Starting phenix.real_space_refine on Tue Mar 12 19:06:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/03_2024/8e44_27879_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/03_2024/8e44_27879.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/03_2024/8e44_27879_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/03_2024/8e44_27879_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/03_2024/8e44_27879_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/03_2024/8e44_27879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/03_2024/8e44_27879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/03_2024/8e44_27879_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/03_2024/8e44_27879_neut_trim_updated.pdb" } resolution = 2.53 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= -0.022 sd= 0.899 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: 8 Type Number sf(0) Gaussians P 3022 5.49 5 S 28 5.16 5 Cl 1 4.86 5 C 34606 2.51 5 N 13701 2.21 5 O 22614 1.98 5 F 1 1.80 5 H 41883 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 84": "OD1" <-> "OD2" Residue "K ASP 121": "OD1" <-> "OD2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 140": "OD1" <-> "OD2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ASP 176": "OD1" <-> "OD2" Residue "M GLU 198": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 88": "OE1" <-> "OE2" Residue "N ASP 108": "OD1" <-> "OD2" Residue "N ASP 181": "OD1" <-> "OD2" Residue "O GLU 31": "OE1" <-> "OE2" Residue "O ASP 49": "OD1" <-> "OD2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "Q TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 115856 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93486 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 278, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1387, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 435, 'rna3p': 2462} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 277, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1388, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 434, 'rna3p': 2463} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 100560 Chain: "J" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3810 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2182 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3170 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3182 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "O" 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: "P" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1775 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 898 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "R" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 794 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'UI9': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" P A G I2061 " occ=0.50 ... (66 atoms not shown) pdb=" H22B G I2061 " occ=0.50 residue: pdb=" P A A I2062 " occ=0.50 ... (64 atoms not shown) pdb=" H2 B A I2062 " occ=0.50 residue: pdb=" P A C I2063 " occ=0.50 ... (60 atoms not shown) pdb=" H6 B C I2063 " occ=0.50 residue: pdb=" P A U I2584 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B U I2584 " occ=0.50 residue: pdb=" P A U I2585 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B U I2585 " occ=0.50 residue: pdb=" P A U I2586 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B U I2586 " occ=0.50 Time building chain proxies: 63.93, per 1000 atoms: 0.55 Number of scatterers: 115856 At special positions: 0 Unit cell: (229.656, 222.221, 190.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 1 17.00 S 28 16.00 P 3022 15.00 F 1 9.00 O 22614 8.00 N 13701 7.00 C 34606 6.00 H 41883 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 79.21 Conformation dependent library (CDL) restraints added in 2.6 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 38 helices and 14 sheets defined 31.5% alpha, 17.6% beta 913 base pairs and 1630 stacking pairs defined. Time for finding SS restraints: 59.72 Creating SS restraints... Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.535A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 16' Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.994A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 30 through 35' Processing helix chain 'K' and resid 131 through 136 Proline residue: K 136 - end of helix Processing helix chain 'K' and resid 197 through 203 removed outlier: 4.582A pdb=" N MET K 201 " --> pdb=" O ASN K 197 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG K 203 " --> pdb=" O GLU K 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 197 through 203' Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.796A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.333A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'L' and resid 37 through 42 removed outlier: 5.657A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.550A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 6.697A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.801A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.526A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 40 removed outlier: 3.648A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 removed outlier: 6.310A pdb=" N THR M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 165 removed outlier: 4.399A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU M 