Starting phenix.real_space_refine (version: dev) on Fri Dec 16 20:09:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/12_2022/7ode_12826_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/12_2022/7ode_12826.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/12_2022/7ode_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_12826/12_2022/7ode_12826_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/12_2022/7ode_12826_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/12_2022/7ode_12826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/12_2022/7ode_12826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/12_2022/7ode_12826_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/12_2022/7ode_12826_trim_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 2 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: 34.43, per 1000 atoms: 0.37 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: 67.40 Conformation dependent library (CDL) restraints added in 2.3 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: 42.59 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: 75.69 Time building geometry restraints manager: 70.72 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 1.805 1.454 0.351 2.00e-02 2.50e+03 3.09e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.638 1.383 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" N3 5MU I 747 " pdb=" C4 5MU I 747 " ideal model delta sigma weight residual 1.179 1.383 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C5 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.150 1.349 -0.199 2.00e-02 2.50e+03 9.88e+01 bond pdb=" C2 1MG I 745 " pdb=" N3 1MG I 745 " ideal model delta sigma weight residual 1.473 1.322 0.151 2.00e-02 2.50e+03 5.69e+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=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C4 1MG I 745 " ideal model delta sigma weight residual 103.27 125.75 -22.48 3.00e+00 1.11e-01 5.61e+01 angle pdb=" C6 5MU I 747 " pdb=" C5 5MU I 747 " pdb=" C5M 5MU I 747 " ideal model delta sigma weight residual 106.12 120.90 -14.78 3.00e+00 1.11e-01 2.43e+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=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C8 1MG I 745 " ideal model delta sigma weight residual 141.41 129.30 12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" N3 5MU I 747 " pdb=" C4 5MU I 747 " pdb=" O4 5MU I 747 " ideal model delta sigma weight residual 107.57 119.11 -11.54 3.00e+00 1.11e-01 1.48e+01 ... (remaining 175565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 37350 35.29 - 70.57: 1088 70.57 - 105.86: 113 105.86 - 141.14: 6 141.14 - 176.43: 9 Dihedral angle restraints: 38566 sinusoidal: 32986 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 38563 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 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. 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.780 Extract box with map and model: 22.830 Check model and map are aligned: 1.030 Convert atoms to be neutral: 0.610 Process input model: 305.840 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 349.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 0.351 61817 Z= 0.193 Angle : 0.389 22.478 93319 Z= 0.205 Chirality : 0.027 0.263 12052 Planarity : 0.008 0.500 4399 Dihedral : 13.109 170.524 29211 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 3.32 % 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 *********************** 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 : 3.384 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 outliers start: 48 outliers final: 11 residues processed: 362 average time/residue: 2.8444 time to fit residues: 1270.4411 Evaluate side-chains 239 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 3.257 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 1.8800 time to fit residues: 10.4824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 155 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 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: 30.0000 chunk 215 optimal weight: 6.9990 chunk 336 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 24 ASN R 58 ASN R 128 ASN X 3 ASN Z 6 GLN c 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.073 61817 Z= 0.433 Angle : 0.655 13.111 93319 Z= 0.338 Chirality : 0.043 0.302 12052 Planarity : 0.006 0.109 4399 Dihedral : 13.318 173.766 25737 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 4.22 % 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: -0.22 (0.20), residues: 1727 helix: 0.26 (0.23), residues: 486 sheet: -0.60 (0.24), residues: 403 loop : 0.03 (0.21), residues: 838 *********************** 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 284 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 223 time to evaluate : 3.244 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 outliers start: 61 outliers final: 24 residues processed: 257 average time/residue: 2.7701 time to fit residues: 883.7365 Evaluate side-chains 238 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 3.214 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 9 average time/residue: 1.2618 time to fit residues: 20.0074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 228 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 363 optimal weight: 9.9990 chunk 299 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 61817 Z= 0.419 Angle : 0.626 13.068 93319 Z= 0.324 Chirality : 0.041 0.311 12052 Planarity : 0.006 0.115 4399 Dihedral : 13.588 175.554 25737 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 3.88 % 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: -0.40 (0.19), residues: 1727 helix: 0.06 (0.23), residues: 494 sheet: -0.64 (0.24), residues: 405 loop : -0.09 (0.21), residues: 828 *********************** 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 273 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 217 time to evaluate : 3.386 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 outliers start: 56 outliers final: 31 residues processed: 250 average time/residue: 3.0175 time to fit residues: 937.2967 Evaluate side-chains 232 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 11 average time/residue: 1.3414 time to fit residues: 25.5055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 0.6980 chunk 253 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 226 optimal weight: 0.6980 chunk 337 optimal weight: 0.7980 chunk 357 optimal weight: 0.6980 chunk 176 optimal weight: 40.0000 chunk 320 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 126 ASN Z 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 61817 Z= 0.129 Angle : 0.488 12.586 93319 Z= 0.264 Chirality : 0.032 0.214 12052 Planarity : 0.004 0.111 4399 Dihedral : 13.345 179.462 25737 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.77 % 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: 0.65 (0.24), residues: 488 sheet: -0.53 (0.25), residues: 394 loop : 0.20 (0.22), residues: 845 *********************** 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 262 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 3.381 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 outliers start: 40 outliers final: 26 residues processed: 249 average time/residue: 2.8233 time to fit residues: 870.9275 Evaluate side-chains 232 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 206 time to evaluate : 3.226 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 1.0734 time to fit residues: 11.5137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 0 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 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: K 117 GLN L 126 ASN Z 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2519 