Starting phenix.real_space_refine on Sat Dec 9 14:05:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/12_2023/8e3m_27868_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/12_2023/8e3m_27868.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/12_2023/8e3m_27868_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/12_2023/8e3m_27868_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/12_2023/8e3m_27868_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/12_2023/8e3m_27868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/12_2023/8e3m_27868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/12_2023/8e3m_27868_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/12_2023/8e3m_27868_neut_trim_updated.pdb" } resolution = 2.25 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= -0.020 sd= 0.705 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: 7 Type Number sf(0) Gaussians P 3016 5.49 5 S 29 5.16 5 C 34590 2.51 5 N 13683 2.21 5 O 22581 1.98 5 F 1 1.80 5 H 41815 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 66": "OD1" <-> "OD2" Residue "K GLU 194": "OE1" <-> "OE2" Residue "K GLU 236": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M GLU 122": "OE1" <-> "OE2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M GLU 197": "OE1" <-> "OE2" Residue "M GLU 198": "OE1" <-> "OE2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ASP 181": "OD1" <-> "OD2" Residue "N GLU 183": "OE1" <-> "OE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ASP 49": "OD1" <-> "OD2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "P ASP 22": "OD1" <-> "OD2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P ASP 109": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 115715 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 279, 'rna2p_pyr': 152, 'rna3p': 15, 'rna3p_pur': 1386, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 437, 'rna3p': 2460} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3805 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 55, 'rna3p_pyr': 46} Link IDs: {'rna2p': 17, 'rna3p': 100} 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 83 Unusual residues: {'UIU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 38.49, per 1000 atoms: 0.33 Number of scatterers: 115715 At special positions: 0 Unit cell: (229.91, 222.44, 190.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 29 16.00 P 3016 15.00 F 1 9.00 O 22581 8.00 N 13683 7.00 C 34590 6.00 H 41815 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: 83.73 Conformation dependent library (CDL) restraints added in 3.3 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: 35 helices and 15 sheets defined 29.9% alpha, 17.1% beta 926 base pairs and 1580 stacking pairs defined. Time for finding SS restraints: 55.88 Creating SS restraints... Processing helix chain 'K' and resid 10 through 17 removed outlier: 3.560A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 17' Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.727A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.543A 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 removed outlier: 3.550A pdb=" N ILE K 135 " --> pdb=" O PRO K 131 " (cutoff:3.500A) Proline residue: K 136 - end of helix No H-bonds generated for 'chain 'K' and resid 131 through 136' Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.807A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.306A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.177A 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 'K' and resid 263 through 268 removed outlier: 6.692A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 263 through 268' Processing helix chain 'K' and resid 197 through 202 removed outlier: 4.079A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 6.889A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.124A 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: 3.552A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.680A 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: 3.511A 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: 3.743A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.504A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 165 removed outlier: 4.537A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU M 164 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N HIS M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.559A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 removed outlier: 3.597A pdb=" N GLU M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.486A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.637A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.449A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.216A 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: 3.672A 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: 4.045A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 122 removed outlier: 3.929A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 4.090A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.917A 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: 3.731A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 5.081A 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 24 removed outlier: 4.171A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.565A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.133A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN K 163 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.075A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'M' and