Starting phenix.real_space_refine on Tue Mar 12 17:18:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/03_2024/8e3m_27868_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/03_2024/8e3m_27868.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/03_2024/8e3m_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_27868/03_2024/8e3m_27868_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/03_2024/8e3m_27868_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/03_2024/8e3m_27868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/03_2024/8e3m_27868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/03_2024/8e3m_27868_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e3m_27868/03_2024/8e3m_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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 38.97, per 1000 atoms: 0.34 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: 84.94 Conformation dependent library (CDL) restraints added in 2.6 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 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: 53.23 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: 140.49 Time building geometry restraints manager: 90.03 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=" 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 angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 106.32 125.94 -19.62 3.00e+00 1.11e-01 4.28e+01 ... (remaining 221363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 54057 35.74 - 71.48: 7331 71.48 - 107.22: 808 107.22 - 142.97: 12 142.97 - 178.71: 7 Dihedral angle restraints: 62215 sinusoidal: 58565 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 62212 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: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.840 Extract box with map and model: 27.560 Check model and map are aligned: 1.220 Set scattering table: 0.780 Process input model: 415.400 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 463.250 ------------------------------------------------------------------------------- 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 : 0.414 28.042 125589 Z= 0.197 Chirality : 0.070 5.692 16430 Planarity : 0.022 0.602 4635 Dihedral : 23.565 178.708 50553 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 : 3.148 Fit side-chains REVERT: O 95 ARG cc_start: 0.8486 (tmm-80) cc_final: 0.8208 (ttp-110) outliers start: 12 outliers final: 10 residues processed: 242 average time/residue: 2.9066 time to fit residues: 897.6399 Evaluate side-chains 240 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 108 SER 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: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 81797 Z= 0.398 Angle : 0.651 27.241 125589 Z= 0.339 Chirality : 0.047 1.996 16430 Planarity : 0.007 0.141 4635 Dihedral : 23.502 179.616 48327 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.47 % Favored : 95.36 % Rotamer: Outliers : 1.91 % Allowed : 16.67 % Favored : 81.42 % 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: 1.30 (0.33), residues: 270 sheet: 0.59 (0.36), residues: 212 loop : -0.16 (0.24), residues: 681 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 0.012 0.001 PHE M 183 TYR 0.010 0.001 TYR K 103 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 240 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 3.021 Fit side-chains revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7814 (tmm-80) outliers start: 18 outliers final: 9 residues processed: 232 average time/residue: 2.9786 time to fit residues: 888.4168 Evaluate side-chains 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 216 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain Q residue 52 ARG 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: 10.0000 chunk 313 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 377 optimal weight: 4.9990 chunk 407 optimal weight: 2.9990 chunk 336 optimal weight: 0.9980 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 M 195 GLN 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: 0.9094 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 81797 Z= 0.193 Angle : 0.606 27.149 125589 Z= 0.320 Chirality : 0.042 2.024 16430 Planarity : 0.006 0.129 4635 Dihedral : 23.593 179.245 48319 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 1.80 % Allowed : 16.03 % 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: 0.41 (0.25), residues: 1163 helix: 1.23 (0.33), residues: 271 sheet: 0.55 (0.37), residues: 201 loop : -0.14 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 78 HIS 0.004 0.001 HIS K 230 PHE 0.010 0.001 PHE M 183 TYR 0.010 0.001 TYR P 38 ARG 0.005 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 236 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 219 time to evaluate : 3.277 Fit side-chains revert: symmetry clash REVERT: O 95 ARG cc_start: 0.8330 (ttp-110) cc_final: 0.8099 (ttp-110) REVERT: Q 52 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7389 (tmm-80) outliers start: 17 outliers final: 13 residues processed: 226 average time/residue: 3.0519 time to fit residues: 878.7470 Evaluate side-chains 231 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 217 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 39 LYS Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain R residue 29 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 3.9990 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: 3.9990 