Starting phenix.real_space_refine on Tue Mar 19 06:52:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/03_2024/7ode_12826_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/03_2024/7ode_12826.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/03_2024/7ode_12826_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/03_2024/7ode_12826_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/03_2024/7ode_12826_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/03_2024/7ode_12826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/03_2024/7ode_12826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/03_2024/7ode_12826_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/03_2024/7ode_12826_trim_updated.pdb" } resolution = 2.84 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= 0.018 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: 6 Type Number sf(0) Gaussians P 1984 5.49 5 S 43 5.16 5 C 27704 2.51 5 N 10576 2.21 5 O 16221 1.98 5 H 35996 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 92524 Number of models: 1 Model: "" Number of chains: 16 Chain: "I" Number of atoms: 64211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1990, 64211 Inner-chain residues flagged as termini: ['pdbres=" A I 547 "', 'pdbres=" G I 962 "', 'pdbres=" U I1971 "', 'pdbres=" A I2033 "', 'pdbres=" G I2156 "'] Classifications: {'RNA': 1990} Modifications used: {'5*END': 5, 'rna2p': 1, 'rna2p_pur': 189, 'rna2p_pyr': 104, 'rna3p': 3, 'rna3p_pur': 975, 'rna3p_pyr': 717} Link IDs: {'rna2p': 293, 'rna3p': 1696} Unresolved chain links: 1 Chain breaks: 19 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3509 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 14, 'TRANS': 211} Chain: "L" Number of atoms: 2813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2813 Classifications: {'peptide': 183} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 1 Chain: "M" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2619 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain breaks: 1 Chain: "R" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2291 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "S" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1950 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "V" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1960 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "X" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1879 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Y" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1967 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "Z" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1655 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "a" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1779 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "b" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1545 Classifications: {'peptide': 93} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "c" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1612 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "g" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1032 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "i" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 907 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "k" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 795 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Time building chain proxies: 31.49, per 1000 atoms: 0.34 Number of scatterers: 92524 At special positions: 0 Unit cell: (201.16, 187.25, 182.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 43 16.00 P 1984 15.00 O 16221 8.00 N 10576 7.00 C 27704 6.00 H 35996 1.00 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: 67.85 Conformation dependent library (CDL) restraints added in 2.6 seconds 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 26 sheets defined 29.1% alpha, 19.4% beta 650 base pairs and 1141 stacking pairs defined. Time for finding SS restraints: 47.28 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 132 through 134 No H-bonds generated for 'chain 'K' and resid 132 through 134' Processing helix chain 'K' and resid 198 through 202 removed outlier: 4.140A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 212 Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'L' and resid 40 through 43 No H-bonds generated for 'chain 'L' and resid 40 through 43' Processing helix chain 'L' and resid 62 through 71 removed outlier: 3.693A pdb=" N ALA L 71 " --> pdb=" O HIS L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 101 Processing helix chain 'L' and resid 121 through 125 Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 Processing helix chain 'M' and resid 98 through 115 removed outlier: 3.514A pdb=" N VAL M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 removed outlier: 3.903A pdb=" N MET M 141 " --> pdb=" O LYS M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 160 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.783A pdb=" N GLU R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 61 No H-bonds generated for 'chain 'R' and resid 59 through 61' Processing helix chain 'R' and resid 68 through 71 No H-bonds generated for 'chain 'R' and resid 68 through 71' Processing helix chain 'R' and resid 89 through 95 Processing helix chain 'R' and resid 97 through 108 removed outlier: 4.062A pdb=" N ILE R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 121 removed outlier: 3.900A pdb=" N LYS R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 135 No H-bonds generated for 'chain 'R' and resid 133 