Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 15:48:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/04_2023/6wyv_21969_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/04_2023/6wyv_21969.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/04_2023/6wyv_21969_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/04_2023/6wyv_21969_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/04_2023/6wyv_21969_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/04_2023/6wyv_21969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/04_2023/6wyv_21969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/04_2023/6wyv_21969_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyv_21969/04_2023/6wyv_21969_neut_updated.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.004 sd= 1.095 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: 6 Type Number sf(0) Gaussians P 3015 5.49 5 S 22 5.16 5 C 33551 2.51 5 N 13326 2.21 5 O 22279 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 23": "OE1" <-> "OE2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ASP 66": "OD1" <-> "OD2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K ASP 121": "OD1" <-> "OD2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 221": "NH1" <-> "NH2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 72194 Number of models: 1 Model: "" Number of chains: 9 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2459} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 60 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'MHV:plan-2': 1, 'DBB:plan-1': 1, '004:plan-2': 1, 'MEA:plan-2': 1, 'MHW:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'O7S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.09, per 1000 atoms: 0.39 Number of scatterers: 72194 At special positions: 0 Unit cell: (228.83, 220.569, 190.003, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 3015 15.00 F 1 9.00 O 22279 8.00 N 13326 7.00 C 33551 6.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 31.48 Conformation dependent library (CDL) restraints added in 1.9 seconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB DBB C 3 " Number of C-beta restraints generated: 1718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 18.8% alpha, 13.2% beta 827 base pairs and 1597 stacking pairs defined. Time for finding SS restraints: 31.85 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 132 through 134 No H-bonds generated for 'chain 'K' and resid 132 through 134' Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 209 through 212 No H-bonds generated for 'chain 'K' and resid 209 through 212' Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.950A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 92 through 98' Processing helix chain 'L' and resid 129 through 137 removed outlier: 3.695A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 removed outlier: 3.568A pdb=" N VAL M 33 " --> pdb=" O HIS M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.644A pdb=" N ALA M 104 " --> pdb=" O MET M 100 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU M 105 " --> pdb=" O TYR M 101 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 removed outlier: 3.745A pdb=" N MET M 141 " --> pdb=" O LYS M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 160 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.732A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 70 Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 125 Processing helix chain 'O' and resid 25 through 36 removed outlier: 4.399A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 66 through 71 removed outlier: 4.430A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 108 removed outlier: 3.555A pdb=" N ARG O 95 " --> pdb=" O GLU O 91 " (cutoff:3.500A) Proline residue: O 97 - end of helix removed outlier: 4.439A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.578A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 103 through 105 removed outlier: 3.509A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.750A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.782A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.962A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'M' and resid 2 through 4 Processing sheet with id= I, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.380A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR M 150 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.617A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 186 through 190 removed outlier: 3.661A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU N 28 " --> pdb=" O LYS N 8 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS N 8 " --> pdb=" O GLU N 28 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 80 through 83 removed outlier: 3.696A pdb=" N ALA N 47 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.567A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) 122 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2034 hydrogen bonds 3336 hydrogen bond angles 0 basepair planarities 827 basepair parallelities 1597 stacking parallelities Total time for adding SS restraints: 134.77 Time building geometry restraints manager: 33.