Starting phenix.real_space_refine on Mon Aug 5 01:00:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khf_37243/08_2024/8khf_37243.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khf_37243/08_2024/8khf_37243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khf_37243/08_2024/8khf_37243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khf_37243/08_2024/8khf_37243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khf_37243/08_2024/8khf_37243.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8khf_37243/08_2024/8khf_37243.cif" } resolution = 3.13 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= 0.016 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 63 5.16 5 C 7967 2.51 5 N 1937 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 ARG 38": "NH1" <-> "NH2" Residue "2 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "4 GLU 58": "OE1" <-> "OE2" Residue "4 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 1": "OD1" <-> "OD2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "5 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 1": "OD1" <-> "OD2" 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 ARG 38": "NH1" <-> "NH2" Residue "7 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 58": "OE1" <-> "OE2" Residue "7 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 38": "NH1" <-> "NH2" Residue "8 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 104": "OD1" <-> "OD2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 19": "OE1" <-> "OE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 133": "OE1" <-> "OE2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 145": "OE1" <-> "OE2" Residue "N PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 203": "OE1" <-> "OE2" 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 TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "T PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12128 Number of models: 1 Model: "" Number of chains: 20 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: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 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: "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 Chain: "4" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.75, per 1000 atoms: 0.72 Number of scatterers: 12128 At special positions: 0 Unit cell: (121.18, 89.79, 135.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 63 16.00 O 2160 8.00 N 1937 7.00 C 7967 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: 4.71 Conformation dependent library (CDL) restraints added in 2.3 seconds 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2898 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 4 sheets defined 76.6% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain '1' and resid 2 through 15 Processing helix chain '1' and resid 17 through 39 removed outlier: 4.057A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 73 removed outlier: 3.860A pdb=" N ALA 1 59 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 removed outlier: 3.674A pdb=" N ALA 2 59 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 16 Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 removed outlier: 3.572A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY 3 61 " --> pdb=" O SER 3 57 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 removed outlier: 3.803A pdb=" N CYS 4 64 " --> pdb=" O MET 4 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL 4 67 " --> pdb=" O PHE 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 16 Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 73 removed outlier: 3.513A pdb=" N GLU 5 58 " --> pdb=" O PHE 5 54 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 17 removed outlier: 4.050A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 39 removed outlier: 4.399A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 16 Processing helix chain '7' and resid 17 through 39 removed outlier: 4.446A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 73 removed outlier: 3.894A pdb=" N ALA 7 59 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE 7 73 " --> pdb=" O PHE 7 69 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 16 Processing helix chain '8' and resid 17 through 39 removed outlier: 4.390A pdb=" N SER 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 42 through 72 removed outlier: 3.672A pdb=" N ALA 8 59 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 48 removed outlier: 3.920A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 