through 135' Processing helix chain 'S' and resid 105 through 107 No H-bonds generated for 'chain 'S' and resid 105 through 107' Processing helix chain 'S' and resid 113 through 118 removed outlier: 3.508A pdb=" N SER S 117 " --> pdb=" O MET S 113 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 113 through 118' Processing helix chain 'V' and resid 14 through 31 Processing helix chain 'V' and resid 38 through 56 removed outlier: 4.275A pdb=" N ARG V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Proline residue: V 50 - end of helix removed outlier: 3.510A pdb=" N LYS V 56 " --> pdb=" O ILE V 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 70 Processing helix chain 'V' and resid 73 through 81 Processing helix chain 'V' and resid 83 through 86 No H-bonds generated for 'chain 'V' and resid 83 through 86' Processing helix chain 'X' and resid 3 through 10 Processing helix chain 'X' and resid 54 through 56 No H-bonds generated for 'chain 'X' and resid 54 through 56' Processing helix chain 'X' and resid 98 through 102 Processing helix chain 'X' and resid 105 through 108 Processing helix chain 'Y' and resid 7 through 20 Processing helix chain 'Y' and resid 26 through 29 Processing helix chain 'Y' and resid 32 through 72 removed outlier: 4.121A pdb=" N GLN Y 37 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG Y 51 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS Y 54 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 85 Processing helix chain 'Y' and resid 92 through 101 Processing helix chain 'Y' and resid 103 through 117 Processing helix chain 'a' and resid 14 through 23 removed outlier: 3.582A pdb=" N LEU a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL a 20 " --> pdb=" O LYS a 16 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 37 Processing helix chain 'a' and resid 42 through 62 Processing helix chain 'a' and resid 89 through 91 No H-bonds generated for 'chain 'a' and resid 89 through 91' Processing helix chain 'b' and resid 4 through 10 removed outlier: 3.518A pdb=" N LYS b 9 " --> pdb=" O GLU b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 27 Processing helix chain 'b' and resid 40 through 50 Processing helix chain 'c' and resid 67 through 69 No H-bonds generated for 'chain 'c' and resid 67 through 69' Processing helix chain 'g' and resid 3 through 8 removed outlier: 4.028A pdb=" N GLU g 8 " --> pdb=" O LYS g 4 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 33 Processing helix chain 'g' and resid 40 through 60 removed outlier: 3.835A pdb=" N VAL g 46 " --> pdb=" O LEU g 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 19 removed outlier: 4.578A pdb=" N HIS i 19 " --> pdb=" O MET i 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 16 Processing helix chain 'k' and resid 18 through 23 Processing helix chain 'k' and resid 25 through 37 Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 101 through 105 removed outlier: 6.328A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.610A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 169 through 172 removed outlier: 4.781A pdb=" N THR L 112 " --> pdb=" O ASP L 200 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASP L 200 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL L 26 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N MET L 11 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL L 24 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG L 13 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE L 22 " --> pdb=" O ARG L 13 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS L 190 " --> pdb=" O VAL L 177 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL L 177 " --> pdb=" O LYS L 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 80 through 83 removed outlier: 6.315A pdb=" N THR L 51 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL L 34 " --> pdb=" O THR L 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 117 through 119 Processing sheet with id= H, first strand: chain 'M' and resid 2 through 4 removed outlier: 3.572A pdb=" N LEU M 3 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU M 12 " --> pdb=" O LEU M 3 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.061A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'R' and resid 15 through 19 removed outlier: 6.380A pdb=" N TYR R 53 " --> pdb=" O TYR R 16 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL R 18 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE R 55 " --> pdb=" O VAL R 18 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 73 through 77 Processing sheet with id= L, first strand: chain 'S' and resid 7 through 9 removed outlier: 6.723A pdb=" N LYS S 40 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL S 24 " --> pdb=" O ILE S 38 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE S 38 " --> pdb=" O VAL S 24 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS S 59 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA S 83 " --> pdb=" O VAL S 63 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'V' and resid 33 through 37 Processing sheet with id= N, first strand: chain 'X' and resid 83 through 88 removed outlier: 6.327A pdb=" N THR X 25 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG X 39 " --> pdb=" O VAL X 32 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N GLU X 44 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE X 64 " --> pdb=" O GLU X 44 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR X 60 " --> pdb=" O ILE X 48 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE X 50 " --> pdb=" O ALA X 58 