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9598 1.33 - 1.45: 36921 1.45 - 1.57: 27463 1.57 - 1.69: 6046 1.69 - 1.81: 42 Bond restraints: 80070 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.413 0.389 2.00e-02 2.50e+03 3.79e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.80e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C05 O7S I3001 " pdb=" C06 O7S I3001 " ideal model delta sigma weight residual 1.606 1.348 0.258 2.00e-02 2.50e+03 1.66e+02 ... (remaining 80065 not shown) Histogram of bond angle deviations from ideal: 99.95 - 107.04: 17945 107.04 - 114.13: 51523 114.13 - 121.22: 33666 121.22 - 128.30: 15465 128.30 - 135.39: 4666 Bond angle restraints: 123265 Sorted by residual: angle pdb=" C06 O7S I3001 " pdb=" C07 O7S I3001 " pdb=" C08 O7S I3001 " ideal model delta sigma weight residual 68.57 120.18 -51.61 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C07 O7S I3001 " pdb=" C09 O7S I3001 " pdb=" C10 O7S I3001 " ideal model delta sigma weight residual 85.73 128.21 -42.48 3.00e+00 1.11e-01 2.00e+02 angle pdb=" C04 O7S I3001 " pdb=" C05 O7S I3001 " pdb=" C06 O7S I3001 " ideal model delta sigma weight residual 85.76 124.77 -39.01 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.74 -35.35 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C08 O7S I3001 " pdb=" C07 O7S I3001 " pdb=" C09 O7S I3001 " ideal model delta sigma weight residual 154.30 122.03 32.27 3.00e+00 1.11e-01 1.16e+02 ... (remaining 123260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 39503 35.47 - 70.93: 1148 70.93 - 106.40: 114 106.40 - 141.87: 16 141.87 - 177.33: 10 Dihedral angle restraints: 40791 sinusoidal: 38093 harmonic: 2698 Sorted by residual: dihedral pdb=" C MHW C 1 " pdb=" N MHW C 1 " pdb=" CA MHW C 1 " pdb=" CB MHW C 1 " ideal model delta harmonic sigma weight residual -122.60 -179.31 56.71 0 2.50e+00 1.60e-01 5.15e+02 dihedral pdb=" N MHW C 1 " pdb=" C MHW C 1 " pdb=" CA MHW C 1 " pdb=" CB MHW C 1 " ideal model delta harmonic sigma weight residual 122.80 179.27 -56.47 0 2.50e+00 1.60e-01 5.10e+02 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 54.67 177.33 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 40788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 15775 0.052 - 0.105: 315 0.105 - 0.157: 38 0.157 - 0.209: 1 0.209 - 0.262: 2 Chirality restraints: 16131 Sorted by residual: chirality pdb=" CA 004 C 7 " pdb=" N 004 C 7 " pdb=" C 004 C 7 " pdb=" CB 004 C 7 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA THR C 2 " pdb=" N THR C 2 " pdb=" C THR C 2 " pdb=" CB THR C 2 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA DBB C 3 " pdb=" N DBB C 3 " pdb=" C DBB C 3 " pdb=" CB DBB C 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 16128 not shown) Planarity restraints: 4353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.027 2.00e-02 2.50e+03 6.05e-01 8.22e+03 pdb=" C4' 2MG I2445 " -0.471 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.803 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.582 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.566 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.245 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.865 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.186 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.960 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 3TD I1915 " -0.925 2.00e-02 2.50e+03 6.02e-01 8.17e+03 pdb=" C4' 3TD I1915 " 0.184 2.00e-02 2.50e+03 pdb=" O4' 3TD I1915 " 0.854 2.00e-02 2.50e+03 pdb=" C3' 3TD I1915 " -0.273 2.00e-02 2.50e+03 pdb=" O3' 3TD I1915 " 0.808 2.00e-02 2.50e+03 pdb=" C2' 3TD I1915 " -0.582 2.00e-02 2.50e+03 pdb=" O2' 3TD I1915 " -0.558 2.00e-02 2.50e+03 pdb=" C1' 3TD I1915 " 0.518 2.00e-02 2.50e+03 pdb=" C5 3TD I1915 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.037 2.00e-02 2.50e+03 5.96e-01 7.99e+03 pdb=" C4' 1MG I 745 " -0.449 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.712 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.588 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.213 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.915 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.209 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.927 2.00e-02 2.50e+03 ... (remaining 4350 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 480 2.52 - 3.11: 50418 3.11 - 3.71: 142582 3.71 - 4.30: 205666 4.30 - 4.90: 269227 Nonbonded interactions: 668373 Sorted by model distance: nonbonded pdb=" O2' G I1980 " pdb=" OP2 U I1982 " model vdw 1.925 2.440 nonbonded pdb=" O2' A I 415 " pdb=" OP1 A I1866 " model vdw 1.930 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 1.952 2.440 nonbonded pdb=" OP2 C I 672 " pdb=" OG SER L 42 " model vdw 1.955 2.440 nonbonded pdb=" O2* PSU I1911 " pdb=" OP1 A I1912 " model vdw 1.958 3.040 ... (remaining 668368 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=1.00 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: 13.130 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: 0.040 Extract box with map and model: 46.850 Check model and map are aligned: 0.810 Set scattering table: 0.460 Process input model: 266.490 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 338.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.006 0.391 80070 Z= 0.343 Angle : 0.508 51.611 123265 Z= 0.226 Chirality : 0.024 0.262 16131 Planarity : 0.031 0.605 4353 Dihedral : 13.148 177.331 39073 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.14 % Favored : 92.75 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.66 (0.21), residues: 952 helix: -4.04 (0.23), residues: 165 sheet: -3.09 (0.35), residues: 164 loop : -2.97 (0.20), residues: 623 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 231 time to evaluate : 2.102 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 240 average time/residue: 1.6299 time to fit residues: 512.9099 Evaluate side-chains 163 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 2.067 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.5468 time to fit residues: 3.7373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 358 optimal weight: 4.