49 through 55 removed outlier: 3.548A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 109 through 117 removed outlier: 3.509A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 180 through 187 removed outlier: 3.548A pdb=" N VAL G 184 " --> pdb=" O SER G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 193 removed outlier: 3.622A pdb=" N SER G 191 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 removed outlier: 3.626A 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: 3.862A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.536A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.389A 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 32 through 48 Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.830A 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 126 through 130 removed outlier: 3.547A pdb=" N MET M 130 " --> pdb=" O PHE M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'N' and resid 6 through 10 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: 3.613A 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 86 Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.751A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 3.834A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 181 removed outlier: 3.816A pdb=" N LEU N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR N 146 " --> pdb=" O VAL N 142 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.801A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA N 166 " --> pdb=" O ALA N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 224 Processing helix chain 'P' and resid 13 through 19 Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'Q' and resid 1 through 8 removed outlier: 5.337A pdb=" N THR Q 6 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N THR Q 7 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL Q 8 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 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: 3.937A 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 79 removed outlier: 4.415A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.789A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' 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: 3.867A 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: 5.258A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS I 44 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 26 through 31 removed outlier: 5.304A pdb=" N ASN H 29 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE H 20 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.297A 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: 7.319A 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 13 933 hydrogen bonds defined for protein. 2747 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: 3.74 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 3767 1.37 - 1.51: 3896 1.51 - 1.65: 4595 1.65 - 1.79: 58 1.79 - 1.93: 58 Bond restraints: 12374 Sorted by residual: bond pdb=" C10 BQ1 4 101 " pdb=" C17 BQ1 4 101 " ideal model delta sigma weight residual 1.437 1.369 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C17 BQ1 4 101 " pdb=" O03 BQ1 4 101 " ideal model delta sigma weight residual 1.330 1.395 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C ILE S 45 " pdb=" N PRO S 46 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.30e-02 5.92e+03 9.88e+00 bond pdb=" C15 BQ1 4 101 " pdb=" C22 BQ1 4 101 " ideal model delta sigma weight residual 1.417 1.366 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" N SER 4 57 " pdb=" CA SER 4 57 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.17e-02 7.31e+03 5.72e+00 ... (remaining 12369 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.80: 252 105.80 - 112.89: 6721 112.89 - 119.98: 4468 119.98 - 127.06: 5222 127.06 - 134.15: 98 Bond angle restraints: 16761 Sorted by residual: angle pdb=" N LYS R 91 " pdb=" CA LYS R 91 " pdb=" C LYS R 91 " ideal model delta sigma weight residual 114.64 108.40 6.24 1.52e+00 4.33e-01 1.69e+01 angle pdb=" N PHE N 26 " pdb=" CA PHE N 26 " pdb=" C PHE N 26 " ideal model delta sigma weight residual 109.81 116.66 -6.85 2.21e+00 2.05e-01 9.60e+00 angle pdb=" CA ALA 4 59 " pdb=" C ALA 4 59 " pdb=" O ALA 4 59 " ideal model delta sigma weight residual 120.90 118.13 2.77 1.03e+00 9.43e-01 7.24e+00 angle pdb=" CA SER 4 57 " pdb=" C SER 4 57 " pdb=" O SER 4 57 " ideal model delta sigma weight residual 121.00 118.28 2.72 1.05e+00 9.07e-01 6.73e+00 angle pdb=" C ALA 2 74 " pdb=" N MET 