Starting phenix.real_space_refine on Fri Mar 15 15:49:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/03_2024/8h9q_34577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/03_2024/8h9q_34577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/03_2024/8h9q_34577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/03_2024/8h9q_34577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/03_2024/8h9q_34577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/03_2024/8h9q_34577.pdb" } resolution = 3.47 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= 0.012 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 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 ASP 1": "OD1" <-> "OD2" 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 ARG 38": "NH1" <-> "NH2" Residue "5 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 1": "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 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 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 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 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 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 "G GLU 37": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 118": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 19": "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 83": "OD1" <-> "OD2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 128": "OD1" <-> "OD2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "N ASP 224": "OD1" <-> "OD2" Residue "R ASP 33": "OD1" <-> "OD2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 77": "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 "T PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 38": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12083 Number of models: 1 Model: "" Number of chains: 19 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: "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: "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: "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} 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: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} 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 Time building chain proxies: 6.02, per 1000 atoms: 0.50 Number of scatterers: 12083 At special positions: 0 Unit cell: (107.31, 112.42, 140.16, 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 2158 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: 4.19 Conformation dependent library (CDL) restraints added in 2.0 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: 65 helices and 4 sheets defined 76.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain '4' and resid 1 through 17 removed outlier: 3.956A 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 removed outlier: 3.874A pdb=" N ALA 4 59 " --> pdb=" O ALA 4 55 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.956A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 removed outlier: 3.829A pdb=" N ILE 5 33 " --> pdb=" O PHE 5 29 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 73 removed outlier: 3.875A pdb=" N ALA 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 17 removed outlier: 3.955A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 removed outlier: 3.507A pdb=" N ILE 6 33 " --> pdb=" O PHE 6 29 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 removed outlier: 3.874A pdb=" N ALA 6 59 " --> pdb=" O ALA 6 55 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 17 removed outlier: 3.955A 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 removed outlier: 3.874A pdb=" N ALA 7 59 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.956A 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 removed outlier: 3.874A pdb=" N ALA 8 59 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.956A 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 removed outlier: 3.524A pdb=" N TYR 1 49 " --> pdb=" O GLN 1 45 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA 1 59 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 3.956A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 removed outlier: 3.566A pdb=" N ILE 2 33 " --> pdb=" O PHE 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 73 removed outlier: 3.874A pdb=" N ALA 2 59 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 17 removed outlier: 3.955A 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 removed outlier: 3.874A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 56 removed outlier: 4.275A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 4.485A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.706A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.662A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 191 Processing helix chain 'G' and resid 197 through 221 removed outlier: 3.509A pdb=" N THR G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) 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: 3.725A 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 9 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 39 removed outlier: 4.415A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.542A 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: 4.696A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.769A 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 '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: 3.700A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 87 removed outlier: 3.506A pdb=" N ALA N 80 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 removed outlier: 3.504A pdb=" N ASN N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Proline residue: N 107 - end of helix removed outlier: 3.899A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 127 Processing helix chain 'N' and resid 134 through 138 removed