resid 2 through 6 removed outlier: 4.883A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 44 through 47 removed outlier: 6.805A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.338A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.227A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.566A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.012A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 105 through 108 removed outlier: 5.906A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.954A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'O' and resid 74 through 78 removed outlier: 3.687A pdb=" N THR O 78 " --> pdb=" O GLY O 83 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY O 83 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'P' and resid 2 through 8 removed outlier: 7.023A pdb=" N VAL P 106 " --> pdb=" O THR P 72 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'P' and resid 80 through 88 removed outlier: 3.666A pdb=" N THR P 100 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG P 92 " --> pdb=" O ARG P 88 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'Q' and resid 28 through 31 removed outlier: 6.521A pdb=" N SER Q 29 " --> pdb=" O LYS Q 37 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS Q 37 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP Q 31 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2313 hydrogen bonds 3618 hydrogen bond angles 0 basepair planarities 926 basepair parallelities 1580 stacking parallelities Total time for adding SS restraints: 135.19 Time building geometry restraints manager: 87.99 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: 41813 1.03 - 1.23: 632 1.23 - 1.42: 43619 1.42 - 1.62: 37492 1.62 - 1.81: 56 Bond restraints: 123612 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 1.367 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.369 0.266 2.00e-02 2.50e+03 1.77e+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 9.46e+01 ... (remaining 123607 not shown) Histogram of bond angle deviations from ideal: 79.96 - 90.95: 4 90.95 - 101.94: 2955 101.94 - 112.93: 132621 112.93 - 123.91: 71124 123.91 - 134.90: 14664 Bond angle restraints: 221368 Sorted by residual: angle pdb=" C1' G7M I2069 " pdb=" N9 G7M I2069 " pdb=" C8 G7M I2069 " ideal model delta sigma weight residual 94.96 128.72 -33.76 3.00e+00 1.11e-01 1.27e+02 angle pdb=" O3* PSU I2504 " pdb=" P G I2505 " pdb=" OP1 G I2505 " ideal model delta sigma weight residual 108.00 79.96 28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" O3' 2MG I2445 " pdb=" P G I2446 " pdb=" OP1 G I2446 " ideal model delta sigma weight residual 108.00 81.39 26.61 3.00e+00 1.11e-01 7.87e+01 angle pdb=" O3' 2MG I2445 " pdb=" P G I2446 " pdb=" OP2 G I2446 " ideal model delta sigma weight residual 108.00 84.78 23.22 3.00e+00 1.11e-01 5.99e+01 angle pdb=" O3* PSU I2504 " pdb=" P G I2505 " pdb=" OP2 G I2505 " ideal model delta sigma weight residual 108.00 85.85 22.15 3.00e+00 1.11e-01 5.45e+01 ... (remaining 221363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 52453 35.74 - 71.48: 5654 71.48 - 107.22: 808 107.22 - 142.97: 12 142.97 - 178.71: 7 Dihedral angle restraints: 58934 sinusoidal: 55284 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 53.29 178.71 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 45.44 -173.44 1 1.70e+01 3.46e-03 6.62e+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 93.82 106.18 1 1.50e+01 4.44e-03 5.46e+01 ... (remaining 58931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.138: 16426 1.138 - 2.277: 2 2.277 - 3.415: 0 3.415 - 4.553: 0 4.553 - 5.692: 2 Chirality restraints: 16430 Sorted by residual: chirality pdb=" C9 UIU I3001 " pdb=" C11 UIU I3001 " pdb=" C13 UIU I3001 " pdb=" C5 UIU I3001 " both_signs ideal model delta sigma weight residual False -2.78 2.92 -5.69 2.00e-01 2.50e+01 8.10e+02 chirality pdb=" C57 UIU I3001 " pdb=" C34 UIU I3001 " pdb=" C6 UIU I3001 " pdb=" C8 UIU I3001 " both_signs ideal model delta sigma weight residual False -2.76 2.78 -5.54 2.00e-01 2.50e+01 7.67e+02 chirality pdb=" P G I2446 " pdb=" OP1 G I2446 " pdb=" OP2 G I2446 " pdb=" O5' G I2446 " both_signs ideal model delta sigma weight residual True 2.41 0.38 2.03 2.00e-01 2.50e+01 1.03e+02 ... (remaining 16427 not shown) Planarity restraints: 8161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.029 2.00e-02 2.50e+03 6.02e-01 8.16e+03 pdb=" C4' OMC I2498 " 0.464 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.773 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.587 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.577 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.233 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.882 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.199 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.950 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.048 2.00e-02 2.50e+03 5.87e-01 7.74e+03 pdb=" C4' 2MG I2445 " -0.442 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.658 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.599 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.594 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.203 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.925 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.221 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.899 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.035 2.00e-02 2.50e+03 