2 75 " pdb=" CA MET 2 75 " ideal model delta sigma weight residual 121.70 126.27 -4.57 1.80e+00 3.09e-01 6.46e+00 ... (remaining 16756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 6676 17.64 - 35.29: 513 35.29 - 52.93: 73 52.93 - 70.57: 11 70.57 - 88.21: 12 Dihedral angle restraints: 7285 sinusoidal: 2743 harmonic: 4542 Sorted by residual: dihedral pdb=" CA THR N 135 " pdb=" C THR N 135 " pdb=" N PRO N 136 " pdb=" CA PRO N 136 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLN S 66 " pdb=" C GLN S 66 " pdb=" N LEU S 67 " pdb=" CA LEU S 67 " ideal model delta harmonic sigma weight residual 180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CG ARG R 45 " pdb=" CD ARG R 45 " pdb=" NE ARG R 45 " pdb=" CZ ARG R 45 " ideal model delta sinusoidal sigma weight residual 180.00 135.14 44.86 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 7282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1519 0.049 - 0.098: 381 0.098 - 0.147: 71 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C07 BQ1 4 101 " pdb=" C06 BQ1 4 101 " pdb=" C10 BQ1 4 101 " pdb=" C12 BQ1 4 101 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA THR N 135 " pdb=" N THR N 135 " pdb=" C THR N 135 " pdb=" CB THR N 135 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA THR Q 14 " pdb=" N THR Q 14 " pdb=" C THR Q 14 " pdb=" CB THR Q 14 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 1971 not shown) Planarity restraints: 2071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE 3 54 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C PHE 3 54 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE 3 54 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA 3 55 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 8 54 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C PHE 8 54 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE 8 54 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA 8 55 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 1 54 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C PHE 1 54 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE 1 54 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA 1 55 " -0.010 2.00e-02 2.50e+03 ... (remaining 2068 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 486 2.72 - 3.26: 13424 3.26 - 3.81: 20226 3.81 - 4.35: 24815 4.35 - 4.90: 42277 Nonbonded interactions: 101228 Sorted by model distance: nonbonded pdb=" O LYS N 55 " pdb=" OG1 THR N 59 " model vdw 2.169 3.040 nonbonded pdb=" OH TYR G 52 " pdb=" OE1 GLN G 205 " model vdw 2.203 3.040 nonbonded pdb=" O MET N 181 " pdb=" OG1 THR N 189 " model vdw 2.207 3.040 nonbonded pdb=" O ASN G 182 " pdb=" OG SER G 186 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR R 50 " pdb=" O GLY R 64 " model vdw 2.231 3.040 ... (remaining 101223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '2' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '3' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '4' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '5' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '6' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '7' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '8' and (resid 1 through 37 or resid 39 through 75)) } 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=0.50 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: 7.660 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 36.720 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.006 0.068 12374 Z= 0.375 Angle : 0.671 6.915 16761 Z= 0.385 Chirality : 0.043 0.245 1974 Planarity : 0.005 0.041 2071 Dihedral : 12.893 88.214 4387 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.18), residues: 1559 helix: -1.59 (0.13), residues: 1130 sheet: -2.01 (0.48), residues: 89 loop : -2.19 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 109 HIS 0.005 0.001 HIS H 51 PHE 0.021 0.002 PHE 7 29 TYR 0.015 0.001 TYR G 44 ARG 0.005 0.001 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: 2 31 SER cc_start: 0.8761 (m) cc_final: 0.8533 (m) REVERT: 7 7 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8487 (mtmt) REVERT: 7 69 PHE cc_start: 0.8195 (m-10) cc_final: 0.7428 (t80) REVERT: 8 7 LYS cc_start: 0.8368 (mtmt) cc_final: 0.7935 (mtpp) REVERT: G 65 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7671 (mtmm) REVERT: G 81 ILE cc_start: 0.8336 (mm) cc_final: 0.8112 (mm) REVERT: G 188 ASP cc_start: 0.7783 (m-30) cc_final: 0.7552 (m-30) REVERT: I 7 GLN cc_start: 0.8450 (mm110) cc_final: 0.7998 (mt0) REVERT: I 21 LYS cc_start: 0.8725 (tttm) cc_final: 0.8377 (tttp) REVERT: I 25 ASP cc_start: 0.8731 (m-30) cc_final: 0.8477 (m-30) REVERT: K 14 TYR cc_start: 0.8557 (m-80) cc_final: 0.8252 (m-80) REVERT: K 19 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7659 (mt-10) REVERT: K 26 TYR cc_start: 0.8241 (t80) cc_final: 0.7931 (t80) REVERT: K 48 LYS cc_start: 0.7737 (tttt) cc_final: 0.6492 (tmtt) REVERT: K 72 LYS cc_start: 0.8203 (mttt) cc_final: 0.7577 (mmtt) REVERT: K 84 LYS cc_start: 0.8106 (mttp) cc_final: 0.7826 (pttp) REVERT: N 57 MET cc_start: 0.8110 (mmm) cc_final: 0.7381 (mmt) REVERT: R 33 ASP cc_start: 0.8513 (t0) cc_final: 0.8297 (t0) REVERT: R 49 ARG cc_start: 0.7741 (ttm170) cc_final: 0.6738 (tmt170) REVERT: R 85 LYS cc_start: 0.7968 (ptmt) cc_final: 0.7545 (pttm) REVERT: S 94 LYS cc_start: 0.7967 (pttt) cc_final: 0.7528 (mtpt) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2650 time to fit residues: 105.1831 Evaluate side-chains 235 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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: 0.6980 chunk 114 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 H 85 ASN I 7 GLN K 88 GLN N 46 GLN N 47 GLN N 61 HIS R 83 HIS S 75 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12374 Z= 0.207 Angle : 0.577 8.157 16761 Z= 0.304 Chirality : 0.041 0.139 1974 Planarity : 0.004 0.044 2071 Dihedral : 5.913 69.332 1716 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.36 % Allowed : 8.93 % Favored : 89.71 % 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: -0.41 (0.20), residues: 1559 helix: 0.29 (0.15), residues: 1140 sheet: -1.88 (0.50), residues: 90 loop : -1.38 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.017 0.001 PHE H 45 TYR 0.012 0.001 TYR G 44 ARG 0.003 0.000 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 252 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 31 SER cc_start: 0.8683 (m) cc_final: 0.8245 (p) REVERT: 4 75 MET cc_start: 0.6681 (mpp) cc_final: 0.6229 (mpp) REVERT: 5 69 PHE cc_start: 0.7865 (m-10) cc_final: 0.7528 (t80) REVERT: 7 7 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8430 (mttt) REVERT: 7 69 PHE cc_start: 0.8097 (m-10) cc_final: 0.7466 (t80) REVERT: 8 7 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7940 (mtpp) REVERT: G 81 ILE cc_start: 0.8375 (mm) cc_final: 0.8129 (mm) REVERT: I 7 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7925 (mt0) REVERT: I 21 LYS cc_start: 0.8692 (tttm) cc_final: 0.8398 (tttp) REVERT: I 25 ASP cc_start: 0.8713 (m-30) cc_final: 0.8489 (m-30) REVERT: I 44 LYS cc_start: 0.8722 (mttm) cc_final: 0.8253 (mttt) REVERT: K 19 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7655 (mt-10) REVERT: K 26 TYR cc_start: 0.8263 (t80) cc_final: 0.7989 (t80) REVERT: K 48 LYS cc_start: 0.7605 (tttt) cc_final: 0.6485 (tmtt) REVERT: K 72 LYS cc_start: 0.8210 (mttt) cc_final: 0.7591 (mmtt) REVERT: K 84 LYS cc_start: 0.8055 (mttp) cc_final: 0.7744 (pttp) REVERT: R 49 ARG cc_start: 0.7719 (ttm170) cc_final: 0.6757 (tmt170) REVERT: R 63 SER cc_start: 0.7981 (m) cc_final: 0.7754 (t) REVERT: R 85 LYS cc_start: 0.7914 (ptmt) cc_final: 0.7493 (pttm) REVERT: S 90 GLU cc_start: 0.8112 (tt0) cc_final: 0.7864 (tt0) outliers start: 17 outliers final: 10 residues processed: 261 average time/residue: 0.2579 time to fit residues: 93.0177 Evaluate side-chains 244 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 234 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12374 Z= 0.252 Angle : 0.573 7.693 16761 Z= 0.299 Chirality : 0.041 0.145 1974 Planarity : 0.004 0.045 2071 Dihedral : 5.608 66.478 1716 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.91 % Allowed : 11.48 % Favored : 86.60 % 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: 0.60 (0.21), residues: 1559 helix: 1.03 (0.15), residues: 1154 sheet: -1.62 (0.52), residues: 91 loop : -1.08 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 PHE 0.019 0.001 PHE H 45 TYR 0.025 0.001 TYR S 100 ARG 0.003 0.000 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7919 (ppp) cc_final: 0.7375 (ppp) REVERT: 3 39 ASN cc_start: 0.8140 (t0) cc_final: 0.7918 (t0) REVERT: 5 69 PHE cc_start: 0.8023 (m-10) cc_final: 0.7544 (t80) REVERT: 7 7 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8376 (mttt) REVERT: 7 69 PHE cc_start: 0.8056 (m-10) cc_final: 0.7473 (t80) REVERT: 8 7 LYS cc_start: 0.8366 (mtmt) cc_final: 0.7933 (mtpp) REVERT: G 166 ARG cc_start: 0.8339 (ttp-110) cc_final: 0.8006 (mtm110) REVERT: I 7 