Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 23 01:03:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/08_2023/7ode_12826_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/08_2023/7ode_12826.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/08_2023/7ode_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_12826/08_2023/7ode_12826_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/08_2023/7ode_12826_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/08_2023/7ode_12826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/08_2023/7ode_12826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/08_2023/7ode_12826_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ode_12826/08_2023/7ode_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-1.21rc1-5044/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: 3 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: 28.72, per 1000 atoms: 0.31 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: 65.43 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: 45.52 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: 74.05 Time building geometry restraints manager: 68.52 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=" N3 1MG I 745 " pdb=" C4 1MG I 745 " ideal model delta sigma weight residual 1.492 1.351 0.141 2.00e-02 2.50e+03 4.95e+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=" C8 1MG I 745 " ideal model delta sigma weight residual 100.16 129.30 -29.14 3.00e+00 1.11e-01 9.43e+01 angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C4 1MG I 745 " ideal model delta sigma weight residual 146.15 125.75 20.40 3.00e+00 1.11e-01 4.62e+01 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 ... (remaining 175565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 37353 35.29 - 70.57: 1093 70.57 - 105.86: 113 105.86 - 141.14: 6 141.14 - 176.43: 9 Dihedral angle restraints: 38574 sinusoidal: 32994 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 38571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 11550 0.053 - 0.105: 414 0.105 - 0.158: 81 0.158 - 0.211: 1 0.211 - 0.263: 2 Chirality restraints: 12048 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 12045 not shown) Planarity restraints: 7700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.037 2.00e-02 2.50e+03 5.54e-01 6.91e+03 pdb=" C4' 1MG I 745 " -0.424 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.570 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.557 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.206 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.907 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.237 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.824 2.00e-02 2.50e+03 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 ... (remaining 7697 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: 4.910 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: 0.760 Extract box with map and model: 23.120 Check model and map are aligned: 1.010 Set scattering table: 0.650 Process input model: 292.060 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 334.470 ------------------------------------------------------------------------------- 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= 0.190 Angle : 0.398 29.140 93319 Z= 0.207 Chirality : 0.027 0.263 12048 Planarity : 0.011 0.554 4400 Dihedral : 13.130 170.524 29219 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 % 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 : 3.132 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: 3.2785 time to fit residues: 1440.2974 Evaluate side-chains 239 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 3.169 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 2.0173 time to fit residues: 10.9066 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.072 61817 Z= 0.434 Angle : 0.660 12.871 93319 Z= 0.342 Chirality : 0.043 0.299 12048 Planarity : 0.006 0.120 4400 Dihedral : 13.287 173.206 25745 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 4.08 % 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: -0.17 (0.20), residues: 1727 helix: 0.31 (0.23), residues: 486 sheet: -0.56 (0.24), residues: 401 loop : 0.04 (0.21), residues: 840 *********************** 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 282 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 223 time to evaluate : 3.111 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 outliers start: 59 outliers final: 24 residues processed: 256 average time/residue: 3.2406 time to fit residues: 1029.2439 Evaluate side-chains 237 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 3.631 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 9 average time/residue: 1.3920 time to fit residues: 22.4942 ------------------------------------------------------------------------------- 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: 0.9980 chunk 92 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN Z 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 61817 Z= 0.351 Angle : 0.593 13.122 93319 Z= 0.314 Chirality : 0.039 0.292 12048 Planarity : 0.006 0.117 4400 Dihedral : 13.501 176.584 25745 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 3.81 % 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: 489 sheet: -0.60 (0.24), residues: 405 loop : 0.03 (0.21), residues: 833 *********************** 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 274 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 219 time to evaluate : 3.189 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 outliers start: 55 outliers final: 30 residues processed: 248 average time/residue: 3.3561 time to fit residues: 1011.1069 Evaluate side-chains 235 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 3.121 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 18 residues processed: 12 average time/residue: 1.4136 time to fit residues: 28.0077 ------------------------------------------------------------------------------- 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: 0.5980 chunk 253 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 226 optimal weight: 0.9980 chunk 337 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 176 optimal weight: 40.0000 chunk 320 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 61817 Z= 0.219 Angle : 0.527 12.694 93319 Z= 0.286 Chirality : 0.034 0.247 12048 Planarity : 0.005 0.114 4400 Dihedral : 13.364 178.363 25745 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 2.91 % 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: 0.04 (0.20), residues: 1727 helix: 0.57 (0.24), residues: 488 sheet: -0.51 (0.25), residues: 383 loop : 0.13 (0.21), residues: 856 *********************** 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 251 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 209 time to evaluate : 3.107 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 outliers start: 42 outliers final: 29 residues processed: 236 average time/residue: 3.3039 time to fit residues: 947.8235 Evaluate side-chains 233 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 7 average time/residue: 0.9808 time to fit residues: 14.5211 ------------------------------------------------------------------------------- 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: 4.9990 chunk 203 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 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: 6.