Starting phenix.real_space_refine on Thu Feb 15 07:04:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/02_2024/8e44_27879_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/02_2024/8e44_27879.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/02_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_27879/02_2024/8e44_27879_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/02_2024/8e44_27879_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/02_2024/8e44_27879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/02_2024/8e44_27879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/02_2024/8e44_27879_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/02_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-5238/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: 67.07, per 1000 atoms: 0.58 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: 81.11 Conformation dependent library (CDL) restraints added in 2.5 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: 58.43 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: 131.83 Time building geometry restraints manager: 85.12 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: 54291 35.63 - 71.25: 7195 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: 0.010 Normalize map: mean=0, sd=1: 4.360 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: 0.880 Extract box with map and model: 28.680 Check model and map are aligned: 1.430 Set scattering table: 0.820 Process input model: 432.600 Find NCS groups from input model: 1.410 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: 0.010 Load rotamer database and sin/cos tables:9.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 479.840 ------------------------------------------------------------------------------- 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 : 0.405 33.891 125732 Z= 0.197 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 : 3.309 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: 2.9585 time to fit residues: 980.3520 Evaluate side-chains 203 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 3.312 ------------------------------------------------------------------------------- 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: 0.9000 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 81884 Z= 0.354 Angle : 0.613 26.897 125732 Z= 0.325 Chirality : 0.045 1.978 16446 Planarity : 0.007 0.137 4636 Dihedral : 23.250 179.413 48386 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer: Outliers : 1.27 % Allowed : 9.55 % Favored : 89.17 % 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: 1.35 (0.33), residues: 272 sheet: 0.62 (0.37), residues: 200 loop : -0.25 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.011 0.001 PHE M 183 TYR 0.011 0.001 TYR P 38 ARG 0.003 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 229 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 217 time to evaluate : 3.237 Fit side-chains revert: symmetry clash REVERT: K 125 LYS cc_start: 0.8483 (ptmm) cc_final: 0.8258 (pttp) REVERT: M 115 GLN cc_start: 0.9194 (mt0) cc_final: 0.8942 (mt0) REVERT: R 14 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8446 (mtm180) outliers start: 12 outliers final: 6 residues processed: 224 average time/residue: 2.8499 time to fit residues: 814.1010 Evaluate side-chains 209 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 202 time to evaluate : 3.203 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 313 optimal weight: 4.9990 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: 0.0030 chunk 374 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 81884 Z= 0.281 Angle : 0.583 26.970 125732 Z= 0.317 Chirality : 0.043 1.974 16446 Planarity : 0.007 0.132 4636 Dihedral : 23.281 176.773 48386 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 1.27 % Allowed : 11.04 % Favored : 87.69 % 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: 0.23 (0.24), residues: 1163 helix: 1.19 (0.32), residues: 273 sheet: 0.52 (0.38), residues: 188 loop : -0.33 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.005 0.001 HIS L 35 PHE 0.009 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.004 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 225 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 213 time to evaluate : 3.229 Fit side-chains revert: symmetry clash REVERT: K 125 LYS cc_start: 0.8477 (ptmm) cc_final: 0.8222 (pttp) REVERT: M 115 GLN cc_start: 0.9131 (mt0) cc_final: 0.8848 (mt0) REVERT: M 171 ASP cc_start: 0.8183 (t70) cc_final: 0.7980 (t0) REVERT: N 81 GLU cc_start: 0.8267 (pt0) cc_final: 0.8018 (pt0) REVERT: N 88 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7903 (mt-10) REVERT: P 109 ASP cc_start: 0.7984 (p0) cc_final: 0.7659 (p0) REVERT: R 14 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8455 (mtm180) outliers start: 12 outliers final: 8 residues processed: 219 average time/residue: 2.9456 time to fit residues: 822.5925 Evaluate side-chains 208 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 57 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 chunk 108 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.9021 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 81884 Z= 0.412 Angle : 0.627 26.905 125732 Z= 0.337 Chirality : 0.047 1.980 16446 Planarity : 0.007 0.138 4636 Dihedral : 23.291 177.638 48386 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 1.80 % Allowed : 12.42 % Favored : 85.77 % 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: 0.09 (0.24), residues: 1163 helix: 1.25 (0.33), residues: 