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= 0.380 Angle : 0.598 12.724 93319 Z= 0.311 Chirality : 0.040 0.293 12052 Planarity : 0.005 0.112 4399 Dihedral : 13.469 176.636 25737 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 3.67 % 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: 0.42 (0.24), residues: 489 sheet: -0.65 (0.25), residues: 395 loop : 0.11 (0.21), residues: 843 *********************** 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 258 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 205 time to evaluate : 3.417 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 outliers start: 53 outliers final: 36 residues processed: 237 average time/residue: 2.8243 time to fit residues: 831.4326 Evaluate side-chains 240 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 24 residues processed: 12 average time/residue: 1.3403 time to fit residues: 26.9087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 88 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 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 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 61817 Z= 0.380 Angle : 0.600 12.737 93319 Z= 0.313 Chirality : 0.040 0.293 12052 Planarity : 0.005 0.112 4399 Dihedral : 13.535 177.593 25737 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 3.53 % 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: -0.22 (0.20), residues: 1727 helix: 0.35 (0.23), residues: 489 sheet: -0.70 (0.25), residues: 401 loop : 0.03 (0.21), residues: 837 *********************** 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 256 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 205 time to evaluate : 3.374 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 outliers start: 51 outliers final: 38 residues processed: 236 average time/residue: 2.7955 time to fit residues: 818.5661 Evaluate side-chains 239 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 201 time to evaluate : 3.223 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 25 residues processed: 13 average time/residue: 1.3887 time to fit residues: 29.3679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 301 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 356 optimal weight: 0.4980 chunk 223 optimal weight: 0.5980 chunk 217 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** Z 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 61817 Z= 0.193 Angle : 0.521 12.660 93319 Z= 0.279 Chirality : 0.034 0.241 12052 Planarity : 0.005 0.111 4399 Dihedral : 13.499 178.120 25737 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 3.11 % 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: -0.01 (0.20), residues: 1727 helix: 0.59 (0.24), residues: 489 sheet: -0.67 (0.25), residues: 395 loop : 0.15 (0.21), residues: 843 *********************** 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 250 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 3.306 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 outliers start: 45 outliers final: 29 residues processed: 236 average time/residue: 2.8457 time to fit residues: 841.7339 Evaluate side-chains 233 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 3.247 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 1.4421 time to fit residues: 15.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 226 optimal weight: 0.0870 chunk 242 optimal weight: 7.9990 chunk 176 optimal weight: 40.0000 chunk 33 optimal weight: 4.9990 chunk 280 optimal weight: 10.0000 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 86 ASN K 117 GLN L 126 ASN X 115 ASN k 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 61817 Z= 0.363 Angle : 0.593 12.759 93319 Z= 0.310 Chirality : 0.039 0.288 12052 Planarity : 0.005 0.112 4399 Dihedral : 13.556 177.734 25737 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 2.98 % 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: 0.44 (0.24), residues: 489 sheet: -0.67 (0.26), residues: 377 loop : -0.03 (0.21), residues: 861 *********************** 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 249 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 3.246 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 outliers start: 43 outliers final: 33 residues processed: 236 average time/residue: 2.7555 time to fit residues: 811.1942 Evaluate side-chains 235 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 3.243 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 24 residues processed: 9 average time/residue: 1.4883 time to fit residues: 22.2508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 4.9990 chunk 341 optimal weight: 0.8980 chunk 311 optimal weight: 5.9990 chunk 332 optimal weight: 0.9990 chunk 200 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 331 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 61817 Z= 0.174 Angle : 0.518 13.566 93319 Z= 0.278 Chirality : 0.034 0.233 12052 Planarity : 0.005 0.111 4399 Dihedral : 13.511 178.767 25737 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.56 % 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: 0.00 (0.20), residues: 1727 helix: 0.66 (0.24), residues: 490 sheet: -0.70 (0.25), residues: 395 loop : 0.14 (0.22), residues: 842 *********************** 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 242 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 3.284 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 outliers start: 37 outliers final: 28 residues processed: 232 average time/residue: 2.7607 time to fit residues: 795.8610 Evaluate side-chains 229 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 3.253 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 1.3744 time to fit residues: 10.9624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 7.9990 chunk 351 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 368 optimal weight: 1.9990 chunk 339 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 61817 Z= 0.272 Angle : 0.541 12.725 93319 Z= 0.288 Chirality : 0.036 0.259 12052 Planarity : 0.005 0.112 4399 Dihedral : 13.472 179.134 25737 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 2.35 % 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: -0.05 (0.20), residues: 1727 helix: 0.60 (0.24), residues: 489 sheet: -0.67 (0.26), residues: 377 loop : 0.06 (0.21), residues: 861 ********************** 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 237 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 3.281 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 outliers start: 34 outliers final: 28 residues processed: 230 average time/residue: 2.8382 time to fit residues: 810.6657 Evaluate side-chains 228 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 1.6990 time to fit residues: 10.0837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 0.0980 chunk 312 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 293 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 Z 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.134292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.099108 restraints weight = 190803.229| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 0.84 r_work: 0.3304 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 61817 Z= 0.294 Angle : 0.552 12.745 93319 Z= 0.292 Chirality : 0.037 0.265 12052 Planarity : 0.005 0.112 4399 Dihedral : 13.485 179.036 25737 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 2.21 % 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: 0.57 (0.24), residues: 489 sheet: -0.68 (0.26), residues: 377 loop : 0.07 (0.21), residues: 861 =============================================================================== Job complete usr+sys time: 25772.66 seconds wall clock time: 445 minutes 28.94 seconds (26728.94 seconds total)