164 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N HIS M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.619A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'N' and resid 56 through 61 removed outlier: 3.521A pdb=" N VAL N 60 " --> pdb=" O LYS N 56 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 61' Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.733A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.301A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 98 through 103' Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'O' and resid 24 through 38 removed outlier: 4.131A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.155A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 123 removed outlier: 3.795A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYS O 123 " --> pdb=" O PHE O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 removed outlier: 4.354A pdb=" N LYS O 72 " --> pdb=" O ASN O 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 67 through 72' Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.584A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.734A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 70 removed outlier: 3.530A pdb=" N LEU P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 65 through 70' Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.748A pdb=" N HIS Q 19 " --> pdb=" O MET Q 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 16 Processing helix chain 'R' and resid 17 through 25 removed outlier: 4.148A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.621A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.314A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY K 179 " --> pdb=" O ARG K 271 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG K 271 " --> pdb=" O GLY K 179 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG K 269 " --> pdb=" O MET K 181 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.215A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 1 through 6 removed outlier: 4.381A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.576A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'N' and resid 11 through 16 removed outlier: 3.970A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER N 199 " --> pdb=" O LYS N 8 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU N 168 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.061A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 179 through 182 Processing sheet with id= 10, first strand: chain 'N' and resid 24 through 28 Processing sheet with id= 11, first strand: chain 'N' and resid 105 through 108 removed outlier: 5.661A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'O' and resid 14 through 19 Processing sheet with id= 13, first strand: chain 'P' and resid 2 through 8 Processing sheet with id= 14, first strand: chain 'Q' and resid 29 through 32 removed outlier: 4.537A pdb=" N GLU Q 36 " --> pdb=" O ASP Q 31 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2277 hydrogen bonds 3580 hydrogen bond angles 0 basepair planarities 913 basepair parallelities 1633 stacking parallelities Total time for adding SS restraints: 143.15 Time building geometry restraints manager: 83.27 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: 41881 1.03 - 1.23: 631 1.23 - 1.42: 39608 1.42 - 1.61: 41591 1.61 - 1.81: 56 Bond restraints: 123767 Sorted by residual: bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.81e+02 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.79e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.349 -0.194 2.00e-02 2.50e+03 9.37e+01 ... (remaining 123762 not shown) Histogram of bond angle deviations from ideal: 67.71 - 82.07: 30 82.07 - 96.43: 2 96.43 - 110.79: 112268 110.79 - 125.15: 97434 125.15 - 139.51: 11933 Bond angle restraints: 221667 Sorted by residual: angle pdb=" O3' G I1341 " pdb=" C3' G I1341 " pdb=" H3' G I1341 " ideal model delta sigma weight residual 109.00 67.71 41.29 3.00e+00 1.11e-01 1.89e+02 angle pdb=" O3'B U I2585 " pdb=" C3'B U I2585 " pdb=" H3'B U I2585 " ideal model delta sigma weight residual 109.00 69.15 39.85 3.00e+00 1.11e-01 1.76e+02 angle pdb=" O3'A U I2585 " pdb=" C3'A U I2585 " pdb=" H3'A U I2585 " ideal model delta sigma weight residual 109.00 70.30 38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C5' G I1341 " pdb=" C4' G I1341 " pdb=" H4' G I1341 " ideal model delta sigma weight residual 109.00 72.35 36.65 3.00e+00 1.11e-01 1.49e+02 angle pdb=" O3' U I1313 " pdb=" C3' U I1313 " pdb=" H3' U I1313 " ideal model delta sigma weight residual 109.00 73.69 35.31 3.00e+00 1.11e-01 1.39e+02 ... (remaining 221662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 54290 35.63 - 71.25: 7196 71.25 - 106.88: 799 106.88 - 142.50: 10 142.50 - 178.13: 4 Dihedral angle restraints: 62299 sinusoidal: 58649 harmonic: 3650 Sorted by residual: dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual 232.00 53.87 178.13 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 40.79 -168.79 1 1.70e+01 3.46e-03 6.58e+01 dihedral pdb=" O4' U I1313 " pdb=" C1' U I1313 " pdb=" N1 U I1313 " pdb=" C2 U I1313 " ideal model delta sinusoidal sigma weight residual 200.00 86.68 113.32 1 1.50e+01 4.44e-03 5.96e+01 ... (remaining 62296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.399: 16436 0.399 - 0.798: 7 0.798 - 1.197: 1 1.197 - 1.596: 0 1.596 - 1.994: 2 Chirality