267 sheet: 0.33 (0.37), residues: 199 loop : -0.47 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.010 0.002 HIS P 7 PHE 0.007 0.001 PHE M 183 TYR 0.015 0.002 TYR P 38 ARG 0.004 0.000 ARG M 170 *********************** 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: 17 poor density : 200 time to evaluate : 3.244 Fit side-chains revert: symmetry clash REVERT: M 115 GLN cc_start: 0.9103 (mt0) cc_final: 0.8803 (mt0) REVERT: M 171 ASP cc_start: 0.8204 (t70) cc_final: 0.7977 (t0) REVERT: R 14 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8509 (mtm180) REVERT: R 29 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: R 41 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8206 (mtp180) outliers start: 17 outliers final: 9 residues processed: 207 average time/residue: 2.8953 time to fit residues: 765.9058 Evaluate side-chains 204 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 3.287 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 227 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 360 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 81884 Z= 0.300 Angle : 0.606 26.949 125732 Z= 0.330 Chirality : 0.044 1.977 16446 Planarity : 0.007 0.135 4636 Dihedral : 23.315 177.711 48386 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.82 % Favored : 95.10 % Rotamer: Outliers : 1.49 % Allowed : 13.48 % 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: 0.07 (0.24), residues: 1163 helix: 1.24 (0.33), residues: 267 sheet: 0.32 (0.37), residues: 192 loop : -0.47 (0.23), residues: 704 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 Q 13 *********************** 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 214 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 3.295 Fit side-chains revert: symmetry clash REVERT: M 115 GLN cc_start: 0.9095 (mt0) cc_final: 0.8801 (mt0) REVERT: M 171 ASP cc_start: 0.8205 (t70) cc_final: 0.7975 (t0) REVERT: R 14 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8502 (mtm180) REVERT: R 29 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: R 41 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8196 (mtp180) outliers start: 14 outliers final: 9 residues processed: 206 average time/residue: 2.9117 time to fit residues: 766.5648 Evaluate side-chains 210 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 198 time to evaluate : 3.263 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 4.9990 chunk 361 optimal weight: 5.9990 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: 4.9990 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: 4.5990 ------------------------------------------------------------------------------- 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: 0.9023 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 81884 Z= 0.417 Angle : 0.633 26.842 125732 Z= 0.340 Chirality : 0.047 1.982 16446 Planarity : 0.007 0.138 4636 Dihedral : 23.344 177.333 48386 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 1.70 % Allowed : 12.74 % Favored : 85.56 % 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: -0.09 (0.24), residues: 1163 helix: 1.11 (0.33), residues: 268 sheet: 0.27 (0.37), residues: 199 loop : -0.61 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.015 0.002 HIS P 7 PHE 0.009 0.001 PHE M 183 TYR 0.016 0.002 TYR P 38 ARG 0.004 0.000 ARG M 170 *********************** 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 220 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 3.176 Fit side-chains revert: symmetry clash REVERT: M 115 GLN cc_start: 0.9063 (mt0) cc_final: 0.8741 (mt0) REVERT: N 81 GLU cc_start: 0.8444 (pt0) cc_final: 0.8122 (pt0) REVERT: N 88 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8007 (mt-10) REVERT: R 14 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8512 (mtm180) REVERT: R 29 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: R 41 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8207 (mtp180) outliers start: 16 outliers final: 9 residues processed: 211 average time/residue: 2.9606 time to fit residues: 799.5896 Evaluate side-chains 205 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 3.265 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 0.3980 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: 2.9990 chunk 184 optimal weight: 7.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 81884 Z= 0.274 Angle : 0.607 26.940 125732 Z= 0.331 Chirality : 0.043 1.979 16446 Planarity : 0.007 0.135 4636 Dihedral : 23.375 177.369 48386 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.80 % Allowed : 13.91 % Favored : 84.29 % 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: -0.05 (0.24), residues: 1163 helix: 1.17 (0.33), residues: 268 sheet: 0.28 (0.37), residues: 205 loop : -0.60 (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 0.003 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 214 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 2.955 Fit side-chains revert: symmetry clash REVERT: M 171 ASP cc_start: 0.8212 (t70) cc_final: 0.7992 (t0) REVERT: R 14 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8489 (mtm180) REVERT: R 29 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: R 41 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8188 (mtp180) outliers start: 17 outliers final: 9 residues processed: 205 average time/residue: 2.9945 time to fit residues: 788.5589 Evaluate side-chains 205 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 3.238 ------------------------------------------------------------------------------- 