outlier: 3.731A pdb=" N LEU N 137 " --> pdb=" O PRO N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 181 removed outlier: 4.119A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.645A 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 9 through 19 removed outlier: 4.077A pdb=" N MET P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Proline residue: P 15 - end of helix removed outlier: 3.699A 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 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 8 through 21 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.942A 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 85 removed outlier: 4.468A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS R 82 " --> pdb=" O SER R 78 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N HIS R 83 " --> pdb=" O PHE R 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.332A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) 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 94 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 4.030A pdb=" N ALA T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.251A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS I 44 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 6.180A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.295A 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 13 948 hydrogen bonds defined for protein. 2796 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: 3.38 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3719 1.34 - 1.46: 2331 1.46 - 1.57: 6159 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12324 Sorted by residual: bond pdb=" N LEU 7 42 " pdb=" CA LEU 7 42 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.30e+00 bond pdb=" N LEU 2 42 " pdb=" CA LEU 2 42 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.93e+00 bond pdb=" N LEU 3 42 " pdb=" CA LEU 3 42 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.18e-02 7.18e+03 7.65e+00 bond pdb=" N VAL 2 28 " pdb=" CA VAL 2 28 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.37e+00 bond pdb=" N VAL 1 28 " pdb=" CA VAL 1 28 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 7.11e+00 ... (remaining 12319 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.45: 311 106.45 - 113.36: 6867 113.36 - 120.27: 4770 120.27 - 127.19: 4648 127.19 - 134.10: 93 Bond angle restraints: 16689 Sorted by residual: angle pdb=" C ILE N 138 " pdb=" CA ILE N 138 " pdb=" CB ILE N 138 " ideal model delta sigma weight residual 113.70 110.15 3.55 9.50e-01 1.11e+00 1.39e+01 angle pdb=" N ILE P 6 " pdb=" CA ILE P 6 " pdb=" C ILE P 6 " ideal model delta sigma weight residual 112.98 108.68 4.30 1.25e+00 6.40e-01 1.18e+01 angle pdb=" N LEU 8 42 " pdb=" CA LEU 8 42 " pdb=" C LEU 8 42 " ideal model delta sigma weight residual 112.72 108.93 3.79 1.14e+00 7.69e-01 1.10e+01 angle pdb=" N LYS R 91 " pdb=" CA LYS R 91 " pdb=" C LYS R 91 " ideal model delta sigma weight residual 114.56 110.38 4.18 1.27e+00 6.20e-01 1.08e+01 angle pdb=" C ILE S 45 " pdb=" CA ILE S 45 " pdb=" CB ILE S 45 " ideal model delta sigma weight residual 114.35 110.88 3.47 1.06e+00 8.90e-01 1.07e+01 ... (remaining 16684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6562 17.97 - 35.95: 580 35.95 - 53.92: 78 53.92 - 71.90: 24 71.90 - 89.87: 5 Dihedral angle restraints: 7249 sinusoidal: 2711 harmonic: 4538 Sorted by residual: dihedral pdb=" CA TYR G 193 " pdb=" C TYR G 193 " pdb=" N ASP G 194 " pdb=" CA ASP G 194 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CB GLU G 92 " pdb=" CG GLU G 92 " pdb=" CD GLU G 92 " pdb=" OE1 GLU G 92 " ideal model delta sinusoidal sigma weight residual 0.00 87.48 -87.48 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASP G 140 " pdb=" CB ASP G 140 " pdb=" CG ASP G 140 " pdb=" OD1 ASP G 140 " ideal model delta sinusoidal sigma weight residual -30.00 -83.84 53.84 1 2.00e+01 2.50e-03 9.84e+00 ... (remaining 7246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1381 0.042 - 0.083: 418 0.083 - 0.125: 126 0.125 - 0.167: 31 0.167 - 0.209: 15 Chirality restraints: 1971 Sorted by residual: chirality pdb=" CA ILE 2 25 " pdb=" N ILE 2 25 " pdb=" C ILE 2 25 " pdb=" CB ILE 2 25 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE 8 25 " pdb=" N ILE 8 25 " pdb=" C ILE 8 25 " pdb=" CB ILE 8 25 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE 3 25 " pdb=" N ILE 3 25 " pdb=" C ILE 3 25 " pdb=" CB ILE 3 25 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1968 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 5 38 " 0.197 9.50e-02 1.11e+02 8.82e-02 4.77e+00 pdb=" NE ARG 5 38 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG 5 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 5 38 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 5 38 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO 7 40 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C PRO 7 40 " 0.036 2.00e-02 2.50e+03 pdb=" O PRO 7 40 " -0.014 2.00e-02 2.50e+03 pdb=" N SER 7 41 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO 5 40 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C PRO 5 40 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO 5 40 " 0.013 2.00e-02 2.50e+03 pdb=" N SER 5 41 " 0.011 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1315 2.74 - 3.28: 13903 3.28 - 3.82: 20522 3.82 - 4.36: 24448 4.36 - 4.90: 41091 Nonbonded interactions: 101279 Sorted by model distance: nonbonded pdb=" ND2 ASN N 101 " pdb=" OG1 THR N 161 " model vdw 2.203 2.520 nonbonded pdb=" OH TYR G 214 " pdb=" O PRO H 23 " model vdw 2.221 2.440 nonbonded pdb=" O ARG H 134 " pdb=" ND2 ASN H 138 " model vdw 2.233 2.520 nonbonded pdb=" OH TYR G 44 " pdb=" OD1 ASN G 211 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR R 50 " pdb=" O GLY R 64 " model vdw 2.254 2.440 ... (remaining 101274 