chunk 401 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 359 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.9137 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 81797 Z= 0.420 Angle : 0.656 26.970 125589 Z= 0.345 Chirality : 0.047 1.983 16430 Planarity : 0.007 0.140 4635 Dihedral : 23.553 178.711 48319 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.99 % Favored : 94.84 % Rotamer: Outliers : 2.12 % Allowed : 15.82 % 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: 1.24 (0.33), residues: 269 sheet: 0.30 (0.35), residues: 218 loop : -0.30 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 78 HIS 0.006 0.001 HIS K 230 PHE 0.015 0.001 PHE M 183 TYR 0.013 0.002 TYR P 38 ARG 0.003 0.000 ARG O 27 *********************** 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 239 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 219 time to evaluate : 3.236 Fit side-chains revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7777 (tmm-80) outliers start: 20 outliers final: 13 residues processed: 226 average time/residue: 3.0975 time to fit residues: 884.5024 Evaluate side-chains 239 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 225 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 39 LYS Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 52 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 360 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.9130 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 81797 Z= 0.384 Angle : 0.644 27.088 125589 Z= 0.340 Chirality : 0.047 2.000 16430 Planarity : 0.007 0.136 4635 Dihedral : 23.571 178.976 48318 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.82 % Favored : 95.01 % Rotamer: Outliers : 2.02 % Allowed : 16.45 % 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: 0.17 (0.25), residues: 1163 helix: 1.20 (0.33), residues: 269 sheet: 0.22 (0.35), residues: 218 loop : -0.32 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 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 0.002 0.000 ARG K 271 *********************** 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 237 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 3.272 Fit side-chains revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7789 (tmm-80) outliers start: 19 outliers final: 12 residues processed: 226 average time/residue: 3.1495 time to fit residues: 914.9475 Evaluate side-chains 230 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 52 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 4.9990 chunk 361 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 401 optimal weight: 9.9990 chunk 333 optimal weight: 1.9990 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 M 195 GLN N 42 ASN P 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 81797 Z= 0.349 Angle : 0.636 27.104 125589 Z= 0.336 Chirality : 0.046 1.998 16430 Planarity : 0.007 0.136 4635 Dihedral : 23.576 178.912 48318 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.73 % Favored : 95.10 % Rotamer: Outliers : 1.91 % Allowed : 16.77 % Favored : 81.32 % 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: 1.23 (0.33), residues: 269 sheet: 0.21 (0.35), residues: 208 loop : -0.29 (0.24), residues: 686 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 N 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 237 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 219 time to evaluate : 3.197 Fit side-chains revert: symmetry clash REVERT: Q 52 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7786 (tmm-80) outliers start: 18 outliers final: 14 residues processed: 225 average time/residue: 3.1364 time to fit residues: 901.3661 Evaluate side-chains 232 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 39 LYS Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain R residue 29 GLN 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: 3.9990 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: 3.9990 ------------------------------------------------------------------------------- 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 42 ASN N 126 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 81797 Z= 0.364 Angle : 0.634 26.988 125589 Z= 0.335 Chirality : 0.046 1.998 16430 Planarity : 0.007 0.135 4635 Dihedral : 23.591 178.373 48318 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.82 % Favored : 95.01 % Rotamer: Outliers : 2.02 % Allowed : 17.09 % 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: 0.15 (0.25), residues: 1163 helix: 1.23 (0.33), residues: 271 sheet: 0.07 (0.36), residues: 205 loop : -0.30 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.015 0.001 PHE M 183 TYR 0.013 0.001 TYR P 38 ARG 0.003 0.000 ARG O 95 *********************** 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 236 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 3.199 Fit side-chains revert: symmetry clash REVERT: M 88 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8352 (mmp80) REVERT: O 131 ASN cc_start: 0.8936 (p0) cc_final: 0.8561 (p0) REVERT: Q 52 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7397 (tmm-80) outliers start: 19 outliers final: 13 residues processed: 225 average time/residue: 3.1710 time to fit residues: 904.0257 Evaluate side-chains 229 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 39 LYS Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 52 ARG 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: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 