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA X 58 " --> pdb=" O ILE X 50 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Z' and resid 11 through 15 removed outlier: 7.443A pdb=" N GLN Z 6 " --> pdb=" O VAL Z 38 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL Z 38 " --> pdb=" O GLN Z 6 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Z' and resid 19 through 22 Processing sheet with id= Q, first strand: chain 'Z' and resid 32 through 35 removed outlier: 6.530A pdb=" N GLU Z 62 " --> pdb=" O ILE Z 98 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE Z 98 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Z' and resid 72 through 76 removed outlier: 3.508A pdb=" N LYS Z 76 " --> pdb=" O LYS Z 85 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS Z 85 " --> pdb=" O LYS Z 76 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'a' and resid 3 through 7 removed outlier: 6.896A pdb=" N SER a 108 " --> pdb=" O VAL a 71 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL a 71 " --> pdb=" O SER a 108 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'a' and resid 82 through 87 Processing sheet with id= U, first strand: chain 'b' and resid 11 through 14 removed outlier: 6.614A pdb=" N LYS b 33 " --> pdb=" O ARG b 12 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL b 31 " --> pdb=" O PRO b 14 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS b 81 " --> pdb=" O VAL b 34 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'b' and resid 67 through 70 Processing sheet with id= W, first strand: chain 'c' and resid 22 through 24 Processing sheet with id= X, first strand: chain 'c' and resid 41 through 44 Processing sheet with id= Y, first strand: chain 'c' and resid 83 through 88 removed outlier: 3.633A pdb=" N ARG c 86 " --> pdb=" O VAL c 93 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'c' and resid 25 through 29 removed outlier: 6.902A pdb=" N ILE c 35 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL c 28 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS c 33 " --> pdb=" O VAL c 28 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1614 hydrogen bonds 2568 hydrogen bond angles 0 basepair planarities 650 basepair parallelities 1141 stacking parallelities Total time for adding SS restraints: 73.25 Time building geometry restraints manager: 70.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 35991 1.03 - 1.22: 393 1.22 - 1.42: 29055 1.42 - 1.61: 32293 1.61 - 1.81: 81 Bond restraints: 97813 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.454 0.348 2.00e-02 2.50e+03 3.04e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.383 0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" N3 5MU I 747 " pdb=" C4 5MU I 747 " ideal model delta sigma weight residual 1.182 1.383 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C5 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.155 1.349 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C2 1MG I 745 " pdb=" N3 1MG I 745 " ideal model delta sigma weight residual 1.467 1.322 0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 97808 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.02: 12101 107.02 - 113.76: 101081 113.76 - 120.50: 36558 120.50 - 127.24: 21489 127.24 - 133.98: 4341 Bond angle restraints: 175570 Sorted by residual: angle pdb=" C6 5MU I 747 " pdb=" C5 5MU I 747 " pdb=" C5M 5MU I 747 " ideal model delta sigma weight residual 106.09 120.90 -14.81 3.00e+00 1.11e-01 2.44e+01 angle pdb=" O4 5MU I 747 " pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 112.86 126.83 -13.97 3.00e+00 1.11e-01 2.17e+01 angle pdb=" N3 5MU I 747 " pdb=" C4 5MU I 747 " pdb=" O4 5MU I 747 " ideal model delta sigma weight residual 107.56 119.11 -11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 112.59 122.69 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C2 5MU I 747 " pdb=" N3 5MU I 747 " pdb=" C4 5MU I 747 " ideal model delta sigma weight residual 118.32 127.30 -8.98 3.00e+00 1.11e-01 8.96e+00 ... (remaining 175565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 42626 35.29 - 70.57: 5099 70.57 - 105.86: 557 105.86 - 141.14: 6 141.14 - 176.43: 9 Dihedral angle restraints: 48297 sinusoidal: 42717 harmonic: 5580 Sorted by residual: dihedral pdb=" O4' U I1255 " pdb=" C1' U I1255 " pdb=" N1 U I1255 " pdb=" C2 U I1255 " ideal model delta sinusoidal sigma weight residual 200.00 40.02 159.98 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U I 846 " pdb=" C1' U I 846 " pdb=" N1 U I 846 " pdb=" C2 U I 846 " ideal model delta sinusoidal sigma weight residual 200.00 40.60 159.40 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U I 573 " pdb=" C1' U I 573 " pdb=" N1 U I 573 " pdb=" C2 U I 573 " ideal model delta sinusoidal sigma weight residual -160.00 -11.25 -148.75 1 1.50e+01 4.44e-03 7.91e+01 ... (remaining 48294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 11554 0.053 - 0.105: 414 0.105 - 0.158: 81 0.158 - 0.211: 1 0.211 - 0.263: 2 Chirality restraints: 12052 Sorted by residual: chirality pdb=" C3* PSU I 746 " pdb=" C4* PSU I 746 " pdb=" O3* PSU I 746 " pdb=" C2* PSU I 746 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C2* PSU I 746 " pdb=" C3* PSU I 746 " pdb=" O2* PSU I 746 " pdb=" C1* PSU I 746 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1' U I 573 " pdb=" O4' U I 573 " pdb=" C2' U I 573 " pdb=" N1 U I 573 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 12049 not shown) Planarity restraints: 7699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU I 747 " 0.012 2.00e-02 2.50e+03 5.00e-01 5.62e+03 pdb=" C4' 5MU I 747 " 0.409 2.00e-02 2.50e+03 pdb=" O4' 