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7916 (mt0) REVERT: I 21 LYS cc_start: 0.8711 (tttm) cc_final: 0.8436 (tttp) REVERT: I 44 LYS cc_start: 0.8743 (mttm) cc_final: 0.8290 (mttt) REVERT: K 19 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7558 (mt-10) REVERT: K 26 TYR cc_start: 0.8285 (t80) cc_final: 0.8018 (t80) REVERT: K 48 LYS cc_start: 0.7608 (tttt) cc_final: 0.6523 (tmtt) REVERT: K 72 LYS cc_start: 0.8238 (mttt) cc_final: 0.7576 (mmtt) REVERT: K 84 LYS cc_start: 0.8050 (mttp) cc_final: 0.7745 (pttp) REVERT: N 64 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8580 (tttp) REVERT: R 49 ARG cc_start: 0.7759 (ttm170) cc_final: 0.6676 (tmt170) REVERT: R 63 SER cc_start: 0.8001 (m) cc_final: 0.7785 (t) REVERT: R 85 LYS cc_start: 0.7882 (ptmt) cc_final: 0.7461 (pttm) outliers start: 24 outliers final: 15 residues processed: 257 average time/residue: 0.2469 time to fit residues: 89.5569 Evaluate side-chains 252 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 0.0030 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 39 ASN I 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12374 Z= 0.180 Angle : 0.539 7.294 16761 Z= 0.280 Chirality : 0.040 0.142 1974 Planarity : 0.004 0.039 2071 Dihedral : 5.280 61.537 1716 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.83 % Allowed : 13.48 % Favored : 84.69 % 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: 1.35 (0.21), residues: 1559 helix: 1.53 (0.15), residues: 1151 sheet: -0.89 (0.58), residues: 83 loop : -0.78 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.002 0.001 HIS H 51 PHE 0.020 0.001 PHE K 24 TYR 0.011 0.001 TYR S 100 ARG 0.002 0.000 ARG N 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7936 (ppp) cc_final: 0.7373 (ppp) REVERT: 5 69 PHE cc_start: 0.8018 (m-10) cc_final: 0.7525 (t80) REVERT: 7 7 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8414 (mttt) REVERT: 7 69 PHE cc_start: 0.7981 (m-10) cc_final: 0.7475 (t80) REVERT: 8 7 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7851 (mtpp) REVERT: G 113 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8380 (ttp80) REVERT: G 166 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.8006 (mtm110) REVERT: I 7 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7916 (mt0) REVERT: I 21 LYS cc_start: 0.8721 (tttm) cc_final: 0.8515 (tttp) REVERT: I 44 LYS cc_start: 0.8721 (mttm) cc_final: 0.8250 (mttt) REVERT: K 19 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7619 (mt-10) REVERT: K 48 LYS cc_start: 0.7550 (tttt) cc_final: 0.6499 (tmtt) REVERT: K 72 LYS cc_start: 0.8186 (mttt) cc_final: 0.7580 (mmtt) REVERT: K 84 LYS cc_start: 0.8033 (mttp) cc_final: 0.7733 (pttp) REVERT: P 39 ARG cc_start: 0.8609 (mtm180) cc_final: 0.8409 (mmm-85) REVERT: R 49 ARG cc_start: 0.7692 (ttm170) cc_final: 0.6689 (tmt170) REVERT: R 63 SER cc_start: 0.7933 (m) cc_final: 0.7692 (t) REVERT: R 85 LYS cc_start: 0.7870 (ptmt) cc_final: 0.7449 (pttm) outliers start: 23 outliers final: 15 residues processed: 258 average time/residue: 0.2645 time to fit residues: 96.8943 Evaluate side-chains 252 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 237 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12374 Z= 0.175 Angle : 0.534 7.983 16761 Z= 0.276 Chirality : 0.040 0.137 1974 Planarity : 0.004 0.088 2071 Dihedral : 5.172 57.879 1716 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.75 % Allowed : 15.23 % Favored : 83.01 % 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: 1559 helix: 1.75 (0.15), residues: 1151 sheet: -0.80 (0.59), residues: 83 loop : -0.61 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.002 0.000 HIS H 51 PHE 0.021 0.001 PHE K 24 TYR 0.011 0.001 TYR R 51 ARG 0.005 0.000 ARG N 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7951 (ppp) cc_final: 0.7333 (ppp) REVERT: 3 39 ASN cc_start: 0.7976 (t0) cc_final: 0.7691 (t0) REVERT: 5 69 PHE cc_start: 0.7985 (m-10) cc_final: 0.7489 (t80) REVERT: 7 7 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8358 (mttt) REVERT: 7 69 PHE cc_start: 0.7962 (m-10) cc_final: 0.7443 (t80) REVERT: 8 7 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7804 (mtpp) REVERT: G 166 ARG cc_start: 0.8292 (ttp-110) cc_final: 0.8009 (mtm110) REVERT: I 7 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7906 (mt0) REVERT: I 44 LYS cc_start: 0.8704 (mttm) cc_final: 0.8240 (mttt) REVERT: K 19 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7620 (mt-10) REVERT: K 48 LYS cc_start: 0.7550 (tttt) cc_final: 0.6528 (tmtt) REVERT: K 72 LYS