5.63e-01 7.12e+03 pdb=" C4' OMG I2251 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.603 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.559 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.209 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.904 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.237 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.847 2.00e-02 2.50e+03 ... (remaining 8158 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 3082 2.11 - 2.73: 135913 2.73 - 3.35: 290421 3.35 - 3.98: 454534 3.98 - 4.60: 643579 Nonbonded interactions: 1527529 Sorted by model distance: nonbonded pdb=" OE1 GLU M 127 " pdb=" H GLU M 127 " model vdw 1.483 1.850 nonbonded pdb=" OE1 GLU N 183 " pdb=" H GLU N 183 " model vdw 1.507 1.850 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.542 1.850 nonbonded pdb=" H ILE L 77 " pdb=" O LYS L 109 " model vdw 1.547 1.850 nonbonded pdb=" OE1 GLU M 16 " pdb=" H GLU M 16 " model vdw 1.564 1.850 ... (remaining 1527524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.940 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: 0.980 Extract box with map and model: 28.090 Check model and map are aligned: 1.170 Set scattering table: 0.750 Process input model: 414.710 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.240 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:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 464.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 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 81797 Z= 0.322 Angle : 0.423 33.763 125589 Z= 0.199 Chirality : 0.070 5.692 16430 Planarity : 0.022 0.602 4635 Dihedral : 22.668 178.708 48169 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.27 % Allowed : 16.67 % Favored : 82.06 % 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: 0.83 (0.26), residues: 1163 helix: 1.59 (0.35), residues: 264 sheet: 1.18 (0.38), residues: 198 loop : 0.01 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 78 HIS 0.004 0.001 HIS M 165 PHE 0.004 0.000 PHE M 124 TYR 0.005 0.001 TYR P 38 ARG 0.018 0.000 ARG O 96 *********************** 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 250 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 238 time to evaluate : 3.230 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 242 average time/residue: 2.9254 time to fit residues: 905.3412 Evaluate side-chains 242 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 232 time to evaluate : 3.291 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 6 average time/residue: 1.1526 time to fit residues: 14.0426 ------------------------------------------------------------------------------- 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: 2.9990 chunk 314 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN M 136 GLN M 156 ASN N 32 ASN N 126 ASN P 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 81797 Z= 0.404 Angle : 0.656 29.018 125589 Z= 0.341 Chirality : 0.046 1.877 16430 Planarity : 0.007 0.138 4635 Dihedral : 22.645 179.718 45929 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.56 % Favored : 95.27 % Rotamer: Outliers : 2.65 % Allowed : 15.82 % Favored : 81.53 % 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: 0.41 (0.25), residues: 1163 helix: 1.30 (0.33), residues: 270 sheet: 0.56 (0.36), residues: 205 loop : -0.18 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE M 183 TYR 0.010 0.001 TYR K 161 ARG 0.007 0.000 ARG O 96 *********************** 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 250 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 225 time to evaluate : 3.248 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 236 average time/residue: 3.1944 time to fit residues: 973.5383 Evaluate side-chains 235 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 220 time to evaluate : 2.977 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 6 residues processed: 10 average time/residue: 1.3322 time to fit residues: 24.5377 ------------------------------------------------------------------------------- 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: 10.0000 chunk 116 optimal weight: 9.9990 chunk 313 optimal weight: 0.5980 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 2.9990 chunk 336 optimal weight: 2.9990 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 115 GLN M 136 GLN M 156 ASN N 126 ASN O 128 ASN P 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 81797 Z= 0.215 Angle : 0.588 27.132 125589 Z= 0.312 Chirality : 0.042 2.000 16430 Planarity : 0.006 0.128 4635 Dihedral : 22.671 177.979 45929 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 1.70 % Allowed : 16.24 % Favored : 82.06 % 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: 0.45 (0.25), residues: 1163 helix: 1.36 (0.33), residues: 271 sheet: 0.51 (0.37), residues: 201 loop : -0.14 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 78 HIS 0.003 0.001 HIS K 230 PHE 0.013 0.001 PHE M 183 TYR 0.009 0.001 TYR P 38 ARG 0.004 0.000 ARG O 96 *********************** 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 233 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 3.244 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 222 average time/residue: 3.1745 time to fit residues: 900.9018 Evaluate side-chains 223 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 3.288 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 6 average time/residue: 1.4407 time to fit residues: 16.1702 ------------------------------------------------------------------------------- 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: 0.8980 chunk 283 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 1.9990 chunk 401 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 359 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 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 M 136 GLN M 156 ASN N 42 ASN P 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 81797 Z= 0.335 Angle : 0.618 27.114 125589 Z= 0.327 Chirality : 0.045 1.991 16430 Planarity : 0.007 0.135 4635 Dihedral : 22.674 178.459 45929 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.82 % Favored : 95.01 % Rotamer: Outliers : 2.34 % Allowed : 15.50 % Favored : 82.17 % 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: 0.38 (0.25), residues: 1163 helix: 1.40 (0.33), residues: 269 sheet: 0.37 (0.37), residues: 200 loop : -0.20 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.013 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.003 0.000 ARG K 271 *********************** 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 243 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 221 time to evaluate : 3.280 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 231 average time/residue: 3.0776 time to fit residues: 902.9821 Evaluate side-chains 240 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 3.271 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 8 average time/residue: 1.4472 time to fit residues: 20.4604 ------------------------------------------------------------------------------- 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: 5.9990 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: 6.9990 chunk 277 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 360 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN M 136 GLN M 156 ASN N 42 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 81797 Z= 0.418 Angle : 0.658 27.203 125589 Z= 0.346 Chirality : 0.048 1.986 16430 Planarity : 0.007 0.138 4635 Dihedral : 22.760 179.195 45929 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 2.23 % Allowed : 15.71 % Favored : 82.06 % 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: 0.22 (0.25), residues: 1163 helix: 1.28 (0.33), residues: 269 sheet: 0.12 (0.37), residues: 205 loop : -0.24 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 78 HIS 0.006 0.001 HIS K 230 PHE 0.015 0.001 PHE M 183 TYR 0.014 0.002 TYR K 161 ARG 0.009 0.000 ARG O 96 *********************** 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 241 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 3.237 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 230 average time/residue: 3.2250 time to fit residues: 938.0064 Evaluate side-chains 228 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 3.292 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 1.2498 time to fit residues: 14.8587 ------------------------------------------------------------------------------- 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: 3.9990 chunk 361 optimal weight: 3.9990 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: 2.9990 chunk 185 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 210 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN M 136 GLN M 156 ASN N 42 ASN N 126 ASN P 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 81797 Z= 0.349 Angle : 0.643 27.122 125589 Z= 0.340 Chirality : 0.046 2.009 16430 Planarity : 0.007 0.137 4635 Dihedral : 22.771 179.247 45929 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.07 % Favored : 94.75 % Rotamer: Outliers : 1.59 % Allowed : 17.41 % Favored : 81.00 % 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: 0.20 (0.25), residues: 1163 helix: 1.27 (0.33), residues: 269 sheet: 0.09 (0.36), residues: 205 loop : -0.26 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.014 0.001 PHE M 183 TYR 0.013 0.001 TYR P 38 ARG 0.011 0.000 ARG O 96 *********************** 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 230 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 215 time to evaluate : 3.228 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 223 average time/residue: 3.1389 time to fit residues: 888.6826 Evaluate side-chains 224 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 3.272 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.3360 time to fit residues: 11.2385 ------------------------------------------------------------------------------- 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: 3.9990 chunk 45 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 338 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 399 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN M 136 GLN M 156 ASN N 42 ASN P 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 81797 Z= 0.316 Angle : 0.634 27.125 125589 Z= 0.337 Chirality : 0.045 2.015 16430 Planarity : 0.007 0.136 4635 Dihedral : 22.776 179.145 45929 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.99 % Favored : 94.84 % Rotamer: Outliers : 1.17 % Allowed : 17.83 % Favored : 81.00 % 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: 0.21 (0.25), residues: 1163 helix: 1.29 (0.33), residues: 269 sheet: 0.09 (0.36), residues: 205 loop : -0.26 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.013 0.001 PHE M 183 TYR 0.013 0.001 TYR P 38 ARG 0.005 0.000 ARG O 96 *********************** 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 225 