5MU I 747 " 0.492 2.00e-02 2.50e+03 pdb=" C3' 5MU I 747 " -0.574 2.00e-02 2.50e+03 pdb=" O3' 5MU I 747 " -0.445 2.00e-02 2.50e+03 pdb=" C2' 5MU I 747 " -0.246 2.00e-02 2.50e+03 pdb=" O2' 5MU I 747 " 0.812 2.00e-02 2.50e+03 pdb=" C1' 5MU I 747 " 0.262 2.00e-02 2.50e+03 pdb=" N1 5MU I 747 " -0.722 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 573 " -0.016 2.00e-02 2.50e+03 9.73e-03 2.84e+00 pdb=" N1 U I 573 " 0.029 2.00e-02 2.50e+03 pdb=" C2 U I 573 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U I 573 " 0.000 2.00e-02 2.50e+03 pdb=" N3 U I 573 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U I 573 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U I 573 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U I 573 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U I 573 " -0.002 2.00e-02 2.50e+03 pdb=" H5 U I 573 " 0.000 2.00e-02 2.50e+03 pdb=" H3 U I 573 " -0.000 2.00e-02 2.50e+03 pdb=" H6 U I 573 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 512 " -0.021 2.00e-02 2.50e+03 8.46e-03 2.50e+00 pdb=" N9 G I 512 " 0.023 2.00e-02 2.50e+03 pdb=" C8 G I 512 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G I 512 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G I 512 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G I 512 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G I 512 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G I 512 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G I 512 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G I 512 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G I 512 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G I 512 " 0.001 2.00e-02 2.50e+03 pdb=" H8 G I 512 " -0.000 2.00e-02 2.50e+03 pdb=" H1 G I 512 " -0.000 2.00e-02 2.50e+03 ... (remaining 7696 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 2755 2.13 - 2.75: 126982 2.75 - 3.37: 239654 3.37 - 3.98: 363926 3.98 - 4.60: 523878 Nonbonded interactions: 1257195 Sorted by model distance: nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.516 1.850 nonbonded pdb=" OP1 G I1266 " pdb=" HE ARG i 16 " model vdw 1.534 1.850 nonbonded pdb=" H1 G I 476 " pdb=" OP2 A I 479 " model vdw 1.545 1.850 nonbonded pdb="HO2' G I 372 " pdb=" O6 G I 400 " model vdw 1.553 1.850 nonbonded pdb=" OD2 ASP c 18 " pdb=" H ASN c 40 " model vdw 1.559 1.850 ... (remaining 1257190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.960 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: 0.750 Extract box with map and model: 19.710 Check model and map are aligned: 1.000 Set scattering table: 0.630 Process input model: 298.420 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.170 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 338.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.003 0.348 61817 Z= 0.191 Angle : 0.380 14.812 93319 Z= 0.203 Chirality : 0.027 0.263 12052 Planarity : 0.008 0.500 4399 Dihedral : 22.757 170.524 36304 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.32 % Allowed : 7.34 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1727 helix: 0.41 (0.23), residues: 485 sheet: -0.50 (0.24), residues: 409 loop : 0.02 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 213 HIS 0.002 0.000 HIS g 41 PHE 0.007 0.001 PHE Z 77 TYR 0.007 0.001 TYR K 103 ARG 0.004 0.000 ARG k 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 335 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 126 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7664 (t0) REVERT: L 174 SER cc_start: 0.8679 (m) cc_final: 0.8432 (t) REVERT: M 23 PHE cc_start: 0.8087 (t80) cc_final: 0.7864 (t80) REVERT: M 149 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8219 (pt) REVERT: R 141 ASP cc_start: 0.5583 (OUTLIER) cc_final: 0.5166 (m-30) REVERT: S 32 TYR cc_start: 0.8002 (m-80) cc_final: 0.7709 (m-80) REVERT: S 84 CYS cc_start: 0.7148 (p) cc_final: 0.6864 (m) REVERT: S 99 ILE cc_start: 0.7707 (mm) cc_final: 0.7067 (mt) REVERT: S 103 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7084 (m) REVERT: V 110 MET cc_start: 0.8921 (mmm) cc_final: 0.8551 (mmm) REVERT: X 9 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7184 (mt-10) REVERT: c 45 HIS cc_start: 0.7827 (m170) cc_final: 0.7138 (m-70) REVERT: i 10 ARG cc_start: 0.5259 (ptt-90) cc_final: 0.4944 (ptm160) outliers start: 48 outliers final: 11 residues processed: 362 average time/residue: 3.2077 time to fit residues: 1403.4130 Evaluate side-chains 246 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 231 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 149 ILE Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain i residue 27 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 4.9990 chunk 280 optimal weight: 0.0870 chunk 155 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 290 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 176 optimal weight: 40.0000 chunk 215 optimal weight: 6.9990 chunk 336 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN M 24 ASN R 58 ASN R 128 ASN X 3 ASN Z 6 GLN c 46 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 61817 Z= 0.363 Angle : 0.608 13.884 93319 Z= 0.317 Chirality : 0.040 0.282 12052 Planarity : 0.006 0.118 4399 Dihedral : 23.238 173.689 32862 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.08 % Allowed : 16.82 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.07 (0.20), residues: 1727 helix: 0.36 (0.23), residues: 492 sheet: -0.52 (0.25), residues: 384 loop : 0.12 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 213 HIS 0.004 0.001 HIS k 16 PHE 0.012 0.002 PHE L 118 TYR 0.017 0.002 TYR Z 2 ARG 0.007 0.001 