Starting phenix.real_space_refine on Sat Dec 9 13:51:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/12_2023/8e44_27879_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/12_2023/8e44_27879.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/12_2023/8e44_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_27879/12_2023/8e44_27879_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/12_2023/8e44_27879_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/12_2023/8e44_27879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/12_2023/8e44_27879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/12_2023/8e44_27879_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e44_27879/12_2023/8e44_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-1.21rc1-5172/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: 64.57, per 1000 atoms: 0.56 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: 77.71 Conformation dependent library (CDL) restraints added in 2.4 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: 56.62 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: 136.72 Time building geometry restraints manager: 81.95 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: 52683 35.63 - 71.25: 5507 71.25 - 106.88: 799 106.88 - 142.50: 10 142.50 - 178.13: 4 Dihedral angle restraints: 59003 sinusoidal: 55353 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 59000 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.830 Extract box with map and model: 27.690 Check model and map are aligned: 1.240 Set scattering table: 0.730 Process input model: 433.630 Find NCS groups from input model: 1.440 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:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 481.240 ------------------------------------------------------------------------------- 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 : 22.336 178.129 48226 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 : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 262 average time/residue: 3.0925 time to fit residues: 1026.5240 Evaluate side-chains 204 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 3.034 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.3126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN R 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 81884 Z= 0.331 Angle : 0.605 26.915 125732 Z= 0.321 Chirality : 0.044 1.974 16446 Planarity : 0.007 0.139 4636 Dihedral : 22.370 179.588 45986 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 1.27 % Allowed : 9.87 % Favored : 88.85 % 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: 0.44 (0.25), residues: 1163 helix: 1.36 (0.33), residues: 272 sheet: 0.89 (0.40), residues: 173 loop : -0.25 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.004 0.001 HIS K 200 PHE 0.010 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 231 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 219 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 226 average time/residue: 2.9628 time to fit residues: 860.1802 Evaluate side-chains 208 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 3.097 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 1.4680 time to fit residues: 9.1515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 374 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 302 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 81884 Z= 0.346 Angle : 0.602 26.936 125732 Z= 0.327 Chirality : 0.045 1.979 16446 Planarity : 0.007 0.135 4636 Dihedral : 22.421 177.116 45986 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 1.59 % Allowed : 11.04 % Favored : 87.37 % 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: 0.25 (0.24), residues: 1163 helix: 1.29 (0.33), residues: 265 sheet: 0.44 (0.37), residues: 198 loop : -0.32 (0.23), residues: 700 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 0.009 0.001 PHE M 183 TYR 0.013 0.001 TYR P 38 ARG 0.010 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 228 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 213 time to evaluate : 2.919 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 220 average time/residue: 2.9786 time to fit residues: 840.3664 Evaluate side-chains 209 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 3.016 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 1.6562 time to fit residues: 12.2818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 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: 4.9990 chunk 108 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 81884 Z= 0.400 Angle : 0.624 26.925 125732 Z= 0.336 Chirality : 0.046 1.981 16446 Planarity : 0.007 0.138 4636 Dihedral : 22.454 177.440 45986 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.49 % Allowed : 12.85 % 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: 0.02 (0.24), residues: 1163 helix: 1.18 (0.33), residues: 267 sheet: 0.30 (0.37), residues: 199 loop : -0.52 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.013 0.002 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 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 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 217 average time/residue: 2.9254 time to fit residues: 813.8434 Evaluate side-chains 202 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 2.958 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 1.6615 time to fit residues: 12.2414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 101 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1707 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= 0.334 Angle : 0.610 26.971 125732 Z= 0.331 Chirality : 0.045 1.978 16446 Planarity : 0.007 0.135 4636 Dihedral : 22.469 177.459 45986 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.06 % Allowed : 13.91 % 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: 0.02 (0.24), residues: 1163 helix: 1.17 (0.33), residues: 267 sheet: 0.32 (0.37), residues: 198 loop : -0.52 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.007 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 O 95 *********************** 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 209 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 3.046 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 204 average time/residue: 2.9833 time to fit residues: 779.6850 Evaluate side-chains 203 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 3.058 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 2.1073 time to fit residues: 5.2227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 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: 