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: 10.350 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: 0.010 Extract box with map and model: 27.500 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 31.630 Find NCS groups from input model: 0.520 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.005 0.039 12324 Z= 0.338 Angle : 0.732 6.674 16689 Z= 0.480 Chirality : 0.048 0.209 1971 Planarity : 0.005 0.088 2066 Dihedral : 13.533 89.871 4353 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % 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: -3.02 (0.19), residues: 1558 helix: -1.76 (0.13), residues: 1126 sheet: -1.94 (0.47), residues: 87 loop : -2.04 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 48 HIS 0.002 0.001 HIS H 51 PHE 0.018 0.001 PHE H 45 TYR 0.016 0.001 TYR G 193 ARG 0.006 0.001 ARG 2 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 548 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 39 ASN cc_start: 0.7857 (t0) cc_final: 0.7595 (t0) REVERT: 8 45 GLN cc_start: 0.7416 (tp40) cc_final: 0.7167 (tp40) REVERT: 1 2 ILE cc_start: 0.6704 (tt) cc_final: 0.6476 (tp) REVERT: 2 39 ASN cc_start: 0.8389 (t0) cc_final: 0.7913 (t0) REVERT: 3 62 LEU cc_start: 0.8459 (mt) cc_final: 0.8178 (mt) REVERT: G 104 MET cc_start: 0.7510 (mmt) cc_final: 0.7007 (mmm) REVERT: G 156 ASP cc_start: 0.8075 (t0) cc_final: 0.7591 (t70) REVERT: G 222 THR cc_start: 0.7707 (m) cc_final: 0.7463 (m) REVERT: H 111 ASN cc_start: 0.8632 (m110) cc_final: 0.8197 (m-40) REVERT: H 135 ILE cc_start: 0.8815 (mt) cc_final: 0.8200 (mm) REVERT: H 139 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7765 (mp0) REVERT: I 14 ARG cc_start: 0.7950 (tpt90) cc_final: 0.7522 (ttm-80) REVERT: K 26 TYR cc_start: 0.7554 (t80) cc_final: 0.6722 (t80) REVERT: K 72 LYS cc_start: 0.8633 (mttt) cc_final: 0.8026 (mmtt) REVERT: K 89 LYS cc_start: 0.8485 (tttt) cc_final: 0.8256 (ttpt) REVERT: M 159 ASN cc_start: 0.7904 (p0) cc_final: 0.7617 (p0) REVERT: N 48 TRP cc_start: 0.8713 (t60) cc_final: 0.8351 (t60) REVERT: N 55 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8441 (mtmt) REVERT: N 145 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7797 (mm-30) REVERT: P 7 LYS cc_start: 0.8315 (tttm) cc_final: 0.8046 (tttm) REVERT: P 23 GLU cc_start: 0.8868 (mp0) cc_final: 0.8520 (mp0) REVERT: Q 3 GLN cc_start: 0.9017 (mp10) cc_final: 0.8672 (mp10) REVERT: Q 22 LEU cc_start: 0.9044 (tt) cc_final: 0.8795 (tp) REVERT: Q 26 LEU cc_start: 0.8975 (mt) cc_final: 0.8621 (mt) REVERT: R 28 TRP cc_start: 0.7161 (t-100) cc_final: 0.6731 (t60) REVERT: R 45 ARG cc_start: 0.7935 (mtm180) cc_final: 0.7117 (ttt180) REVERT: R 49 ARG cc_start: 0.7106 (ttm170) cc_final: 0.6750 (ttt-90) REVERT: S 70 LYS cc_start: 0.6891 (tptt) cc_final: 0.6624 (tppt) REVERT: S 90 GLU cc_start: 0.8376 (tt0) cc_final: 0.7499 (tm-30) REVERT: T 16 TYR cc_start: 0.7299 (m-80) cc_final: 0.6897 (m-10) REVERT: T 21 LEU cc_start: 0.8615 (mt) cc_final: 0.8338 (pp) REVERT: T 29 ARG cc_start: 0.7947 (ttt180) cc_final: 0.7695 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.2587 time to fit residues: 194.3225 Evaluate side-chains 413 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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: 0.2980 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 HIS G 163 ASN G 202 GLN H 85 ASN H 111 ASN N 46 GLN N 47 GLN N 101 ASN N 172 HIS ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS S 75 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12324 Z= 0.223 Angle : 0.678 8.462 16689 Z= 0.335 Chirality : 0.043 0.230 1971 Planarity : 0.004 0.045 2066 Dihedral : 4.131 19.475 1686 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.19 % Allowed : 16.04 % Favored : 80.77 % 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: -0.05 (0.21), residues: 1558 helix: 0.57 (0.15), residues: 1110 sheet: -1.25 (0.51), residues: 90 loop : -1.35 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 68 HIS 0.004 0.001 HIS R 83 PHE 0.018 0.002 PHE H 45 TYR 0.015 0.001 TYR R 47 ARG 0.007 0.001 ARG G 36 *********************** 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 471 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 431 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 39 ASN cc_start: 0.7890 (t0) cc_final: 0.7460 (t0) REVERT: 8 45 GLN cc_start: 0.7140 (tp40) cc_final: 0.6859 (tp-100) REVERT: 2 39 ASN cc_start: 0.8203 (t0) cc_final: 0.7745 (t0) REVERT: G 104 MET cc_start: 0.7505 (mmt) cc_final: 0.6977 (mmm) REVERT: G 222 THR cc_start: 0.7487 (m) cc_final: 0.7279 (m) REVERT: H 111 ASN cc_start: 0.8542 (m-40) cc_final: 0.8341 (m-40) REVERT: H 136 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8259 (mt-10) REVERT: I 14 ARG cc_start: 0.8100 (tpt90) cc_final: 0.7700 (ttm-80) REVERT: I 18 ILE cc_start: 0.9002 (mt) cc_final: 0.8712 (mm) REVERT: K 13 ARG cc_start: 0.8277 (mtp85) cc_final: 0.8031 (mtp85) REVERT: K 26 TYR cc_start: 0.7488 (t80) cc_final: 0.6800 (t80) REVERT: K 72 LYS cc_start: 0.8574 (mttt) cc_final: 0.7963 (mmtt) REVERT: M 128 ASP cc_start: 0.8732 (p0) cc_final: 0.8360 (p0) REVERT: M 159 ASN cc_start: 0.8060 (p0) cc_final: 0.7778 (p0) REVERT: N 55 LYS cc_start: 0.8871 (mtpp) cc_final: 0.8389 (mtmt) REVERT: N 115 MET cc_start: 0.8850 (ppp) cc_final: 0.8619 (ppp) REVERT: N 145 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7760 (mm-30) REVERT: N 152 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8445 (mm-40) REVERT: P 22 GLN cc_start: 0.8051 (pt0) cc_final: 0.7796 (pt0) REVERT: Q 3 GLN cc_start: 0.8877 (mp10) cc_final: 0.8662 (mp10) REVERT: Q 22 LEU cc_start: 0.9077 (tt) cc_final: 0.8865 (tp) REVERT: Q 29 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8999 (mm) REVERT: R 28 TRP cc_start: 0.7210 (t-100) cc_final: 0.6741 (t60) REVERT: R 45 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7118 (ttt180) REVERT: R 