restraints: 16446 Sorted by residual: chirality pdb=" P G I2505 " pdb=" OP1 G I2505 " pdb=" OP2 G I2505 " pdb=" O5' G I2505 " both_signs ideal model delta sigma weight residual True 2.41 0.42 1.99 2.00e-01 2.50e+01 9.94e+01 chirality pdb=" P G I1339 " pdb=" OP1 G I1339 " pdb=" OP2 G I1339 " pdb=" O5' G I1339 " both_signs ideal model delta sigma weight residual True 2.41 0.42 1.99 2.00e-01 2.50e+01 9.93e+01 chirality pdb=" C3'B U I2584 " pdb=" C4'B U I2584 " pdb=" O3'B U I2584 " pdb=" C2'B U I2584 " both_signs ideal model delta sigma weight residual False -2.48 -1.65 -0.83 2.00e-01 2.50e+01 1.71e+01 ... (remaining 16443 not shown) Planarity restraints: 8167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.034 2.00e-02 2.50e+03 6.03e-01 8.18e+03 pdb=" C4' OMC I2498 " 0.463 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.759 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.589 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.586 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.226 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.894 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.199 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.949 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.045 2.00e-02 2.50e+03 5.70e-01 7.31e+03 pdb=" C4' 2MG I2445 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.602 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.580 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.200 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.921 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.234 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.860 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.036 2.00e-02 2.50e+03 5.62e-01 7.11e+03 pdb=" C4' OMG I2251 " 0.428 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.598 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.561 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.207 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.906 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.237 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.845 2.00e-02 2.50e+03 ... (remaining 8164 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 3955 2.16 - 2.77: 148604 2.77 - 3.38: 290620 3.38 - 3.99: 448780 3.99 - 4.60: 635279 Nonbonded interactions: 1527238 Sorted by model distance: nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.545 1.850 nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.553 1.850 nonbonded pdb=" OP1 A I2883 " pdb=" HH TYR Q 49 " model vdw 1.594 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.599 1.850 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.600 1.850 ... (remaining 1527233 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 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: 0.850 Extract box with map and model: 28.090 Check model and map are aligned: 1.230 Set scattering table: 0.780 Process input model: 445.980 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.280 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:9.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 493.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.390 81884 Z= 0.326 Angle : 0.396 26.804 125732 Z= 0.195 Chirality : 0.035 1.994 16446 Planarity : 0.021 0.603 4636 Dihedral : 23.260 178.129 50622 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.11 % Allowed : 0.00 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.26), residues: 1163 helix: 1.81 (0.36), residues: 250 sheet: 1.26 (0.41), residues: 174 loop : 0.01 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 248 HIS 0.002 0.001 HIS O 76 PHE 0.010 0.001 PHE K 67 TYR 0.007 0.001 TYR L 58 ARG 0.009 0.000 ARG K 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 LYS cc_start: 0.8491 (ptmm) cc_final: 0.8258 (pttp) REVERT: M 145 ASP cc_start: 0.7951 (t70) cc_final: 0.7490 (t70) REVERT: M 171 ASP cc_start: 0.8302 (t70) cc_final: 0.7963 (t0) REVERT: M 194 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8499 (mmtt) outliers start: 1 outliers final: 1 residues processed: 262 average time/residue: 3.0203 time to fit residues: 999.3387 Evaluate side-chains 203 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 69 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 0.8980 chunk 314 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 325 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 81884 Z= 0.346 Angle : 0.619 26.898 125732 Z= 0.330 Chirality : 0.045 1.977 16446 Planarity : 0.007 0.140 4636 Dihedral : 23.268 178.989 48386 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 1.38 % Allowed : 9.66 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.25), residues: 1163 helix: 1.32 (0.33), residues: 270 sheet: 0.55 (0.37), residues: 203 loop : -0.21 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS K 200 PHE 0.011 0.001 PHE M 183 TYR 0.010 0.001 TYR P 38 ARG 0.004 0.000 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 125 LYS cc_start: 0.8480 (ptmm) cc_final: 0.8256 (pttp) REVERT: M 115 GLN cc_start: 0.9195 (mt0) cc_final: 0.8912 (mt0) REVERT: M 171 ASP cc_start: 0.8259 (t70) cc_final: 0.7981 (t0) REVERT: R 14 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8446 (mtm180) outliers start: 13 outliers final: 8 residues processed: 237 average time/residue: 2.8456 time to fit residues: 863.4765 Evaluate side-chains 213 