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 231 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: K 82 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7585 (mt-10) REVERT: L 126 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7810 (t0) REVERT: L 174 SER cc_start: 0.8785 (m) cc_final: 0.8366 (t) REVERT: M 47 LYS cc_start: 0.4825 (OUTLIER) cc_final: 0.4540 (tmmt) REVERT: M 134 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8695 (tp) REVERT: R 90 GLU cc_start: 0.6551 (pp20) cc_final: 0.6316 (pp20) REVERT: R 91 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7460 (mm-30) REVERT: R 141 ASP cc_start: 0.5371 (OUTLIER) cc_final: 0.4905 (m-30) REVERT: S 7 MET cc_start: 0.7315 (mmm) cc_final: 0.6353 (mmt) REVERT: S 84 CYS cc_start: 0.7196 (p) cc_final: 0.6895 (m) REVERT: S 103 VAL cc_start: 0.7487 (OUTLIER) cc_final: 0.7079 (m) REVERT: X 9 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7245 (mt-10) REVERT: X 78 SER cc_start: 0.7861 (t) cc_final: 0.7624 (p) REVERT: X 89 ARG cc_start: 0.7490 (mmm160) cc_final: 0.7287 (mmm160) REVERT: Z 81 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.5688 (mmtm) REVERT: c 24 LYS cc_start: 0.7255 (ttpt) cc_final: 0.6393 (pptt) REVERT: c 45 HIS cc_start: 0.7706 (m170) cc_final: 0.7117 (m-70) REVERT: i 10 ARG cc_start: 0.5327 (ptt-90) cc_final: 0.5083 (ptm160) outliers start: 59 outliers final: 22 residues processed: 263 average time/residue: 3.0815 time to fit residues: 991.2391 Evaluate side-chains 248 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 219 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 81 LYS Chi-restraints excluded: chain a residue 2 GLU Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain c residue 15 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN c 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 61817 Z= 0.471 Angle : 0.675 13.197 93319 Z= 0.346 Chirality : 0.044 0.327 12052 Planarity : 0.006 0.116 4399 Dihedral : 23.332 175.429 32852 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.64 % Allowed : 17.51 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.19), residues: 1727 helix: 0.03 (0.23), residues: 489 sheet: -0.67 (0.24), residues: 405 loop : -0.06 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 213 HIS 0.005 0.001 HIS i 38 PHE 0.017 0.002 PHE X 43 TYR 0.018 0.002 TYR Z 2 ARG 0.010 0.001 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7187 (mt-10) REVERT: K 82 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7662 (mt-10) REVERT: L 13 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7555 (ptm160) REVERT: L 43 ASP cc_start: 0.7630 (m-30) cc_final: 0.7395 (m-30) REVERT: L 49 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: L 174 SER cc_start: 0.8725 (m) cc_final: 0.8268 (t) REVERT: M 134 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8807 (tp) REVERT: M 156 ASN cc_start: 0.8176 (m-40) cc_final: 0.7963 (t0) REVERT: R 141 ASP cc_start: 0.5237 (OUTLIER) cc_final: 0.4561 (m-30) REVERT: S 7 MET cc_start: 0.7272 (mmm) cc_final: 0.6981 (mmm) REVERT: S 20 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.5138 (tmt) REVERT: a 95 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6406 (mtp180) REVERT: c 45 HIS cc_start: 0.7795 (m170) cc_final: 0.7161 (m90) REVERT: i 10 ARG cc_start: 0.5581 (ptt-90) cc_final: 0.5207 (ptm160) outliers start: 67 outliers final: 36 residues processed: 260 average time/residue: 3.6945 time to fit residues: 1188.8003 Evaluate side-chains 251 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 209 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 49 GLN Chi-restraints excluded: chain L residue 114 LYS Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 20 MET Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain V residue 2 ARG Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain X residue 103 ARG Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 81 LYS Chi-restraints excluded: chain a residue 2 GLU Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain k residue 22 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 226 optimal weight: 0.2980 chunk 337 optimal weight: 0.5980 chunk 357 optimal weight: 0.6980 chunk 176 optimal weight: 40.0000 chunk 320 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 126 ASN Z 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 61817 Z= 0.127 Angle : 0.496 12.734 93319 Z= 0.269 Chirality : 0.032 0.215 12052 Planarity : 0.004 0.112 4399 Dihedral : 23.192 179.594 32850 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.98 % Allowed : 20.21 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1727 helix: 0.60 (0.24), residues: 490 sheet: -0.54 (0.25), residues: 399 loop : 0.18 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 213 HIS 0.007 0.001 HIS Z 82 PHE 0.008 0.001 PHE Z 53 TYR 0.008 0.001 TYR a 38 ARG 0.008 0.000 ARG b 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7222 (mt-10) REVERT: K 82 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7524 (mt-10) REVERT: K 117 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8236 (tp40) REVERT: L 43 ASP cc_start: 0.7614 (m-30) cc_final: 0.7395 (m-30) REVERT: L 49 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: L 174 SER cc_start: 0.8677 (m) cc_final: 0.8211 (t) REVERT: M 156 ASN cc_start: 0.8120 (m-40) cc_final: 0.7900 (t0) REVERT: R 141 ASP cc_start: 0.5168 (OUTLIER) cc_final: 0.4586 (m-30) REVERT: S 103 VAL cc_start: 0.7491 (OUTLIER) cc_final: 0.7086 (m) REVERT: c 24 LYS cc_start: 0.7337 (ttpt) cc_final: 0.6433 (pptt) REVERT: c 45 HIS cc_start: 0.7705 (m170) cc_final: 0.7154 (m-70) REVERT: c 85 