49 ARG cc_start: 0.7117 (ttm170) cc_final: 0.6783 (ttt-90) REVERT: S 47 ARG cc_start: 0.9043 (mmm160) cc_final: 0.8740 (ttp80) REVERT: S 70 LYS cc_start: 0.6834 (tptt) cc_final: 0.6276 (mttp) REVERT: S 90 GLU cc_start: 0.8452 (tt0) cc_final: 0.7440 (tm-30) REVERT: T 16 TYR cc_start: 0.7480 (m-80) cc_final: 0.7133 (m-10) REVERT: T 29 ARG cc_start: 0.8136 (ttt180) cc_final: 0.7767 (tpp-160) outliers start: 40 outliers final: 19 residues processed: 448 average time/residue: 0.2413 time to fit residues: 152.3800 Evaluate side-chains 406 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 386 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain I residue 42 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain R residue 76 SER 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: 6.9990 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN R 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12324 Z= 0.212 Angle : 0.641 14.330 16689 Z= 0.314 Chirality : 0.042 0.209 1971 Planarity : 0.004 0.045 2066 Dihedral : 4.041 18.068 1686 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.03 % Allowed : 18.20 % Favored : 78.77 % 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: 1.11 (0.22), residues: 1558 helix: 1.41 (0.16), residues: 1103 sheet: -0.83 (0.55), residues: 87 loop : -0.82 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 25 HIS 0.005 0.001 HIS R 83 PHE 0.020 0.002 PHE 3 54 TYR 0.016 0.001 TYR 2 49 ARG 0.006 0.000 ARG H 59 *********************** 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 453 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 415 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8518 (t) cc_final: 0.8101 (m) REVERT: 6 49 TYR cc_start: 0.7702 (m-10) cc_final: 0.7448 (m-80) REVERT: 6 60 MET cc_start: 0.6898 (mmm) cc_final: 0.6642 (mmt) REVERT: 7 58 GLU cc_start: 0.7874 (tt0) cc_final: 0.7665 (tp30) REVERT: 8 66 MET cc_start: 0.7663 (ttp) cc_final: 0.6787 (mmt) REVERT: 1 62 LEU cc_start: 0.7730 (mt) cc_final: 0.7358 (mt) REVERT: 2 39 ASN cc_start: 0.8194 (t0) cc_final: 0.7764 (t0) REVERT: G 36 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7512 (ttp80) REVERT: G 104 MET cc_start: 0.7616 (mmt) cc_final: 0.7131 (mmm) REVERT: H 25 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7328 (tm-30) REVERT: H 136 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8440 (mt-10) REVERT: H 139 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8446 (mt-10) REVERT: I 14 ARG cc_start: 0.8087 (tpt90) cc_final: 0.7707 (ttm-80) REVERT: I 18 ILE cc_start: 0.9040 (mt) cc_final: 0.8719 (mm) REVERT: K 26 TYR cc_start: 0.7528 (t80) cc_final: 0.6780 (t80) REVERT: M 159 ASN cc_start: 0.8127 (p0) cc_final: 0.7915 (p0) REVERT: N 55 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8374 (mtmt) REVERT: N 115 MET cc_start: 0.8875 (ppp) cc_final: 0.8549 (ppp) REVERT: N 118 ARG cc_start: 0.6901 (mtp180) cc_final: 0.5471 (mmt-90) REVERT: N 145 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7658 (mm-30) REVERT: Q 3 GLN cc_start: 0.9024 (mp10) cc_final: 0.8738 (mp10) REVERT: R 28 TRP cc_start: 0.7145 (t-100) cc_final: 0.6579 (t60) REVERT: R 45 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7109 (ttt180) REVERT: R 49 ARG cc_start: 0.7127 (ttm170) cc_final: 0.6782 (ttt-90) REVERT: R 62 ILE cc_start: 0.8396 (tp) cc_final: 0.8038 (mt) REVERT: S 44 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7988 (mm-30) REVERT: S 70 LYS cc_start: 0.6906 (tptt) cc_final: 0.6693 (tppt) REVERT: S 71 GLU cc_start: 0.8344 (mp0) cc_final: 0.7908 (pm20) REVERT: T 21 LEU cc_start: 0.8676 (mt) cc_final: 0.8118 (tt) REVERT: T 29 ARG cc_start: 0.7999 (ttt180) cc_final: 0.7798 (tpp-160) outliers start: 38 outliers final: 21 residues processed: 432 average time/residue: 0.2516 time to fit residues: 156.3231 Evaluate side-chains 407 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 386 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 57 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 42 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN R 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12324 Z= 0.200 Angle : 0.648 10.358 16689 Z= 0.313 Chirality : 0.042 0.194 1971 Planarity : 0.004 0.041 2066 Dihedral : 4.046 17.477 1686 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.99 % Allowed : 20.27 % Favored : 75.74 % 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: 1.44 (0.22), residues: 1558 helix: 1.64 (0.16), residues: 1104 sheet: -0.58 (0.56), residues: 87 loop : -0.67 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 25 HIS 0.003 0.001 HIS R 83 PHE 0.029 0.002 PHE S 64 TYR 0.015 0.001 TYR 4 49 ARG 0.006 0.000 ARG P 39 *********************** 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 454 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 404 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.8021 (mttm) cc_final: 0.7714 (mttm) REVERT: 4 48 SER cc_start: 0.8493 (t) cc_final: 0.8057 (m) REVERT: 6 45 GLN cc_start: 0.6172 (tp40) cc_final: 0.5970 (tp40) REVERT: 6 49 TYR cc_start: 0.7607 (m-10) cc_final: 0.7353 (m-80) REVERT: 6 60 MET cc_start: 0.6817 (mmm) cc_final: 0.6551 (mmt) REVERT: 7 45 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7665 (tm-30) REVERT: 7 58 GLU cc_start: 0.7995 (tt0) cc_final: 0.7562 (tp30) REVERT: 8 66 MET cc_start: 0.7662 (ttp) cc_final: 0.6768 (mmt) REVERT: 2 39 ASN cc_start: 0.8185 (t0) cc_final: 0.7773 (t0) REVERT: 3 1 ASP cc_start: 0.7218 (p0) cc_final: 0.6631 (t70) REVERT: G 104 MET cc_start: 0.7621 (mmt) cc_final: 0.7095 (mmm) REVERT: H 25 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7384 (tm-30) REVERT: H 136 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8340 (mt-10) REVERT: H 139 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8351 (mt-10) REVERT: I 14 ARG cc_start: 0.8064 (tpt90) cc_final: 0.7696 (ttm-80) REVERT: I 18 ILE cc_start: 0.9018 (mt) cc_final: 0.8737 (mm) REVERT: K 13 ARG cc_start: 0.8349 (mtp85) cc_final: 0.8114 (mtp85) REVERT: K 26 TYR cc_start: 0.7578 (t80) cc_final: 0.6941 (t80) REVERT: K 87 GLU cc_start: 0.8307 (pp20) cc_final: 0.8070 (pt0) REVERT: N 55 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8424 (mtmt) REVERT: N 118 ARG cc_start: 0.6705 (mtp180) cc_final: 0.5657 (mmt-90) REVERT: N 145 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7649 (mm-30) REVERT: P 13 MET cc_start: 0.8546 (mmm) cc_final: 0.7824 (mmm) REVERT: Q 3 GLN cc_start: 0.8997 (mp10) cc_final: 0.8720 (mp10) REVERT: R 45 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7110 (ttt180) REVERT: R 49 ARG cc_start: 0.7138 (ttm170) cc_final: 0.6806 (ttt-90) REVERT: R 62 ILE cc_start: 0.8393 (tp) cc_final: 0.8032 (mt) REVERT: S 47 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7956 (ttp80) REVERT: S 70 LYS cc_start: 0.6877 (tptt) cc_final: 0.6606 (tppt) REVERT: S 71 GLU cc_start: 0.8262 (mp0) cc_final: 0.7813 (pm20) REVERT: S 90 GLU cc_start: 0.8254 (tt0) cc_final: 0.7327 (tm-30) REVERT: T 5 VAL cc_start: 0.8670 (t) cc_final: 0.8465 (t) REVERT: T 21 LEU cc_start: 0.8678 (mt) cc_final: 0.8104 (tt) outliers start: 50 outliers final: 31 residues processed: 424 average time/residue: 0.2418 time to fit residues: 144.5259 Evaluate side-chains 416 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 385 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 57 SER Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain I residue 42 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain T residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 159 ASN ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN R 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12324 Z= 0.201 Angle : 0.642 9.862 16689 Z= 0.313 Chirality : 0.041 0.219 1971 Planarity : 0.004 0.043 2066 Dihedral : 4.015 17.275 1686 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.23 % Allowed : 21.87 % 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: 1.61 (0.22), residues: 1558 helix: 1.61 (0.16), residues: 1129 sheet: -0.47 (0.56), residues: 90 loop : -0.16 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 28 HIS 0.004 0.001 HIS R 83 PHE 0.021 0.002 PHE 7 63 TYR 0.018 0.001 TYR K 44 ARG 0.006 0.000 ARG P 39 *********************** 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 458 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 405 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.8024 (mttm) cc_final: 0.7759 (mttm) REVERT: 4 48 SER cc_start: 0.8495 (t) cc_final: 0.8042 (m) REVERT: 4 54 PHE cc_start: 0.8033 (t80) cc_final: 0.7563 (t80) REVERT: 6 49 TYR cc_start: 0.7562 (m-10) cc_final: 0.7326 (m-80) REVERT: 6 60 MET cc_start: 0.6762 (mmm) cc_final: 0.6428 (mmt) REVERT: 7 45 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7789 (tm-30) REVERT: 7 58 GLU cc_start: 0.8117 (tt0) cc_final: 0.7645 (tp30) REVERT: 8 66 MET cc_start: 0.7678 (ttp) cc_final: 0.6771 (mmt) REVERT: 2 39 ASN cc_start: 0.8201 (t0) cc_final: 0.7792 (t0) REVERT: 3 1 ASP cc_start: 0.7157 (p0) cc_final: 0.6590 (t70) REVERT: G 104 MET cc_start: 0.7663 (mmt) cc_final: 0.7345 (mmm) REVERT: H 25 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7317 (tm-30) REVERT: H 136 GLU cc_start: 0.8719 (mt-10) cc_final: 0.7964 (mt-10) REVERT: H 139 GLU cc_start: 0.8686 (mt-10) cc_final: 0.7963 (mp0) REVERT: I 13 ILE cc_start: 0.8990 (mm) cc_final: 0.8674 (mm) REVERT: I 14 ARG cc_start: 0.8057 (tpt90) cc_final: 0.7646 (ttm-80) REVERT: I 18 ILE cc_start: 0.8997 (mt) cc_final: 0.8606 (mp) REVERT: K 26 TYR cc_start: 0.7598 (t80) cc_final: 0.6904 (t80) REVERT: K 84 LYS cc_start: 0.8839 (ttmt) cc_final: 0.7816 (ttpt) REVERT: K 85 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8764 (tt) REVERT: K 88 GLN cc_start: 0.8289 (mp10) cc_final: 0.7767 (mp10) REVERT: N 55 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8431 (mtmt) REVERT: N 118 ARG cc_start: 0.6976 (mtp180) cc_final: 0.5643 (mmt-90) REVERT: N 145 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7657 (mm-30) REVERT: Q 3 GLN cc_start: 0.8986 (mp10) cc_final: 0.8701 (mp10) REVERT: R 30 LEU cc_start: 0.7938 (pp) cc_final: 0.7519 (mp) REVERT: R 45 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7133 (ttt180) REVERT: R 49 ARG cc_start: 0.7154 (ttm170) cc_final: 0.6822 (ttt-90) REVERT: R 62 ILE cc_start: 0.8378 (tp) cc_final: 0.8017 (mt) REVERT: S 47 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8178 (ttp80) REVERT: S 54 LYS cc_start: 0.9419 (mmmt) cc_final: 0.9118 (tptp) REVERT: S 90 GLU cc_start: 0.8288 (tt0) cc_final: 0.7372 (tm-30) REVERT: T 21 LEU cc_start: 0.8702 (mt) cc_final: 0.8170 (tt) outliers start: 53 outliers final: 36 residues processed: 426 average time/residue: 0.2398 time to fit residues: 143.6257 Evaluate side-chains 421 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 384 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 57 SER Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 4.9990 chunk 131 optimal weight: 0.4980 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN 8 44 GLN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12324 Z= 0.221 Angle : 0.647 9.320 16689 Z= 0.316 Chirality : 0.042 0.214 1971 Planarity : 0.004 0.046 2066 Dihedral : 3.998 17.174 1686 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.23 % Allowed : 23.38 % Favored : 72.39 % 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: 1.66 (0.22), residues: 1558 helix: 1.63 (0.16), residues: 1131 sheet: -0.37 (0.57), residues: 90 loop : -0.13 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 28 HIS 0.004 0.001 HIS R 83 PHE 0.026 0.002 PHE 7 63 TYR 0.019 0.001 TYR 3 49 ARG 0.006 0.000 ARG P 39 *********************** 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 460 