cc_start: 0.8176 (mttt) cc_final: 0.7564 (mmtt) REVERT: K 84 LYS cc_start: 0.8022 (mttp) cc_final: 0.7727 (pttp) REVERT: N 64 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8576 (tttp) REVERT: R 49 ARG cc_start: 0.7689 (ttm170) cc_final: 0.6733 (tmt170) REVERT: R 63 SER cc_start: 0.7963 (m) cc_final: 0.7723 (t) REVERT: R 85 LYS cc_start: 0.7911 (ptmt) cc_final: 0.7492 (pttm) outliers start: 22 outliers final: 13 residues processed: 257 average time/residue: 0.2580 time to fit residues: 93.7359 Evaluate side-chains 257 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 243 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.9980 chunk 131 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12374 Z= 0.181 Angle : 0.539 7.674 16761 Z= 0.276 Chirality : 0.040 0.137 1974 Planarity : 0.004 0.057 2071 Dihedral : 5.096 53.790 1716 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.15 % Allowed : 15.87 % Favored : 81.98 % 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: 1.78 (0.22), residues: 1559 helix: 2.02 (0.15), residues: 1113 sheet: -0.82 (0.58), residues: 85 loop : -0.95 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.023 0.001 PHE K 24 TYR 0.012 0.001 TYR G 44 ARG 0.007 0.000 ARG P 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 247 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7915 (ppp) cc_final: 0.7354 (ppp) REVERT: 3 39 ASN cc_start: 0.7978 (t0) cc_final: 0.7699 (t0) REVERT: 4 75 MET cc_start: 0.6607 (mpp) cc_final: 0.6118 (mpp) REVERT: 5 69 PHE cc_start: 0.7976 (m-10) cc_final: 0.7497 (t80) REVERT: 5 75 MET cc_start: 0.4945 (ptt) cc_final: 0.4334 (ptp) REVERT: 7 7 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8361 (mttt) REVERT: 7 69 PHE cc_start: 0.7934 (m-10) cc_final: 0.7405 (t80) REVERT: 8 7 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7807 (mtpp) REVERT: G 113 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8381 (ttp80) REVERT: G 166 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7998 (mtm110) REVERT: I 7 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7922 (mt0) REVERT: I 44 LYS cc_start: 0.8713 (mttm) cc_final: 0.8263 (mttt) REVERT: K 19 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7685 (mt-10) REVERT: K 48 LYS cc_start: 0.7551 (tttt) cc_final: 0.6517 (tmtt) REVERT: K 72 LYS cc_start: 0.8180 (mttt) cc_final: 0.7565 (mmtt) REVERT: K 84 LYS cc_start: 0.8012 (mttp) cc_final: 0.7692 (pttp) REVERT: N 154 MET cc_start: 0.8618 (mtp) cc_final: 0.8415 (mtm) REVERT: R 49 ARG cc_start: 0.7697 (ttm170) cc_final: 0.6770 (tmt170) REVERT: R 63 SER cc_start: 0.7974 (m) cc_final: 0.7731 (t) REVERT: R 85 LYS cc_start: 0.7907 (ptmt) cc_final: 0.7487 (pttm) outliers start: 27 outliers final: 17 residues processed: 261 average time/residue: 0.2510 time to fit residues: 93.3933 Evaluate side-chains 261 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 244 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 106 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12374 Z= 0.219 Angle : 0.554 7.573 16761 Z= 0.283 Chirality : 0.040 0.139 1974 Planarity : 0.004 0.042 2071 Dihedral : 5.124 53.936 1716 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.15 % Allowed : 16.11 % Favored : 81.74 % 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: 1.77 (0.22), residues: 1559 helix: 2.01 (0.15), residues: 1112 sheet: -0.84 (0.58), residues: 85 loop : -0.94 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 PHE 0.021 0.001 PHE K 24 TYR 0.013 0.001 TYR G 44 ARG 0.006 0.000 ARG P 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 246 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7919 (ppp) cc_final: 0.7333 (ppp) REVERT: 2 31 SER cc_start: 0.8560 (m) cc_final: 0.8284 (p) REVERT: 4 65 LEU cc_start: 0.7958 (mm) cc_final: 0.7661 (mt) REVERT: 4 75 MET cc_start: 0.6721 (mpp) cc_final: 0.6279 (mpp) REVERT: 5 69 PHE cc_start: 0.8003 (m-10) cc_final: 0.7501 (t80) REVERT: 5 75 MET cc_start: 0.5022 (ptt) cc_final: 0.4405 (ptp) REVERT: 7 7 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8363 (mttt) REVERT: 7 69 PHE cc_start: 0.7946 (m-10) cc_final: 0.7405 (t80) REVERT: 8 7 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7825 (mtpp) REVERT: G 113 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8374 (ttp80) REVERT: G 166 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.8000 (mtm110) REVERT: I 7 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7932 (mt0) REVERT: I 44 LYS cc_start: 0.8740 (mttm) cc_final: 0.8293 (mttt) REVERT: K 19 