PHE cc_start: 0.7440 (m-80) cc_final: 0.6954 (m-80) REVERT: i 10 ARG cc_start: 0.5487 (ptt-90) cc_final: 0.5132 (ptm160) outliers start: 43 outliers final: 26 residues processed: 244 average time/residue: 3.1774 time to fit residues: 945.3528 Evaluate side-chains 242 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 49 GLN Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain Z residue 82 HIS Chi-restraints excluded: chain a residue 2 GLU Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain i residue 15 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 321 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 126 ASN Z 43 ASN c 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 61817 Z= 0.383 Angle : 0.602 12.785 93319 Z= 0.313 Chirality : 0.040 0.295 12052 Planarity : 0.005 0.113 4399 Dihedral : 23.194 177.655 32850 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 3.74 % Allowed : 20.14 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.11 (0.20), residues: 1727 helix: 0.43 (0.24), residues: 489 sheet: -0.65 (0.25), residues: 407 loop : 0.11 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 213 HIS 0.030 0.001 HIS Z 82 PHE 0.012 0.002 PHE L 127 TYR 0.014 0.002 TYR Z 2 ARG 0.006 0.001 ARG b 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 214 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: K 82 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7631 (mt-10) REVERT: K 117 GLN cc_start: 0.8471 (tt0) cc_final: 0.8165 (tp40) REVERT: L 43 ASP cc_start: 0.7631 (m-30) cc_final: 0.7416 (m-30) REVERT: L 49 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: L 56 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7630 (ptpt) REVERT: L 174 SER cc_start: 0.8688 (m) cc_final: 0.8286 (t) REVERT: M 115 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: M 156 ASN cc_start: 0.8146 (m-40) cc_final: 0.7910 (t0) REVERT: R 141 ASP cc_start: 0.5276 (OUTLIER) cc_final: 0.4613 (m-30) REVERT: c 24 LYS cc_start: 0.7353 (ttpt) cc_final: 0.6416 (pptt) REVERT: c 45 HIS cc_start: 0.7693 (m170) cc_final: 0.7160 (m90) REVERT: i 10 ARG cc_start: 0.5562 (ptt-90) cc_final: 0.5212 (ptm160) outliers start: 54 outliers final: 36 residues processed: 246 average time/residue: 3.1579 time to fit residues: 946.2117 Evaluate side-chains 253 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 49 GLN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 115 GLN Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain V residue 2 ARG Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 41 ILE Chi-restraints excluded: chain a residue 2 GLU Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 91 LYS Chi-restraints excluded: chain i residue 15 MET Chi-restraints excluded: chain k residue 22 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 357 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 86 ASN L 58 ASN ** M 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 115 ASN Z 82 HIS k 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 61817 Z= 0.375 Angle : 0.602 12.861 93319 Z= 0.314 Chirality : 0.040 0.290 12052 Planarity : 0.006 0.113 4399 Dihedral : 23.244 179.004 32850 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.74 % Allowed : 20.62 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.27 (0.20), residues: 1727 helix: 0.28 (0.23), residues: 494 sheet: -0.70 (0.26), residues: 381 loop : -0.04 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 213 HIS 0.023 0.001 HIS Z 82 PHE 0.009 0.002 PHE R 4 TYR 0.020 0.002 TYR Z 2 ARG 0.010 0.001 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 218 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: K 82 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7578 (mt-10) REVERT: K 199 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: K 201 MET cc_start: 0.8177 (ptm) cc_final: 0.7967 (ptm) REVERT: L 43 ASP cc_start: 0.7608 (m-30) cc_final: 0.7379 (m-30) REVERT: L 49 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: L 56 LYS cc_start: 0.7960 (ptpt) cc_final: 0.7669 (ptpt) REVERT: L 174 SER cc_start: 0.8686 (m) cc_final: 0.8309 (t) REVERT: M 6 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8049 (mtmt) REVERT: M 156 ASN cc_start: 0.8162 (m-40) cc_final: 0.7915 (t0) REVERT: R 141 ASP cc_start: 0.5331 (OUTLIER) cc_final: 0.4615 (m-30) REVERT: S 1 MET cc_start: 0.5311 (ttt) cc_final: 0.5086 (ttt) REVERT: S 20 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.5049 (tmt) REVERT: Z 84 ARG cc_start: 0.5570 (OUTLIER) cc_final: 0.5299 (ptt180) REVERT: a 95 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6265 (ttp-170) REVERT: c 24 LYS cc_start: 0.7384 (ttpt) cc_final: 0.6420 (pptt) REVERT: i 10 ARG cc_start: 0.5614 (ptt-90) cc_final: 0.5267 (ptm160) REVERT: k 41 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.7455 (ttp-170) outliers start: 54 outliers final: 38 residues processed: 247 average time/residue: 3.2293 time to fit residues: 966.7938 Evaluate side-chains 254 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 208 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 49 GLN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 20 MET Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain V residue 2 ARG Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain Z residue 84 ARG Chi-restraints excluded: chain a residue 2 GLU Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 91 LYS Chi-restraints excluded: chain i residue 15 MET Chi-restraints excluded: chain k residue 22 MET Chi-restraints excluded: chain k residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 301 