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 214 time to evaluate : 3.244 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 221 average time/residue: 3.2782 time to fit residues: 930.5959 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 212 time to evaluate : 3.298 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.7896 time to fit residues: 13.1657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 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: 4.9990 chunk 197 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN M 136 GLN M 156 ASN N 42 ASN P 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 81797 Z= 0.400 Angle : 0.646 27.147 125589 Z= 0.341 Chirality : 0.047 1.986 16430 Planarity : 0.007 0.138 4635 Dihedral : 22.772 178.581 45929 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.82 % Favored : 95.01 % Rotamer: Outliers : 1.70 % Allowed : 17.41 % Favored : 80.89 % 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: 0.13 (0.25), residues: 1163 helix: 1.23 (0.33), residues: 271 sheet: 0.07 (0.36), residues: 205 loop : -0.32 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.015 0.001 PHE M 183 TYR 0.013 0.002 TYR P 38 ARG 0.009 0.000 ARG O 96 *********************** 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 231 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 3.233 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 225 average time/residue: 3.2185 time to fit residues: 924.2252 Evaluate side-chains 214 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 3.256 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.3579 time to fit residues: 11.2823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 0.5980 chunk 383 optimal weight: 5.9990 chunk 349 optimal weight: 3.9990 chunk 372 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 chunk 371 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN M 156 ASN N 42 ASN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 81797 Z= 0.228 Angle : 0.620 27.022 125589 Z= 0.331 Chirality : 0.043 2.026 16430 Planarity : 0.007 0.133 4635 Dihedral : 22.807 178.735 45929 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.82 % Favored : 95.01 % Rotamer: Outliers : 1.27 % Allowed : 17.94 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1163 helix: 1.27 (0.33), residues: 271 sheet: 0.22 (0.37), residues: 200 loop : -0.35 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.015 0.001 PHE M 183 TYR 0.013 0.001 TYR P 38 ARG 0.008 0.000 ARG O 96 *********************** 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 217 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 205 time to evaluate : 3.240 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 212 average time/residue: 3.1273 time to fit residues: 845.9148 Evaluate side-chains 221 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 3.301 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.9444 time to fit residues: 13.5221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 3.9990 chunk 394 optimal weight: 0.0070 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 413 optimal weight: 3.9990 chunk 380 optimal weight: 2.9990 chunk 329 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN M 136 GLN M 156 ASN N 42 ASN P 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 81797 Z= 0.274 Angle : 0.618 27.058 125589 Z= 0.329 Chirality : 0.044 2.013 16430 Planarity : 0.007 0.133 4635 Dihedral : 22.796 178.475 45929 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer: Outliers : 0.85 % Allowed : 18.05 % Favored : 81.10 % 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: 0.18 (0.25), residues: 1163 helix: 1.26 (0.33), residues: 271 sheet: 0.23 (0.37), residues: 200 loop : -0.34 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.013 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.019 0.000 ARG O 96 ********************** 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 219 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 211 time to evaluate : 3.260 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 218 average time/residue: 3.1285 time to fit residues: 868.5180 Evaluate side-chains 217 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 210 time to evaluate : 3.252 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 2.5229 time to fit residues: 5.7759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 100 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 329 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 338 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN M 136 GLN M 156 ASN N 42 ASN P 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.063478 restraints weight = 224141.312| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 0.46 r_work: 0.2567 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 81797 Z= 0.270 Angle : 0.616 27.021 125589 Z= 0.328 Chirality : 0.044 2.006 16430 Planarity : 0.007 0.133 4635 Dihedral : 22.792 178.347 45929 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 0.96 % Allowed : 17.94 % Favored : 81.10 % 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: 0.19 (0.25), residues: 1163 helix: 1.26 (0.33), residues: 271 sheet: 0.24 (0.37), residues: 200 loop : -0.33 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.012 0.001 PHE M 183 TYR 0.012 0.001 TYR P 38 ARG 0.014 0.000 ARG O 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33826.04 seconds wall clock time: 581 minutes 20.41 seconds (34880.41 seconds total)