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.2546 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= 0.358 Angle : 0.597 12.787 93319 Z= 0.316 Chirality : 0.039 0.292 12048 Planarity : 0.006 0.115 4400 Dihedral : 13.516 176.854 25745 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 3.94 % 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: 0.40 (0.24), residues: 489 sheet: -0.62 (0.25), residues: 385 loop : 0.08 (0.21), residues: 853 *********************** 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 266 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 209 time to evaluate : 3.116 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 outliers start: 57 outliers final: 38 residues processed: 240 average time/residue: 3.2401 time to fit residues: 963.5287 Evaluate side-chains 242 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 3.110 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 23 residues processed: 15 average time/residue: 1.4333 time to fit residues: 35.5493 ------------------------------------------------------------------------------- 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: 0.5980 chunk 70 optimal weight: 9.9990 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: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN Y 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2607 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= 0.350 Angle : 0.592 12.797 93319 Z= 0.313 Chirality : 0.039 0.286 12048 Planarity : 0.005 0.114 4400 Dihedral : 13.524 177.624 25745 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 3.18 % 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: -0.14 (0.20), residues: 1727 helix: 0.42 (0.24), residues: 489 sheet: -0.62 (0.26), residues: 383 loop : 0.03 (0.21), residues: 855 *********************** 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 252 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 206 time to evaluate : 3.204 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: 46 outliers final: 32 residues processed: 234 average time/residue: 3.1934 time to fit residues: 915.5082 Evaluate side-chains 234 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 3.137 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 8 average time/residue: 1.4087 time to fit residues: 19.7423 ------------------------------------------------------------------------------- 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: 9.9990 chunk 199 optimal weight: 2.9990 chunk 356 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 217 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 Y 20 GLN Z 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 61817 Z= 0.295 Angle : 0.568 12.768 93319 Z= 0.304 Chirality : 0.037 0.272 12048 Planarity : 0.005 0.114 4400 Dihedral : 13.520 177.748 25745 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 3.25 % 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: -0.10 (0.20), residues: 1727 helix: 0.47 (0.24), residues: 489 sheet: -0.61 (0.26), residues: 383 loop : 0.05 (0.21), residues: 855 *********************** 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 254 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 207 time to evaluate : 3.090 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 outliers start: 47 outliers final: 34 residues processed: 234 average time/residue: 3.1484 time to fit residues: 901.5694 Evaluate side-chains 236 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 202 time to evaluate : 3.153 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 24 residues processed: 10 average time/residue: 1.5082 time to fit residues: 24.7722 ------------------------------------------------------------------------------- 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: 2.9990 chunk 212 optimal weight: 0.9990 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: 7.9990 chunk 176 optimal weight: 40.0000 chunk 33 optimal weight: 4.9990 chunk 280 optimal weight: 8.9990 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 Y 20 GLN k 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 61817 Z= 0.295 Angle : 0.567 12.786 93319 Z= 0.303 Chirality : 0.037 0.272 12048 Planarity : 0.005 0.114 4400 Dihedral : 13.508 178.153 25745 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: -0.07 (0.20), residues: 1727 helix: 0.50 (0.24), residues: 488 sheet: -0.61 (0.26), residues: 383 loop : 0.07 (0.21), residues: 856 *********************** 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: 45 poor density : 204 time to evaluate : 3.099 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: 45 outliers final: 32 residues processed: 233 average time/residue: 3.1743 time to fit residues: 904.7835 Evaluate side-chains 233 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 9 average time/residue: 1.4228 time to fit residues: 21.7287 ------------------------------------------------------------------------------- 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: 2.9990 chunk 341 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 332 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 331 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 Y 20 GLN Z 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 61817 Z= 0.165 Angle : 0.527 12.691 93319 Z= 0.287 Chirality : 0.033 0.237 12048 Planarity : 0.005 0.113 4400 Dihedral : 13.486 178.433 25745 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 2.70 % 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: 0.03 (0.20), residues: 1727 helix: 0.65 (0.24), residues: 489 sheet: -0.62 (0.26), residues: 383 loop : 0.13 (0.21), residues: 855 *********************** 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 244 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 205 time to evaluate : 3.118 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: 39 outliers final: 27 residues processed: 231 average time/residue: 3.2924 time to fit residues: 925.0664 Evaluate side-chains 231 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 22 residues processed: 5 average time/residue: 1.2446 time to fit residues: 12.8682 ------------------------------------------------------------------------------- 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: 2.9990 chunk 214 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 368 optimal weight: 1.9990 chunk 339 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 Y 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 61817 Z= 0.247 Angle : 0.541 12.750 93319 Z= 0.291 Chirality : 0.035 0.251 12048 Planarity : 0.005 0.114 4400 Dihedral : 13.432 179.193 25745 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 2.15 % 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: 0.04 (0.20), residues: 1727 helix: 0.61 (0.24), residues: 495 sheet: -0.64 (0.26), residues: 376 loop : 0.17 (0.21), residues: 856 ********************** 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 235 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 3.149 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: 31 outliers final: 23 residues processed: 228 average time/residue: 3.3765 time to fit residues: 943.4549 Evaluate side-chains 225 residues out of total 1445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 2.0776 time to fit residues: 8.4409 ------------------------------------------------------------------------------- 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: 5.9990 chunk 312 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 293 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 301 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 54 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 86 ASN K 117 GLN L 58 ASN L 126 ASN Z 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.132435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.097395 restraints weight = 190397.722| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.00 r_work: 0.3267 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.076 61817 Z= 0.466 Angle : 0.666 12.864 93319 Z= 0.345 Chirality : 0.043 0.311 12048 Planarity : 0.006 0.115 4400 Dihedral : 13.734 177.233 25745 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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: -0.33 (0.20), residues: 1727 helix: 0.24 (0.23), residues: 489 sheet: -0.76 (0.26), residues: 380 loop : -0.06 (0.21), residues: 858 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27274.90 seconds wall clock time: 472 minutes 13.56 seconds (28333.56 seconds total)