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 204 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain R residue 14 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 81884 Z= 0.378 Angle : 0.615 26.942 125732 Z= 0.332 Chirality : 0.046 1.980 16446 Planarity : 0.007 0.138 4636 Dihedral : 23.313 177.187 48386 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.91 % Allowed : 11.15 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1163 helix: 1.26 (0.33), residues: 265 sheet: 0.42 (0.38), residues: 192 loop : -0.39 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.008 0.002 HIS P 7 PHE 0.009 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 ARG 0.005 0.000 ARG M 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 115 GLN cc_start: 0.9100 (mt0) cc_final: 0.8824 (mt0) REVERT: R 14 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8492 (mtm180) REVERT: R 41 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8206 (mtp180) outliers start: 18 outliers final: 10 residues processed: 211 average time/residue: 2.8791 time to fit residues: 778.0741 Evaluate side-chains 210 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 198 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 41 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 1.9990 chunk 401 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 359 optimal weight: 5.9990 chunk 108 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 81884 Z= 0.331 Angle : 0.606 26.891 125732 Z= 0.329 Chirality : 0.045 1.979 16446 Planarity : 0.007 0.135 4636 Dihedral : 23.320 177.163 48386 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 1.59 % Allowed : 12.74 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1163 helix: 1.19 (0.33), residues: 267 sheet: 0.35 (0.37), residues: 192 loop : -0.48 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.010 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 ARG 0.003 0.000 ARG Q 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 2.749 Fit side-chains revert: symmetry clash REVERT: M 115 GLN cc_start: 0.9099 (mt0) cc_final: 0.8802 (mt0) REVERT: R 14 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8489 (mtm180) REVERT: R 29 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: R 41 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8197 (mtp180) outliers start: 15 outliers final: 9 residues processed: 208 average time/residue: 2.8477 time to fit residues: 764.8486 Evaluate side-chains 212 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 41 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 360 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 81884 Z= 0.401 Angle : 0.626 26.952 125732 Z= 0.338 Chirality : 0.047 1.982 16446 Planarity : 0.007 0.139 4636 Dihedral : 23.360 177.341 48386 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.49 % Allowed : 12.63 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1163 helix: 1.11 (0.33), residues: 268 sheet: 0.26 (0.37), residues: 199 loop : -0.59 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.015 0.002 HIS P 7 PHE 0.008 0.001 PHE M 183 TYR 0.015 0.002 TYR P 38 ARG 0.004 0.000 ARG M 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 3.037 Fit side-chains revert: symmetry clash REVERT: M 115 GLN cc_start: 0.9068 (mt0) cc_final: 0.8746 (mt0) REVERT: R 14 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8508 (mtm180) REVERT: R 29 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: R 41 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8208 (mtp180) outliers start: 14 outliers final: 9 residues processed: 203 average time/residue: 2.9270 time to fit residues: 762.5503 Evaluate side-chains 205 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 41 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 4.9990 chunk 361 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 333 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 210 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 81884 Z= 0.363 Angle : 0.619 26.934 125732 Z= 0.335 Chirality : 0.046 1.977 16446 Planarity : 0.007 0.138 4636 Dihedral : 23.364 177.382 48386 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 1.70 % Allowed : 13.59 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1163 helix: 1.14 (0.33), residues: 268 sheet: 0.23 (0.37), residues: 199 loop : -0.60 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.008 0.001 HIS P 7 PHE 0.009 0.001 PHE M 183 TYR 0.015 0.001 TYR P 38 ARG 0.003 0.000 ARG M 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 14 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8500 (mtm180) REVERT: R 29 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: R 41 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8204 (mtp180) outliers start: 16 outliers final: 10 residues processed: 201 average time/residue: 2.9678 time to fit residues: 758.8113 Evaluate side-chains 206 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 41 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 338 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 399 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 81884 Z= 0.284 Angle : 0.603 26.926 125732 Z= 0.330 Chirality : 0.043 1.979 16446 Planarity : 0.007 0.136 4636 Dihedral : 23.383 177.374 48386 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 1.59 % Allowed : 13.80 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1163 helix: 1.16 (0.33), residues: 