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 407 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8496 (t) cc_final: 0.8039 (m) REVERT: 6 60 MET cc_start: 0.6740 (mmm) cc_final: 0.6457 (mmt) REVERT: 7 58 GLU cc_start: 0.8122 (tt0) cc_final: 0.7572 (tp30) REVERT: 7 60 MET cc_start: 0.6333 (tpp) cc_final: 0.5870 (tpt) REVERT: 8 66 MET cc_start: 0.7755 (ttp) cc_final: 0.6819 (mmt) REVERT: 2 39 ASN cc_start: 0.8263 (t0) cc_final: 0.7847 (t0) REVERT: 3 1 ASP cc_start: 0.7144 (p0) cc_final: 0.6657 (t70) REVERT: 3 60 MET cc_start: 0.7203 (mtm) cc_final: 0.6880 (mtp) REVERT: G 104 MET cc_start: 0.7717 (mmt) cc_final: 0.7274 (mmm) REVERT: G 181 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8144 (tt) REVERT: H 25 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7395 (tm-30) REVERT: H 32 ASN cc_start: 0.8451 (m-40) cc_final: 0.8003 (t0) REVERT: H 135 ILE cc_start: 0.8821 (mm) cc_final: 0.7649 (mm) REVERT: H 136 GLU cc_start: 0.8710 (mt-10) cc_final: 0.7979 (mt-10) REVERT: H 139 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8021 (mp0) REVERT: I 14 ARG cc_start: 0.8159 (tpt90) cc_final: 0.7694 (mmp80) REVERT: K 26 TYR cc_start: 0.7623 (t80) cc_final: 0.6957 (t80) REVERT: N 22 LEU cc_start: 0.8615 (mp) cc_final: 0.8314 (tt) REVERT: N 55 LYS cc_start: 0.8892 (mtpp) cc_final: 0.8438 (mtmt) REVERT: N 118 ARG cc_start: 0.7049 (mtp180) cc_final: 0.5716 (mmt-90) REVERT: N 145 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7678 (mm-30) REVERT: P 13 MET cc_start: 0.8578 (mmm) cc_final: 0.8192 (mmm) REVERT: Q 3 GLN cc_start: 0.9006 (mp10) cc_final: 0.8722 (mp10) REVERT: R 20 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8270 (p) REVERT: R 30 LEU cc_start: 0.7941 (pp) cc_final: 0.7519 (mp) REVERT: R 45 ARG cc_start: 0.7932 (mtm180) cc_final: 0.7109 (ttt180) REVERT: R 49 ARG cc_start: 0.7196 (ttm170) cc_final: 0.6887 (ttt-90) REVERT: R 62 ILE cc_start: 0.8402 (tp) cc_final: 0.8030 (mt) REVERT: S 44 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7762 (mm-30) REVERT: S 47 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8183 (ttp80) REVERT: S 54 LYS cc_start: 0.9426 (mmmt) cc_final: 0.9147 (tptp) REVERT: S 90 GLU cc_start: 0.8352 (tt0) cc_final: 0.7400 (tm-30) REVERT: T 21 LEU cc_start: 0.8675 (mt) cc_final: 0.8155 (tt) REVERT: T 41 ARG cc_start: 0.8598 (mtm180) cc_final: 0.8309 (mtm180) outliers start: 53 outliers final: 38 residues processed: 435 average time/residue: 0.2559 time to fit residues: 157.7405 Evaluate side-chains 431 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 391 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12324 Z= 0.249 Angle : 0.665 10.348 16689 Z= 0.325 Chirality : 0.042 0.183 1971 Planarity : 0.004 0.052 2066 Dihedral : 4.089 21.148 1686 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.39 % Allowed : 23.70 % Favored : 71.91 % 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: 1.67 (0.22), residues: 1558 helix: 1.65 (0.15), residues: 1129 sheet: -0.45 (0.57), residues: 89 loop : -0.15 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 28 HIS 0.004 0.001 HIS R 83 PHE 0.030 0.002 PHE 4 54 TYR 0.025 0.002 TYR 3 49 ARG 0.006 0.000 ARG P 39 *********************** 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 449 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 394 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.7988 (mttm) cc_final: 0.7778 (mttm) REVERT: 4 48 SER cc_start: 0.8480 (t) cc_final: 0.8011 (m) REVERT: 6 60 MET cc_start: 0.6782 (mmm) cc_final: 0.6527 (mmt) REVERT: 7 58 GLU cc_start: 0.8224 (tt0) cc_final: 0.7826 (tp30) REVERT: 8 66 MET cc_start: 0.7762 (ttp) cc_final: 0.6827 (mmt) REVERT: 2 39 ASN cc_start: 0.8248 (t0) cc_final: 0.7866 (t0) REVERT: 3 1 ASP cc_start: 0.7049 (p0) cc_final: 0.6572 (t70) REVERT: G 125 LEU cc_start: 0.8355 (tp) cc_final: 0.8126 (mp) REVERT: G 181 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8168 (tt) REVERT: H 25 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7460 (tm-30) REVERT: H 32 ASN cc_start: 0.8436 (m-40) cc_final: 0.7701 (t0) REVERT: H 135 ILE cc_start: 0.8815 (mm) cc_final: 0.7655 (mm) REVERT: H 136 GLU cc_start: 0.8752 (mt-10) cc_final: 0.7992 (mt-10) REVERT: H 139 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8035 (mp0) REVERT: I 14 ARG cc_start: 0.7996 (tpt90) cc_final: 0.7698 (ttm-80) REVERT: K 26 TYR cc_start: 0.7631 (t80) cc_final: 0.6906 (t80) REVERT: N 22 LEU cc_start: 0.8629 (mp) cc_final: 0.8307 (tt) REVERT: N 55 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8461 (mtmt) REVERT: N 118 ARG cc_start: 0.7112 (mtp180) cc_final: 0.5802 (mpt180) REVERT: N 145 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7702 (mm-30) REVERT: P 13 MET cc_start: 0.8624 (mmm) cc_final: 0.8148 (mmm) REVERT: Q 3 GLN cc_start: 0.9022 (mp10) cc_final: 0.8730 (mp10) REVERT: R 20 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8180 (p) REVERT: R 30 LEU cc_start: 0.7981 (pp) cc_final: 0.7580 (mp) REVERT: R 45 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7113 (ttt180) REVERT: R 49 ARG cc_start: 0.7253 (ttm170) cc_final: 0.6825 (ttt-90) REVERT: R 62 ILE cc_start: 0.8402 (tp) cc_final: 0.8080 (mt) REVERT: S 44 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7844 (mm-30) REVERT: S 47 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8254 (ttp80) REVERT: S 54 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9166 (tptp) REVERT: S 90 GLU cc_start: 0.8346 (tt0) cc_final: 0.7382 (tm-30) REVERT: T 21 LEU cc_start: 0.8623 (mt) cc_final: 0.8125 (tt) REVERT: T 42 ARG cc_start: 0.7656 (tmm-80) cc_final: 0.7435 (ppt170) outliers start: 55 outliers final: 42 residues processed: 420 average time/residue: 0.2532 time to fit residues: 151.1417 Evaluate side-chains 423 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 379 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 64 