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7676 (mt-10) REVERT: K 48 LYS cc_start: 0.7601 (tttt) cc_final: 0.6557 (tmtt) REVERT: K 72 LYS cc_start: 0.8179 (mttt) cc_final: 0.7554 (mmtt) REVERT: K 84 LYS cc_start: 0.8059 (mttp) cc_final: 0.7746 (pttp) REVERT: R 49 ARG cc_start: 0.7713 (ttm170) cc_final: 0.6782 (tmt170) REVERT: R 63 SER cc_start: 0.8008 (m) cc_final: 0.7759 (t) REVERT: R 85 LYS cc_start: 0.7917 (ptmt) cc_final: 0.7487 (pttm) outliers start: 27 outliers final: 18 residues processed: 262 average time/residue: 0.2498 time to fit residues: 93.3868 Evaluate side-chains 259 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 2 residue 64 CYS Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain 8 residue 71 ILE Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 150 LEU Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.0770 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12374 Z= 0.165 Angle : 0.536 8.424 16761 Z= 0.273 Chirality : 0.040 0.197 1974 Planarity : 0.004 0.038 2071 Dihedral : 5.035 51.362 1716 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.67 % Allowed : 17.22 % Favored : 81.10 % 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: 1.94 (0.22), residues: 1559 helix: 2.13 (0.15), residues: 1111 sheet: -0.73 (0.59), residues: 85 loop : -0.85 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 28 HIS 0.002 0.000 HIS H 51 PHE 0.020 0.001 PHE K 24 TYR 0.011 0.001 TYR R 51 ARG 0.009 0.000 ARG G 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 250 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7955 (ppp) cc_final: 0.7377 (ppp) REVERT: 4 65 LEU cc_start: 0.7865 (mm) cc_final: 0.7657 (mt) REVERT: 4 75 MET cc_start: 0.6715 (mpp) cc_final: 0.6302 (mpp) REVERT: 5 69 PHE cc_start: 0.8001 (m-10) cc_final: 0.7518 (t80) REVERT: 5 75 MET cc_start: 0.4948 (ptt) cc_final: 0.4399 (ptp) REVERT: 7 7 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8321 (mttt) REVERT: 7 69 PHE cc_start: 0.7917 (m-10) cc_final: 0.7393 (t80) REVERT: 8 7 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7796 (mtpp) REVERT: G 87 LYS cc_start: 0.8264 (pptt) cc_final: 0.7977 (ptmm) REVERT: G 166 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.8005 (mtm110) REVERT: I 7 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7916 (mt0) REVERT: I 44 LYS cc_start: 0.8751 (mttm) cc_final: 0.8296 (mttt) REVERT: K 17 ILE cc_start: 0.8762 (mm) cc_final: 0.8532 (mm) REVERT: K 19 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7682 (mt-10) REVERT: K 48 LYS cc_start: 0.7574 (tttt) cc_final: 0.6533 (tmtt) REVERT: K 72 LYS cc_start: 0.8178 (mttt) cc_final: 0.7567 (mmtt) REVERT: N 154 MET cc_start: 0.8616 (mtp) cc_final: 0.8415 (mtm) REVERT: R 49 ARG cc_start: 0.7681 (ttm170) cc_final: 0.6743 (tmt170) REVERT: R 63 SER cc_start: 0.7959 (m) cc_final: 0.7724 (t) REVERT: R 85 LYS cc_start: 0.7897 (ptmt) cc_final: 0.7472 (pttm) outliers start: 21 outliers final: 14 residues processed: 258 average time/residue: 0.2332 time to fit residues: 85.3509 Evaluate side-chains 254 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 240 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 2 residue 64 CYS Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12374 Z= 0.179 Angle : 0.552 9.810 16761 Z= 0.279 Chirality : 0.040 0.176 1974 Planarity : 0.004 0.035 2071 Dihedral : 4.985 48.948 1716 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.91 % Allowed : 17.54 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1559 helix: 2.10 (0.15), residues: 1135 sheet: -0.78 (0.58), residues: 86 loop : -0.51 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 28 HIS 0.003 0.000 HIS H 51 PHE 0.019 0.001 PHE 1 69 TYR 0.011 0.001 TYR G 44 ARG 0.006 0.000 ARG G 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 246 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7946 (ppp) cc_final: 0.7364 (ppp) REVERT: 4 65 LEU cc_start: 0.7861 (mm) cc_final: 0.7639 (mt) REVERT: 4 75 MET cc_start: 0.6729 (mpp) cc_final: 0.6328 (mpp) REVERT: 5 69 PHE cc_start: 0.8023 (m-10) cc_final: 0.7508 (t80) REVERT: 5 75 MET cc_start: 0.4877 (ptt) cc_final: 0.4316 (ptp) REVERT: 7 7 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8335 (mttt) REVERT: 7 69 PHE cc_start: 0.7927 (m-10) cc_final: 0.7403 (t80) REVERT: 8 7 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7826 (mtpp) REVERT: G 46 LEU cc_start: 0.8421 (mt) cc_final: 0.8157 (mt) REVERT: G 87 LYS cc_start: 0.8257 (pptt) cc_final: 0.7985 (ptmt) REVERT: G 166 