115 GLN M 156 ASN N 42 ASN P 31 GLN R 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 81797 Z= 0.380 Angle : 0.647 27.151 125589 Z= 0.342 Chirality : 0.047 1.996 16430 Planarity : 0.007 0.138 4635 Dihedral : 23.621 178.912 48318 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer: Outliers : 1.91 % Allowed : 17.62 % Favored : 80.47 % 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: 1.20 (0.33), residues: 269 sheet: 0.01 (0.35), residues: 213 loop : -0.29 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.014 0.001 PHE M 183 TYR 0.013 0.002 TYR P 38 ARG 0.012 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: 18 poor density : 213 time to evaluate : 3.243 Fit side-chains revert: symmetry clash REVERT: M 88 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8362 (mmp80) REVERT: O 131 ASN cc_start: 0.8941 (p0) cc_final: 0.8591 (p0) REVERT: Q 52 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7390 (tmm-80) outliers start: 18 outliers final: 12 residues processed: 220 average time/residue: 3.1237 time to fit residues: 871.2671 Evaluate side-chains 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 39 LYS Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 52 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 3.9990 chunk 383 optimal weight: 4.9990 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: 10.0000 chunk 114 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 chunk 371 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.9129 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 81797 Z= 0.334 Angle : 0.637 27.083 125589 Z= 0.338 Chirality : 0.045 2.008 16430 Planarity : 0.007 0.136 4635 Dihedral : 23.630 178.933 48318 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.07 % Favored : 94.75 % Rotamer: Outliers : 1.70 % Allowed : 17.94 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1163 helix: 1.15 (0.33), residues: 271 sheet: 0.01 (0.35), residues: 213 loop : -0.33 (0.24), residues: 679 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 0.013 0.001 PHE M 183 TYR 0.013 0.001 TYR P 38 ARG 0.018 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 230 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 3.194 Fit side-chains revert: symmetry clash REVERT: M 88 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8358 (mmp80) REVERT: O 131 ASN cc_start: 0.8936 (p0) cc_final: 0.8588 (p0) REVERT: Q 52 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7392 (tmm-80) outliers start: 16 outliers final: 13 residues processed: 221 average time/residue: 3.0636 time to fit residues: 858.3463 Evaluate side-chains 227 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 39 LYS Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain R residue 29 GLN 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: 4.9990 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 413 optimal weight: 5.9990 chunk 380 optimal weight: 0.9980 chunk 329 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 81797 Z= 0.355 Angle : 0.640 27.109 125589 Z= 0.338 Chirality : 0.046 1.999 16430 Planarity : 0.007 0.136 4635 Dihedral : 23.627 178.862 48318 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.99 % Favored : 94.84 % Rotamer: Outliers : 1.91 % Allowed : 17.62 % Favored : 80.47 % 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: 0.15 (0.25), residues: 1163 helix: 1.33 (0.33), residues: 264 sheet: -0.03 (0.35), residues: 218 loop : -0.30 (0.24), residues: 681 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 0.013 0.001 PHE M 183 TYR 0.013 0.001 TYR P 38 ARG 0.018 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 231 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 3.196 Fit side-chains revert: symmetry clash REVERT: M 88 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8359 (mmp80) REVERT: N 184 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8641 (mtp85) REVERT: O 131 ASN cc_start: 0.8935 (p0) cc_final: 0.8589 (p0) REVERT: Q 52 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7401 (tmm-80) outliers start: 18 outliers final: 13 residues processed: 222 average time/residue: 3.1397 time to fit residues: 880.5423 Evaluate side-chains 229 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 88 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 39 LYS Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 108 SER Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain R residue 29 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 329 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 338 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.098551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.062640 restraints weight = 224228.502| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 0.49 r_work: 0.2549 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 81797 Z= 0.311 Angle : 0.632 27.046 125589 Z= 0.336 Chirality : 0.045 2.013 16430 Planarity : 0.007 0.136 4635 Dihedral : 23.632 178.845 48318 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.99 % Favored : 94.84 % Rotamer: Outliers : 1.91 % Allowed : 17.52 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1163 helix: 1.16 (0.33), residues: 271 sheet: 0.02 (0.35), residues: 213 loop : -0.33 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.020 0.000 ARG O 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33601.23 seconds wall clock time: 578 minutes 10.14 seconds (34690.14 seconds total)