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN K 143 ASN K 153 GLN K 197 ASN K 226 ASN K 251 GLN L 104 GLN M 41 GLN N 32 ASN N 164 GLN O 47 HIS O 86 GLN O 138 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.080 80070 Z= 0.520 Angle : 0.867 26.309 123265 Z= 0.447 Chirality : 0.045 0.310 16131 Planarity : 0.009 0.146 4353 Dihedral : 14.565 179.128 37270 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 7.08 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.40 (0.23), residues: 952 helix: -2.74 (0.30), residues: 177 sheet: -1.96 (0.38), residues: 162 loop : -2.29 (0.22), residues: 613 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 212 time to evaluate : 2.061 Fit side-chains outliers start: 54 outliers final: 22 residues processed: 251 average time/residue: 1.5345 time to fit residues: 514.3883 Evaluate side-chains 206 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 4 average time/residue: 0.8674 time to fit residues: 7.1315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 244 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 359 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 356 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 197 ASN K 200 HIS K 251 GLN M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN N 134 HIS N 136 ASN O 138 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 80070 Z= 0.240 Angle : 0.644 20.427 123265 Z= 0.351 Chirality : 0.032 0.272 16131 Planarity : 0.008 0.133 4353 Dihedral : 14.309 177.255 37270 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 6.82 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.59 (0.24), residues: 952 helix: -1.74 (0.34), residues: 183 sheet: -1.59 (0.38), residues: 169 loop : -1.80 (0.23), residues: 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 199 time to evaluate : 2.109 Fit side-chains outliers start: 52 outliers final: 25 residues processed: 236 average time/residue: 1.5205 time to fit residues: 482.2682 Evaluate side-chains 211 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 2.107 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.5708 time to fit residues: 6.0023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 360 optimal weight: 0.4980 chunk 381 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN K 251 GLN M 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 80070 Z= 0.382 Angle : 0.753 20.767 123265 Z= 0.399 Chirality : 0.038 0.299 16131 Planarity : 0.009 0.140 4353 Dihedral : 14.704 177.722 37270 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.46 % Favored : 92.44 % Rotamer Outliers : 9.04 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.32 (0.25), residues: 952 helix: -1.55 (0.35), residues: 175 sheet: -1.50 (0.38), residues: 162 loop : -1.59 (0.23), residues: 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 192 time to evaluate : 2.100 Fit side-chains outliers start: 69 outliers final: 36 residues processed: 240 average time/residue: 1.6471 time to fit residues: 525.7900 Evaluate side-chains 207 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 8 average time/residue: 0.8828 time to fit residues: 12.9123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 5.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 325 optimal weight: 0.8980 chunk 263 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 ASN K 251 GLN L 104 GLN M 41 GLN M 94 GLN N 49 GLN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 80070 Z= 0.411 Angle : 0.763 20.632 123265 Z= 0.405 Chirality : 0.040 0.318 16131 Planarity : 0.009 0.140 4353 Dihedral : 15.001 179.918 37270 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.77 % Favored : 92.02 % Rotamer Outliers : 9.17 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.17 (0.25), residues: 952 helix: -1.36 (0.36), residues: 174 sheet: -1.46 (0.37), residues: 162 loop : -1.49 (0.24), residues: 616 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 181 time to evaluate : 2.174 Fit side-chains outliers start: 70 outliers final: 41 residues processed: 233 average time/residue: 1.5315 time to fit residues: 481.0181 Evaluate side-chains 207 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 2.125 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 34 residues processed: 8 average time/residue: 0.9364 time to fit residues: 13.4078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 7.9990 chunk 343 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 chunk 317 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 GLN M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 80070 Z= 0.377 Angle : 0.736 19.055 123265 Z= 0.393 Chirality : 0.038 0.302 16131 Planarity : 0.009 0.139 4353 Dihedral : 14.978 177.624 37270 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.77 % Favored : 92.12 % Rotamer Outliers : 9.44 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.06 (0.25), residues: 952 helix: -1.29 (0.36), residues: 177 sheet: -1.37 (0.38), residues: 162 loop : -1.42 (0.24), residues: 613 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 173 time to evaluate : 2.116 Fit side-chains outliers start: 72 outliers final: 41 residues processed: 222 average time/residue: 1.5102 time to fit residues: 451.0932 Evaluate side-chains 207 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 33 residues processed: 9 average time/residue: 0.9000 time to fit residues: 14.2787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 30.0000 chunk 279 optimal weight: 20.0000 chunk 216 optimal weight: 40.0000 chunk 321 optimal weight: 1.