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.8009 (mtm110) REVERT: H 111 ASN cc_start: 0.7727 (t0) cc_final: 0.7316 (m110) REVERT: I 7 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7921 (mt0) REVERT: I 44 LYS cc_start: 0.8760 (mttm) cc_final: 0.8298 (mttt) REVERT: K 19 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7671 (mt-10) REVERT: K 48 LYS cc_start: 0.7590 (tttt) cc_final: 0.6527 (tmtt) REVERT: K 72 LYS cc_start: 0.8173 (mttt) cc_final: 0.7555 (mmtt) REVERT: N 154 MET cc_start: 0.8617 (mtp) cc_final: 0.8411 (mtm) REVERT: R 49 ARG cc_start: 0.7683 (ttm170) cc_final: 0.6744 (tmt170) REVERT: R 63 SER cc_start: 0.7977 (m) cc_final: 0.7743 (t) REVERT: R 85 LYS cc_start: 0.7923 (ptmt) cc_final: 0.7499 (pttm) outliers start: 24 outliers final: 18 residues processed: 259 average time/residue: 0.2459 time to fit residues: 90.0188 Evaluate side-chains 259 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 2 residue 64 CYS Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 0.0970 chunk 150 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12374 Z= 0.195 Angle : 0.576 11.491 16761 Z= 0.288 Chirality : 0.040 0.185 1974 Planarity : 0.004 0.035 2071 Dihedral : 4.997 46.719 1716 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.91 % Allowed : 17.38 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.22), residues: 1559 helix: 2.08 (0.15), residues: 1135 sheet: -0.79 (0.58), residues: 86 loop : -0.51 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.019 0.001 PHE 1 69 TYR 0.012 0.001 TYR G 44 ARG 0.007 0.000 ARG H 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3118 Ramachandran restraints generated. 1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 241 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 66 MET cc_start: 0.7940 (ppp) cc_final: 0.7360 (ppp) REVERT: 2 31 SER cc_start: 0.8544 (m) cc_final: 0.8294 (p) REVERT: 4 65 LEU cc_start: 0.7882 (mm) cc_final: 0.7655 (mt) REVERT: 4 75 MET cc_start: 0.6808 (mpp) cc_final: 0.6388 (mpp) REVERT: 5 69 PHE cc_start: 0.8022 (m-10) cc_final: 0.7507 (t80) REVERT: 5 75 MET cc_start: 0.4884 (ptt) cc_final: 0.4393 (ptp) REVERT: 7 7 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8286 (mttt) REVERT: 7 69 PHE cc_start: 0.7912 (m-10) cc_final: 0.7359 (t80) REVERT: 8 7 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7827 (mtpp) REVERT: G 46 LEU cc_start: 0.8423 (mt) cc_final: 0.8149 (mt) REVERT: G 87 LYS cc_start: 0.8246 (pptt) cc_final: 0.8024 (ptpt) REVERT: G 166 ARG cc_start: 0.8240 (ttp-110) cc_final: 0.8013 (mtm110) REVERT: I 7 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7903 (mt0) REVERT: I 44 LYS cc_start: 0.8732 (mttm) cc_final: 0.8260 (mttt) REVERT: K 19 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7645 (mt-10) REVERT: K 48 LYS cc_start: 0.7594 (tttt) cc_final: 0.6527 (tmtt) REVERT: K 72 LYS cc_start: 0.8179 (mttt) cc_final: 0.7562 (mmtt) REVERT: R 31 MET cc_start: 0.8608 (mmm) cc_final: 0.7624 (ttt) REVERT: R 49 ARG cc_start: 0.7693 (ttm170) cc_final: 0.6749 (tmt170) REVERT: R 63 SER cc_start: 0.7993 (m) cc_final: 0.7759 (t) REVERT: R 85 LYS cc_start: 0.7930 (ptmt) cc_final: 0.7506 (pttm) outliers start: 24 outliers final: 18 residues processed: 254 average time/residue: 0.2384 time to fit residues: 86.2548 Evaluate side-chains 259 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 PHE Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 31 SER Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 66 MET Chi-restraints excluded: chain 8 residue 67 VAL Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 179 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 74 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106759 restraints weight = 17465.338| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.26 r_work: 0.3172 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 12374 Z= 0.211 Angle : 0.852 59.181 16761 Z= 0.495 Chirality : 0.040 0.185 1974 Planarity : 0.004 0.035 2071 Dihedral : 5.001 46.711 1716 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.52 % Allowed : 17.70 % Favored : 80.78 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.22), residues: 1559 helix: 2.08 (0.15), residues: 1135 sheet: -0.79 (0.58), residues: 86 loop : -0.51 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 28 HIS 0.003 0.000 HIS H 51 PHE 0.018 0.001 PHE 1 69 TYR 0.012 0.001 TYR G 44 ARG 0.008 0.000 ARG R 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3291.52 seconds wall clock time: 59 minutes 19.99 seconds (3559.99 seconds total)