3.7988 ------------------------------------------------------------------------------- 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: 0.9012 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 81884 Z= 0.351 Angle : 0.609 26.975 125732 Z= 0.330 Chirality : 0.045 1.979 16446 Planarity : 0.007 0.136 4636 Dihedral : 22.472 177.173 45986 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.17 % Allowed : 13.80 % 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: 0.01 (0.24), residues: 1163 helix: 1.17 (0.33), residues: 267 sheet: 0.31 (0.37), residues: 198 loop : -0.53 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.007 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 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: 11 poor density : 199 time to evaluate : 3.328 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 205 average time/residue: 3.0209 time to fit residues: 799.7574 Evaluate side-chains 206 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 197 time to evaluate : 3.017 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 1.8478 time to fit residues: 10.3489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 0.8980 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: 0.8980 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: 2.5586 ------------------------------------------------------------------------------- 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: 0.9000 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 81884 Z= 0.241 Angle : 0.591 27.004 125732 Z= 0.324 Chirality : 0.042 1.979 16446 Planarity : 0.007 0.133 4636 Dihedral : 22.499 177.249 45986 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 0.96 % Allowed : 13.91 % Favored : 85.14 % 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: 1.20 (0.33), residues: 268 sheet: 0.31 (0.37), residues: 198 loop : -0.51 (0.23), residues: 697 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 0.015 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: 9 poor density : 199 time to evaluate : 3.033 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 205 average time/residue: 2.9192 time to fit residues: 771.2622 Evaluate side-chains 202 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 3.003 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.3266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.9086 > 50: distance: 174 - 185: 8.698 distance: 185 - 186: 8.003 distance: 185 - 192: 14.503 distance: 185 - 432: 10.235 distance: 186 - 187: 12.383 distance: 186 - 189: 9.810 distance: 186 - 193: 9.315 distance: 187 - 188: 15.580 distance: 187 - 201: 7.965 distance: 188 - 429: 19.983 distance: 189 - 190: 11.758 distance: 189 - 191: 9.329 distance: 189 - 194: 4.880 distance: 190 - 195: 12.921 distance: 190 - 196: 4.489 distance: 191 - 198: 5.786 distance: 191 - 199: 3.011 distance: 191 - 200: 4.719 distance: 201 - 202: 11.293 distance: 201 - 211: 12.138 distance: 202 - 203: 12.735 distance: 202 - 205: 19.536 distance: 202 - 212: 3.945 distance: 203 - 204: 16.346 distance: 203 - 218: 42.836 distance: 205 - 206: 7.969 distance: 205 - 213: 11.740 distance: 205 - 214: 9.655 distance: 206 - 207: 11.334 distance: 206 - 208: 6.179 distance: 207 - 209: 4.766 distance: 207 - 215: 8.078 distance: 208 - 210: 6.828 distance: 208 - 216: 5.104 distance: 209 - 210: 5.456 distance: 209 - 217: 4.887 distance: 218 - 219: 3.335 distance: 218 - 226: 18.735 distance: 219 - 220: 4.695 distance: 219 - 222: 8.843 distance: 219 - 227: 6.920 distance: 220 - 221: 10.111 distance: 220 - 232: 6.431 distance: 222 - 223: 16.931 distance: 222 - 228: 11.065 distance: 222 - 229: 14.671 distance: 223 - 224: 15.393 distance: 223 - 225: 19.947 distance: 225 - 230: 11.717 distance: 225 - 231: 23.632 distance: 232 - 239: 12.671 distance: 233 - 234: 20.368 distance: 233 - 236: 4.617 distance: 233 - 240: 14.483 distance: 234 - 235: 10.699 distance: 234 - 248: 20.838 distance: 236 - 237: 6.727 distance: 236 - 238: 11.707 distance: 236 - 241: 8.817 distance: 237 - 242: 5.896 distance: 237 - 243: 9.526 distance: 237 - 244: 16.106 distance: 238 - 245: 20.673 distance: 238 - 246: 9.812 distance: 238 - 247: 11.567 distance: 248 - 249: 8.017 distance: 248 - 257: 8.853 distance: 249 - 250: 11.879 distance: 249 - 252: 9.195 distance: 249 - 258: 5.092 distance: 250 - 251: 7.051 distance: 250 - 263: 10.103 distance: 252 - 253: 6.157 distance: 252 - 259: 8.894 distance: 252 - 260: 4.392 distance: 253 - 254: 5.896 distance: 253 - 261: 4.347 distance: 254 - 255: 8.144 distance: 263 - 264: 11.364 distance: 263 - 271: 17.804 distance: 264 - 265: 27.834 distance: 264 - 267: 6.258 distance: 264 - 272: 17.074 distance: 265 - 266: 12.320 distance: 265 - 280: 18.645 distance: 267 - 268: 7.835 distance: 267 - 273: 21.091 distance: 267 - 274: 18.832 distance: 268 - 269: 8.774 distance: 268 - 276: 11.721 distance: 269 - 270: 4.922 distance: 270 - 278: 3.872 distance: 280 - 281: 5.266 distance: 280 - 289: 24.958 distance: 281 - 282: 22.152 distance: 281 - 284: 7.526 distance: 281 - 290: 19.840 distance: 282 - 283: 11.196 distance: 282 - 302: 12.397 distance: 284 - 285: 16.020 distance: 284 - 291: 17.630 distance: 284 - 292: 18.568 distance: 285 - 286: 6.198 distance: 285 - 293: 21.915 distance: 285 - 294: 19.624 distance: 286 - 287: 8.353 distance: 286 - 295: 9.720 distance: 286 - 296: 5.347 distance: 287 - 288: 9.225 distance: 287 - 297: 10.465 distance: 287 - 298: 10.110 distance: 288 - 299: 8.205 distance: 288 - 300: 6.940 distance: 288 - 301: 7.041 distance: 302 - 308: 7.641 distance: 303 - 304: 15.848 distance: 303 - 306: 8.325 distance: 303 - 309: 8.168 distance: 304 - 305: 14.770 distance: 304 - 316: 23.117 distance: 306 - 307: 3.872 distance: 306 - 310: 13.991 distance: 306 - 311: 11.811 distance: 307 - 308: 5.402 distance: 307 - 312: 8.114 distance: 307 - 313: 10.096 distance: 308 - 314: 12.347 distance: 308 - 315: 10.140 distance: 316 - 317: 12.020 distance: 316 - 320: 28.674 distance: 317 - 318: 16.261 distance: 317 - 321: 17.251 distance: 317 - 322: 6.917 distance: 318 - 319: 26.625 distance: 318 - 323: 11.471 distance: 323 - 324: 6.218 distance: 323 - 332: 6.483 distance: 324 - 325: 3.044 distance: 324 - 327: 5.411 distance: 324 - 333: 5.203 distance: 325 - 326: 13.936 distance: 325 - 345: 7.315 distance: 327 - 328: 20.897 distance: 327 - 334: 14.192 distance: 327 - 335: 11.476 distance: 328 - 329: 4.667 distance: 328 - 336: 3.307 distance: 328 - 337: 7.224 distance: 329 - 330: 8.979 distance: 329 - 338: 9.201 distance: 329 - 339: 7.389 distance: 330 - 331: 3.161 distance: 330 - 340: 7.060 distance: 330 - 341: 9.625