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN ** K 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 GLN M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 GLN O 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.070 80070 Z= 0.458 Angle : 0.804 18.372 123265 Z= 0.423 Chirality : 0.042 0.405 16131 Planarity : 0.009 0.143 4353 Dihedral : 15.279 178.304 37270 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.30 % Favored : 91.60 % Rotamer Outliers : 8.78 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.04 (0.25), residues: 952 helix: -1.35 (0.36), residues: 172 sheet: -1.21 (0.41), residues: 137 loop : -1.44 (0.23), residues: 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 173 time to evaluate : 2.091 Fit side-chains outliers start: 67 outliers final: 40 residues processed: 220 average time/residue: 1.4636 time to fit residues: 437.3062 Evaluate side-chains 197 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 31 residues processed: 9 average time/residue: 0.9294 time to fit residues: 14.3931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 GLN M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN O 136 GLN O 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.061 80070 Z= 0.411 Angle : 0.756 16.784 123265 Z= 0.402 Chirality : 0.040 0.382 16131 Planarity : 0.009 0.141 4353 Dihedral : 15.195 177.959 37270 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.98 % Favored : 91.91 % Rotamer Outliers : 7.08 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.05 (0.25), residues: 952 helix: -1.28 (0.36), residues: 179 sheet: -1.24 (0.40), residues: 145 loop : -1.45 (0.23), residues: 628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 167 time to evaluate : 2.122 Fit side-chains outliers start: 54 outliers final: 33 residues processed: 207 average time/residue: 1.5077 time to fit residues: 421.9969 Evaluate side-chains 184 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 2.099 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 2 average time/residue: 1.3127 time to fit residues: 5.3555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.9990 chunk 364 optimal weight: 8.9990 chunk 332 optimal weight: 0.9990 chunk 354 optimal weight: 5.9990 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 40.0000 chunk 320 optimal weight: 5.9990 chunk 335 optimal weight: 0.9980 chunk 353 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 143 ASN ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 GLN M 24 ASN M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN O 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 80070 Z= 0.237 Angle : 0.677 16.749 123265 Z= 0.372 Chirality : 0.034 0.317 16131 Planarity : 0.008 0.133 4353 Dihedral : 15.126 176.382 37270 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer Outliers : 6.29 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.93 (0.25), residues: 952 helix: -1.16 (0.36), residues: 179 sheet: -1.28 (0.39), residues: 157 loop : -1.33 (0.24), residues: 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 2.132 Fit side-chains outliers start: 48 outliers final: 34 residues processed: 198 average time/residue: 1.4729 time to fit residues: 397.6454 Evaluate side-chains 197 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 30 residues processed: 5 average time/residue: 1.1300 time to fit residues: 9.9099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 10.0000 chunk 375 optimal weight: 1.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 260 optimal weight: 6.9990 chunk 393 optimal weight: 0.9980 chunk 362 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 80070 Z= 0.351 Angle : 0.726 16.367 123265 Z= 0.389 Chirality : 0.037 0.333 16131 Planarity : 0.009 0.138 4353 Dihedral : 15.123 177.637 37270 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.40 % Favored : 91.49 % Rotamer Outliers : 5.37 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.92 (0.25), residues: 952 helix: -1.17 (0.36), residues: 179 sheet: -1.33 (0.39), residues: 155 loop : -1.31 (0.24), residues: 618 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 2.130 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 30 residues processed: 205 average time/residue: 1.4990 time to fit residues: 414.8599 Evaluate side-chains 191 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 2 average time/residue: 0.6004 time to fit residues: 3.8076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 7.9990 chunk 333 optimal weight: 0.1980 chunk 95 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 322 optimal weight: 0.2980 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 GLN ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN O 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.121796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.092607 restraints weight = 155781.327| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.60 r_work: 0.3202 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 80070 Z= 0.257 Angle : 0.682 16.369 123265 Z= 0.372 Chirality : 0.034 0.289 16131 Planarity : 0.008 0.135 4353 Dihedral : 15.090 176.943 37270 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.46 % Favored : 92.44 % Rotamer Outliers : 4.85 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.76 (0.26), residues: 952 helix: -1.07 (0.37), residues: 177 sheet: -1.25 (0.39), residues: 155 loop : -1.18 (0.24), residues: 620 =============================================================================== Job complete usr+sys time: 11946.65 seconds wall clock time: 213 minutes 56.69 seconds (12836.69 seconds total)