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=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: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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: 0.9010 moved from start: 0.1823 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= 0.347 Angle : 0.609 26.925 125732 Z= 0.330 Chirality : 0.045 1.978 16446 Planarity : 0.007 0.136 4636 Dihedral : 23.367 176.866 48386 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.59 % Allowed : 13.69 % 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: -0.06 (0.24), residues: 1163 helix: 1.19 (0.33), residues: 268 sheet: 0.27 (0.37), residues: 199 loop : -0.61 (0.23), residues: 696 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 0.001 TYR P 38 ARG 0.003 0.000 ARG M 69 *********************** 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 209 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 3.236 Fit side-chains revert: symmetry clash REVERT: R 14 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8489 (mtm180) REVERT: R 29 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: R 41 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8205 (mtp180) outliers start: 15 outliers final: 9 residues processed: 200 average time/residue: 2.8713 time to fit residues: 731.8520 Evaluate side-chains 205 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 3.216 ------------------------------------------------------------------------------- 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: 3.9990 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: 4.9990 chunk 352 optimal weight: 3.9990 chunk 371 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.1883 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= 0.347 Angle : 0.605 26.929 125732 Z= 0.328 Chirality : 0.045 1.978 16446 Planarity : 0.007 0.132 4636 Dihedral : 23.380 178.267 48386 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.80 % Allowed : 13.80 % Favored : 84.39 % 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: 269 sheet: 0.30 (0.37), residues: 205 loop : -0.62 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.010 0.001 HIS P 7 PHE 0.008 0.001 PHE M 183 TYR 0.015 0.002 TYR P 38 ARG 0.003 0.000 ARG L 69 *********************** 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 213 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 2.941 Fit side-chains revert: symmetry clash REVERT: R 14 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8481 (mtm180) REVERT: R 29 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: R 41 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8207 (mtp180) outliers start: 17 outliers final: 10 residues processed: 205 average time/residue: 2.9250 time to fit residues: 766.0601 Evaluate side-chains 206 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 3.303 ------------------------------------------------------------------------------- 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 197 GLU 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: 2.9990 chunk 394 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 413 optimal weight: 3.9990 chunk 380 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 81884 Z= 0.300 Angle : 0.597 26.937 125732 Z= 0.325 Chirality : 0.043 1.978 16446 Planarity : 0.007 0.133 4636 Dihedral : 23.389 176.724 48386 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.38 % Allowed : 14.54 % Favored : 84.08 % 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: -0.05 (0.24), residues: 1163 helix: 1.18 (0.33), residues: 269 sheet: 0.29 (0.37), residues: 205 loop : -0.62 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.008 0.001 HIS P 7 PHE 0.009 0.001 PHE M 183 TYR 0.014 0.001 TYR P 38 ARG 0.003 0.000 ARG O 99 ********************** 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 207 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 14 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8479 (mtm180) REVERT: R 29 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: R 41 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8192 (mtp180) outliers start: 13 outliers final: 9 residues processed: 200 average time/residue: 3.0002 time to fit residues: 772.3979 Evaluate side-chains 204 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 3.226 ------------------------------------------------------------------------------- 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 197 GLU 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: 1.9990 chunk 138 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.107492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.067770 restraints weight = 370312.937| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 0.64 r_work: 0.2558 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 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 = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 81884 Z= 0.351 Angle : 0.606 26.893 125732 Z= 0.328 Chirality : 0.045 1.979 16446 Planarity : 0.007 0.139 4636 Dihedral : 23.380 176.718 48386 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 1.59 % Allowed : 14.33 % Favored : 84.08 % 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: 1.29 (0.33), residues: 263 sheet: 0.26 (0.37), residues: 205 loop : -0.65 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.008 0.001 HIS P 7 PHE 0.009 0.001 PHE M 183 TYR 0.013 0.002 TYR P 38 ARG 0.003 0.000 ARG L 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32949.42 seconds wall clock time: 567 minutes 0.80 seconds (34020.80 seconds total)