CYS Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 0.0670 chunk 28 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN 3 45 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12324 Z= 0.208 Angle : 0.682 11.883 16689 Z= 0.331 Chirality : 0.043 0.257 1971 Planarity : 0.004 0.053 2066 Dihedral : 4.075 18.000 1686 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.51 % Allowed : 25.22 % Favored : 71.27 % 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: 1.73 (0.22), residues: 1558 helix: 1.68 (0.15), residues: 1131 sheet: -0.43 (0.58), residues: 89 loop : -0.05 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 10 HIS 0.004 0.001 HIS R 83 PHE 0.032 0.002 PHE 7 63 TYR 0.023 0.002 TYR T 32 ARG 0.008 0.000 ARG P 39 *********************** 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 445 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 401 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.7923 (mttm) cc_final: 0.7713 (mttm) REVERT: 4 16 VAL cc_start: 0.8078 (t) cc_final: 0.7870 (t) REVERT: 4 48 SER cc_start: 0.8466 (t) cc_final: 0.7996 (m) REVERT: 6 49 TYR cc_start: 0.7536 (m-80) cc_final: 0.6916 (m-80) REVERT: 6 60 MET cc_start: 0.6717 (mmm) cc_final: 0.6465 (mmt) REVERT: 7 58 GLU cc_start: 0.8124 (tt0) cc_final: 0.7858 (tp30) REVERT: 8 66 MET cc_start: 0.7798 (ttp) cc_final: 0.6843 (mmt) REVERT: 2 39 ASN cc_start: 0.8189 (t0) cc_final: 0.7807 (t0) REVERT: 3 1 ASP cc_start: 0.7017 (p0) cc_final: 0.6546 (t70) REVERT: G 125 LEU cc_start: 0.8388 (tp) cc_final: 0.8168 (mp) REVERT: G 181 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8169 (tt) REVERT: H 25 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7453 (tm-30) REVERT: H 32 ASN cc_start: 0.8461 (m-40) cc_final: 0.7718 (t0) REVERT: H 109 LYS cc_start: 0.8860 (tptp) cc_final: 0.8494 (mtpt) REVERT: H 135 ILE cc_start: 0.8811 (mm) cc_final: 0.7737 (mm) REVERT: H 136 GLU cc_start: 0.8710 (mt-10) cc_final: 0.7891 (mt-10) REVERT: H 139 GLU cc_start: 0.8671 (mt-10) cc_final: 0.7996 (mp0) REVERT: I 14 ARG cc_start: 0.7872 (tpt90) cc_final: 0.7648 (ttm-80) REVERT: I 15 TYR cc_start: 0.8499 (t80) cc_final: 0.8275 (t80) REVERT: K 26 TYR cc_start: 0.7651 (t80) cc_final: 0.6964 (t80) REVERT: N 22 LEU cc_start: 0.8625 (mp) cc_final: 0.8303 (tt) REVERT: N 55 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8438 (mtmt) REVERT: N 118 ARG cc_start: 0.7220 (mtp180) cc_final: 0.5807 (mpt180) REVERT: N 145 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7687 (mm-30) REVERT: P 13 MET cc_start: 0.8465 (mmm) cc_final: 0.7945 (mmm) REVERT: Q 3 GLN cc_start: 0.8990 (mp10) cc_final: 0.8713 (mp10) REVERT: R 30 LEU cc_start: 0.7960 (pp) cc_final: 0.7565 (mp) REVERT: R 45 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7128 (ttt180) REVERT: R 49 ARG cc_start: 0.7198 (ttm170) cc_final: 0.6855 (ttt-90) REVERT: R 62 ILE cc_start: 0.8370 (tp) cc_final: 0.8037 (mt) REVERT: S 50 GLN cc_start: 0.9197 (mt0) cc_final: 0.8864 (mt0) REVERT: S 54 LYS cc_start: 0.9451 (mmmt) cc_final: 0.9195 (tptp) REVERT: S 90 GLU cc_start: 0.8351 (tt0) cc_final: 0.7420 (tm-30) REVERT: T 21 LEU cc_start: 0.8604 (mt) cc_final: 0.8148 (tt) REVERT: T 41 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8094 (ptt-90) outliers start: 44 outliers final: 31 residues processed: 427 average time/residue: 0.2505 time to fit residues: 151.5118 Evaluate side-chains 414 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 382 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN 8 44 GLN 2 45 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12324 Z= 0.216 Angle : 0.722 19.136 16689 Z= 0.348 Chirality : 0.044 0.348 1971 Planarity : 0.004 0.054 2066 Dihedral : 4.082 17.563 1686 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.43 % Allowed : 25.54 % Favored : 71.03 % 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: 1.72 (0.22), residues: 1558 helix: 1.67 (0.15), residues: 1134 sheet: -0.32 (0.58), residues: 87 loop : -0.11 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 68 HIS 0.004 0.001 HIS R 83 PHE 0.036 0.002 PHE 4 54 TYR 0.025 0.002 TYR T 32 ARG 0.008 0.000 ARG P 39 *********************** 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 437 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 394 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8443 (t) cc_final: 0.7989 (m) REVERT: 6 45 GLN cc_start: 0.6230 (OUTLIER) cc_final: 0.5953 (tp40) REVERT: 6 49 TYR cc_start: 0.7580 (m-80) cc_final: 0.7014 (m-80) REVERT: 6 60 MET cc_start: 0.6702 (mmm) cc_final: 0.6307 (mmt) REVERT: 7 58 GLU cc_start: 0.8106 (tt0) cc_final: 0.7798 (tp30) REVERT: 8 66 MET cc_start: 0.7781 (ttp) cc_final: 0.6813 (mmt) REVERT: 2 39 ASN cc_start: 0.8174 (t0) cc_final: 0.7819 (t0) REVERT: 3 1 ASP cc_start: 0.6983 (p0) cc_final: 0.6544 (t70) REVERT: G 37 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7814 (tm-30) REVERT: G 104 MET cc_start: 0.7744 (mmt) cc_final: 0.7371 (mmm) REVERT: G 181 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8181 (tt) REVERT: H 25 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7444 (tm-30) REVERT: H 32 ASN cc_start: 0.8456 (m-40) cc_final: 0.7728 (t0) REVERT: H 135 ILE cc_start: 0.8864 (mm) cc_final: 0.7650 (mm) REVERT: H 136 GLU cc_start: 0.8713 (mt-10) cc_final: 0.7926 (mt-10) REVERT: H 139 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8017 (mp0) REVERT: I 14 ARG cc_start: 0.7868 (tpt90) cc_final: 0.7625 (ttm-80) REVERT: K 7 GLU cc_start: 0.7314 (tt0) cc_final: 0.7033 (tp30) REVERT: K 26 TYR cc_start: 0.7607 (t80) cc_final: 0.6860 (t80) REVERT: K 85 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8906 (tt) REVERT: K 88 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: N 22 LEU cc_start: 0.8618 (mp) cc_final: 0.8285 (tt) REVERT: N 55 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8660 (ttpt) REVERT: N 118 ARG cc_start: 0.7272 (mtp180) cc_final: 0.5790 (mpt180) REVERT: N 145 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7689 (mm-30) REVERT: P 22 GLN cc_start: 0.8392 (pm20) cc_final: 0.8154 (pm20) REVERT: Q 3 GLN cc_start: 0.8996 (mp10) cc_final: 0.8716 (mp10) REVERT: R 30 LEU cc_start: 0.7949 (pp) cc_final: 0.7541 (mp) REVERT: R 45 ARG cc_start: 0.7952 (mtm180) cc_final: 0.7139 (ttt180) REVERT: R 49 ARG cc_start: 0.7135 (ttm170) cc_final: 0.6861 (ttt-90) REVERT: R 62 ILE cc_start: 0.8379 (tp) cc_final: 0.8056 (mt) REVERT: S 54 LYS cc_start: 0.9463 (mmmt) cc_final: 0.9210 (tptp) REVERT: S 90 GLU cc_start: 0.8351 (tt0) cc_final: 0.7438 (tm-30) REVERT: T 21 LEU cc_start: 0.8653 (mt) cc_final: 0.8202 (tt) REVERT: T 41 ARG cc_start: 0.8597 (mtm180) cc_final: 0.8315 (mtm110) outliers start: 43 outliers final: 36 residues processed: 413 average time/residue: 0.2463 time to fit residues: 143.3394 Evaluate side-chains 420 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 380 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 45 GLN Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 9 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 64 CYS Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 88 GLN Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12324 Z= 0.228 Angle : 0.742 19.005 16689 Z= 0.354 Chirality : 0.045 0.333 1971 Planarity : 0.004 0.054 2066 Dihedral : 4.101 17.219 1686 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.27 % Allowed : 26.26 % Favored : 70.47 % 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: 1.66 (0.22), residues: 1558 helix: 1.61 (0.15), residues: 1141 sheet: -0.28 (0.57), residues: 87 loop : -0.14 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 68 HIS 0.005 0.001 HIS R 83 PHE 0.045 0.002 PHE 4 54 TYR 0.024 0.002 TYR T 32 ARG 0.008 0.001 ARG P 39 ********************** 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 427 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 386 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8456 (t) cc_final: 0.8014 (m) REVERT: 4 75 MET cc_start: 0.5862 (mpp) cc_final: 0.5549 (mpp) REVERT: 6 49 TYR cc_start: 0.7556 (m-80) cc_final: 0.7122 (m-80) REVERT: 7 58 GLU cc_start: 0.8095 (tt0) cc_final: 0.7792 (tp30) REVERT: 8 66 MET cc_start: 0.7758 (ttp) cc_final: 0.6754 (mmt) REVERT: 2 39 ASN cc_start: 0.8138 (t0) cc_final: 0.7769 (t0) REVERT: 2 47 PHE cc_start: 0.8140 (t80) cc_final: 0.7639 (t80) REVERT: 3 1 ASP cc_start: 0.6981 (p0) cc_final: 0.6581 (t70) REVERT: G 125 LEU cc_start: 0.8465 (tp) cc_final: 0.8184 (mp) REVERT: G 181 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8187 (tt) REVERT: H 25 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7436 (tm-30) REVERT: H 32 ASN cc_start: 0.8465 (m-40) cc_final: 0.7743 (t0) REVERT: H 130 GLU cc_start: 0.8047 (tp30) cc_final: 0.7818 (tp30) REVERT: H 135 ILE cc_start: 0.8872 (mm) cc_final: 0.7669 (mm) REVERT: H 139 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8014 (mp0) REVERT: I 14 ARG cc_start: 0.7892 (tpt90) cc_final: 0.7633 (ttm-80) REVERT: K 44 TYR cc_start: 0.8328 (t80) cc_final: 0.8128 (t80) REVERT: K 85 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8908 (tt) REVERT: K 88 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: N 22 LEU cc_start: 0.8633 (mp) cc_final: 0.8278 (tt) REVERT: N 55 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8451 (mtpt) REVERT: N 118 ARG cc_start: 0.7268 (mtp180) cc_final: 0.5791 (mpt180) REVERT: N 145 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7707 (mm-30) REVERT: P 13 MET cc_start: 0.8397 (mmm) cc_final: 0.7636 (mmm) REVERT: Q 3 GLN cc_start: 0.9023 (mp10) cc_final: 0.8740 (mp10) REVERT: R 30 LEU cc_start: 0.7949 (pp) cc_final: 0.7538 (mp) REVERT: R 45 ARG cc_start: 0.7958 (mtm180) cc_final: 0.7143 (ttt180) REVERT: R 49 ARG cc_start: 0.7149 (ttm170) cc_final: 0.6877 (ttt-90) REVERT: R 62 ILE cc_start: 0.8392 (tp) cc_final: 0.8074 (mt) REVERT: S 54 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9213 (tptp) REVERT: S 77 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8071 (pp) REVERT: S 90 GLU cc_start: 0.8344 (tt0) cc_final: 0.7412 (tm-30) REVERT: T 21 LEU cc_start: 0.8645 (mt) cc_final: 0.8200 (tt) REVERT: T 41 ARG cc_start: 0.8579 (mtm180) cc_final: 0.8317 (mtm110) outliers start: 41 outliers final: 34 residues processed: 405 average time/residue: 0.2386 time to fit residues: 136.4887 Evaluate side-chains 414 residues out of total 1255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 376 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 9 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 64 CYS Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 64 CYS Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 88 GLN Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.5980 chunk 110 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 0.0170 chunk 6 optimal weight: 5.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 HIS ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117823 restraints weight = 22794.909| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.82 r_work: 0.3517 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12324 Z= 0.213 Angle : 0.742 19.343 16689 Z= 0.353 Chirality : 0.044 0.331 1971 Planarity : 0.004 0.056 2066 Dihedral : 4.122 17.362 1686 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.19 % Allowed : 26.34 % Favored : 70.47 % 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: 1.80 (0.22), residues: 1558 helix: 1.71 (0.15), residues: 1145 sheet: -0.23 (0.56), residues: 87 loop : -0.09 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 68 HIS 0.006 0.001 HIS N 127 PHE 0.052 0.002 PHE 4 54 TYR 0.024 0.002 TYR K 26 ARG 0.009 0.001 ARG K 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3606.48 seconds wall clock time: 65 minutes 38.27 seconds (3938.27 seconds total)