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 223 optimal weight: 0.0870 chunk 217 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 58 ASN L 126 ASN ** M 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN Z 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 61817 Z= 0.273 Angle : 0.558 12.785 93319 Z= 0.296 Chirality : 0.036 0.267 12052 Planarity : 0.005 0.113 4399 Dihedral : 23.255 179.054 32850 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.50 % Allowed : 19.79 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.19 (0.20), residues: 1727 helix: 0.42 (0.24), residues: 494 sheet: -0.70 (0.26), residues: 381 loop : -0.00 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 213 HIS 0.009 0.001 HIS Z 82 PHE 0.008 0.001 PHE X 59 TYR 0.014 0.001 TYR Z 2 ARG 0.013 0.001 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 212 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: K 82 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7562 (mt-10) REVERT: K 199 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6892 (mt-10) REVERT: K 201 MET cc_start: 0.8161 (ptm) cc_final: 0.7957 (ptm) REVERT: L 49 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: L 174 SER cc_start: 0.8712 (m) cc_final: 0.8307 (t) REVERT: M 6 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8059 (mtmt) REVERT: M 156 ASN cc_start: 0.8144 (m-40) cc_final: 0.7907 (t0) REVERT: R 141 ASP cc_start: 0.5319 (OUTLIER) cc_final: 0.4851 (m-30) REVERT: S 1 MET cc_start: 0.5343 (ttt) cc_final: 0.5036 (ttt) REVERT: S 20 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.5042 (tmt) REVERT: a 95 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6262 (ttp-170) REVERT: c 24 LYS cc_start: 0.7387 (ttpt) cc_final: 0.6423 (pptt) REVERT: i 10 ARG cc_start: 0.5596 (OUTLIER) cc_final: 0.5253 (ptm160) outliers start: 65 outliers final: 38 residues processed: 249 average time/residue: 3.3045 time to fit residues: 1010.8816 Evaluate side-chains 253 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 207 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 49 GLN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 20 MET Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain V residue 2 ARG Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 48 ILE Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 91 LYS Chi-restraints excluded: chain i residue 10 ARG Chi-restraints excluded: chain i residue 15 MET Chi-restraints excluded: chain k residue 22 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 176 optimal weight: 40.0000 chunk 33 optimal weight: 4.9990 chunk 280 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 126 ASN ** M 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 61817 Z= 0.309 Angle : 0.568 12.817 93319 Z= 0.300 Chirality : 0.038 0.275 12052 Planarity : 0.005 0.113 4399 Dihedral : 23.212 179.651 32850 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.01 % Allowed : 20.62 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.18 (0.20), residues: 1727 helix: 0.49 (0.24), residues: 488 sheet: -0.73 (0.26), residues: 388 loop : -0.01 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 213 HIS 0.008 0.001 HIS Z 82 PHE 0.009 0.001 PHE c 85 TYR 0.012 0.001 TYR Z 2 ARG 0.014 0.001 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 210 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: K 82 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7577 (mt-10) REVERT: K 199 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: K 201 MET cc_start: 0.8184 (ptm) cc_final: 0.7981 (ptm) REVERT: L 49 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: L 174 SER cc_start: 0.8711 (m) cc_final: 0.8305 (t) REVERT: M 6 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8054 (mtmt) REVERT: M 156 ASN cc_start: 0.8154 (m-40) cc_final: 0.7913 (t0) REVERT: R 141 ASP cc_start: 0.5265 (OUTLIER) cc_final: 0.4717 (m-30) REVERT: S 1 MET cc_start: 0.5339 (ttt) cc_final: 0.5077 (ttt) REVERT: S 20 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.5044 (tmt) REVERT: Z 81 LYS cc_start: 0.6348 (mmtt) cc_final: 0.6118 (mmtt) REVERT: a 95 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6149 (ttp-170) REVERT: i 10 ARG cc_start: 0.5592 (OUTLIER) cc_final: 0.5254 (ptm160) outliers start: 58 outliers final: 37 residues processed: 243 average time/residue: 3.2471 time to fit residues: 960.0454 Evaluate side-chains 251 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 206 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 101 ARG Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 49 GLN Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 20 MET Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain V residue 2 ARG Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain X residue 24 ASP Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain a residue 2 GLU Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain a residue 95 ARG Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 91 LYS Chi-restraints excluded: chain i residue 10 ARG Chi-restraints excluded: chain i residue 15 MET Chi-restraints excluded: chain k residue 22 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 0.6980 chunk 341 optimal weight: 0.9980 chunk 311 optimal weight: 5.9990 chunk 332 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 331 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 58 ASN L 126 ASN Z 43 ASN Z 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 61817 Z= 0.133 Angle : 0.487 12.684 93319 Z= 0.263 Chirality : 0.032 0.217 12052 Planarity : 0.004 0.112 4399 Dihedral : 23.133 177.127 32850 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.11 % Allowed : 21.73 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.18 (0.20), residues: 1727 helix: 0.85 (0.24), residues: 490 sheet: -0.62 (0.26), residues: 377 loop : 0.21 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 125 HIS 0.009 0.001 HIS Z 82 PHE 0.026 0.001 PHE L 127 TYR 0.008 0.001 TYR a 38 ARG 0.010 0.000 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: K 82 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7574 (mt-10) REVERT: K 201 MET cc_start: 0.8185 (ptm) cc_final: 0.7982 (ptm) REVERT: L 49 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: L 174 SER cc_start: 0.8658 (m) cc_final: 0.8298 (t) REVERT: M 6 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8067 (mtmt) REVERT: M 156 ASN cc_start: 0.8117 (m-40) cc_final: 0.7886 (t0) REVERT: R 141 ASP cc_start: 0.5284 (OUTLIER) cc_final: 0.4736 (m-30) REVERT: S 1 MET cc_start: 0.5103 (ttt) cc_final: 0.4819 (ttt) REVERT: S 103 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7079 (m) REVERT: c 24 LYS cc_start: 0.7297 (ttpt) cc_final: 0.6354 (pptt) REVERT: i 10 ARG cc_start: 0.5413 (OUTLIER) cc_final: 0.5096 (ptm160) REVERT: k 41 ARG cc_start: 0.7750 (mtp-110) cc_final: 0.7509 (ttp-110) outliers start: 45 outliers final: 28 residues processed: 238 average time/residue: 3.1123 time to fit residues: 903.4867 Evaluate side-chains 240 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 206 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 49 GLN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain V residue 2 ARG Chi-restraints excluded: chain V residue 24 MET Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 91 LYS Chi-restraints excluded: chain i residue 10 ARG Chi-restraints excluded: chain i residue 15 MET Chi-restraints excluded: chain k residue 22 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 4.9990 chunk 351 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 368 optimal weight: 2.9990 chunk 339 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 58 ASN ** M 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 61817 Z= 0.292 Angle : 0.543 12.686 93319 Z= 0.287 Chirality : 0.036 0.257 12052 Planarity : 0.005 0.112 4399 Dihedral : 23.127 179.618 32850 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.04 % Allowed : 21.66 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.08 (0.20), residues: 1727 helix: 0.74 (0.24), residues: 489 sheet: -0.63 (0.26), residues: 384 loop : 0.16 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 213 HIS 0.009 0.001 HIS Z 82 PHE 0.029 0.002 PHE Z 53 TYR 0.010 0.001 TYR a 38 ARG 0.011 0.000 ARG k 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3454 Ramachandran restraints generated. 1727 Oldfield, 0 Emsley, 1727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 210 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 79 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: K 82 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7504 (mt-10) REVERT: K 201 MET cc_start: 0.8221 (ptm) cc_final: 0.8004 (ptm) REVERT: L 49 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: L 174 SER cc_start: 0.8697 (m) cc_final: 0.8312 (t) REVERT: M 6 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8075 (mtmt) REVERT: M 156 ASN cc_start: 0.8146 (m-40) cc_final: 0.7905 (t0) REVERT: R 141 ASP cc_start: 0.5233 (OUTLIER) cc_final: 0.4697 (m-30) REVERT: S 103 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7114 (m) REVERT: Z 81 LYS cc_start: 0.6422 (mmtt) cc_final: 0.6213 (mmtt) REVERT: c 24 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6355 (pptt) REVERT: i 10 ARG cc_start: 0.5525 (OUTLIER) cc_final: 0.5195 (ptm160) outliers start: 44 outliers final: 31 residues processed: 237 average time/residue: 3.2472 time to fit residues: 934.0913 Evaluate side-chains 241 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 49 GLN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 35 TYR Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain R residue 14 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain V residue 2 ARG Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 58 ARG Chi-restraints excluded: chain Y residue 71 GLN Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain c residue 91 LYS Chi-restraints excluded: chain i residue 10 ARG Chi-restraints excluded: chain i residue 15 MET Chi-restraints excluded: chain k residue 22 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 5.9990 chunk 312 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 293 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 58 ASN ** M 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 GLN Z 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.133242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097682 restraints weight = 190465.649| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 0.91 r_work: 0.3251 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 61817 Z= 0.382 Angle : 0.608 12.752 93319 Z= 0.316 Chirality : 0.040 0.289 12052 Planarity : 0.006 0.112 4399 Dihedral : 23.205 178.885 32850 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.91 % Allowed : 22.01 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.16 (0.20), residues: 1727 helix: 0.48 (0.24), residues: 489 sheet: -0.66 (0.26), residues: 380 loop : -0.03 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 213 HIS 0.012 0.001 HIS Z 82 PHE 0.022 0.002 PHE Z 53 TYR 0.013 0.002 TYR Z 2 ARG 0.008 0.001 ARG b 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27883.60 seconds wall clock time: 483 minutes 8.16 seconds (28988.16 seconds total)