268 sheet: 0.24 (0.37), residues: 199 loop : -0.59 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.009 0.001 PHE M 183 TYR 0.015 0.001 TYR P 38 ARG 0.003 0.000 ARG M 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 14 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8491 (mtm180) REVERT: R 29 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: R 41 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8208 (mtp180) outliers start: 15 outliers final: 10 residues processed: 200 average time/residue: 3.0332 time to fit residues: 783.6471 Evaluate side-chains 214 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 41 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 314 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 81884 Z= 0.346 Angle : 0.608 26.936 125732 Z= 0.330 Chirality : 0.045 1.978 16446 Planarity : 0.007 0.136 4636 Dihedral : 23.373 177.071 48386 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.59 % Allowed : 13.59 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1163 helix: 1.17 (0.33), residues: 268 sheet: 0.27 (0.37), residues: 205 loop : -0.58 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.008 0.001 HIS P 7 PHE 0.009 0.001 PHE M 183 TYR 0.015 0.001 TYR P 38 ARG 0.004 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 3.086 Fit side-chains revert: symmetry clash REVERT: R 14 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8489 (mtm180) REVERT: R 29 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8171 (mt0) REVERT: R 41 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8202 (mtp180) outliers start: 15 outliers final: 9 residues processed: 200 average time/residue: 2.9703 time to fit residues: 753.7547 Evaluate side-chains 203 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 41 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 4.9990 chunk 383 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 336 optimal weight: 0.0770 chunk 352 optimal weight: 4.9990 chunk 371 optimal weight: 4.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 81884 Z= 0.283 Angle : 0.599 26.920 125732 Z= 0.327 Chirality : 0.044 1.980 16446 Planarity : 0.007 0.136 4636 Dihedral : 23.383 177.110 48386 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.38 % Allowed : 13.59 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1163 helix: 1.19 (0.33), residues: 268 sheet: 0.26 (0.37), residues: 205 loop : -0.57 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.006 0.001 HIS P 7 PHE 0.009 0.001 PHE M 183 TYR 0.015 0.001 TYR P 38 ARG 0.003 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 3.060 Fit side-chains revert: symmetry clash REVERT: R 14 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8483 (mtm180) REVERT: R 29 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8171 (mt0) REVERT: R 41 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8208 (mtp180) outliers start: 13 outliers final: 9 residues processed: 198 average time/residue: 2.8673 time to fit residues: 728.3287 Evaluate side-chains 203 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 41 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 3.9990 chunk 394 optimal weight: 0.0270 chunk 240 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 413 optimal weight: 4.9990 chunk 380 optimal weight: 0.0970 chunk 329 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 81884 Z= 0.205 Angle : 0.586 26.898 125732 Z= 0.323 Chirality : 0.042 1.981 16446 Planarity : 0.006 0.133 4636 Dihedral : 23.408 177.088 48386 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 1.17 % Allowed : 13.91 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1163 helix: 1.23 (0.33), residues: 268 sheet: 0.26 (0.37), residues: 205 loop : -0.55 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.006 0.001 HIS P 7 PHE 0.010 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 ARG 0.003 0.000 ARG M 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 200 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 14 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8469 (mtm180) REVERT: R 29 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: R 41 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8204 (mtp180) outliers start: 11 outliers final: 8 residues processed: 205 average time/residue: 2.8946 time to fit residues: 760.0199 Evaluate side-chains 210 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain R residue 14 ARG Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 41 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 329 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.068202 restraints weight = 338961.289| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 0.60 r_work: 0.2567 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 81884 Z= 0.335 Angle : 0.601 26.887 125732 Z= 0.327 Chirality : 0.045 1.977 16446 Planarity : 0.007 0.134 4636 Dihedral : 23.370 176.479 48386 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 1.38 % Allowed : 14.01 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1163 helix: 1.18 (0.33), residues: 269 sheet: 0.24 (0.37), residues: 205 loop : -0.58 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.009 0.001 HIS P 7 PHE 0.009 0.001 PHE M 183 TYR 0.015 0.002 TYR P 38 ARG 0.004 0.000 ARG P 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32790.37 seconds wall clock time: 564 minutes 25.87 seconds (33865.87 seconds total)