Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 21:42:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/04_2023/7af3_11751_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/04_2023/7af3_11751.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/04_2023/7af3_11751_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/04_2023/7af3_11751_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/04_2023/7af3_11751_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/04_2023/7af3_11751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/04_2023/7af3_11751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/04_2023/7af3_11751_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/04_2023/7af3_11751_neut_updated.pdb" } resolution = 2.82 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= -0.000 sd= 0.002 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 Zn 1 6.06 5 P 456 5.49 5 Mg 51 5.21 5 S 28 5.16 5 C 9858 2.51 5 N 3453 2.21 5 O 4733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 18580 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 37, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 211, 'rna3p_pyr': 171} Link IDs: {'rna2p': 71, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 803 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.77, per 1000 atoms: 0.58 Number of scatterers: 18580 At special positions: 0 Unit cell: (113.4, 150.15, 126, 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) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 51 11.99 O 4733 8.00 N 3453 7.00 C 9858 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=0, symmetry=0 Time building additional restraints: 10.13 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 9 sheets defined 43.2% alpha, 12.4% beta 140 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 8.52 Creating SS restraints... Processing helix chain 'C' and resid 9 through 11 No H-bonds generated for 'chain 'C' and resid 9 through 11' Processing helix chain 'C' and resid 26 through 50 removed outlier: 4.574A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 79 through 94 removed outlier: 6.221A pdb=" N ASP C 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL C 84 " --> pdb=" O GLY C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 52 removed outlier: 3.756A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 66 removed outlier: 3.583A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 removed outlier: 3.866A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 135 through 147 Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 43 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 90 Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'J' and resid 15 through 31 removed outlier: 4.260A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 88 removed outlier: 4.038A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 21 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 62 removed outlier: 4.094A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 removed outlier: 3.586A pdb=" N GLU M 72 " --> pdb=" O ASP M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 92 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 16 Processing helix chain 'N' and resid 21 through 31 Processing helix chain 'N' and resid 38 through 50 removed outlier: 3.799A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 81 through 89 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.652A pdb=" N SER S 25 " --> pdb=" O LYS S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 71 through 73 No H-bonds generated for 'chain 'S' and resid 71 through 73' Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 62 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 207 through 226 Processing sheet with id= A, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.312A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 164 through 171 Processing sheet with id= C, first strand: chain 'G' and resid 73 through 75 Processing sheet with id= D, first strand: chain 'I' and resid 6 through 12 Processing sheet with id= E, first strand: chain 'J' and resid 96 through 101 removed outlier: 4.449A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 42 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= G, first strand: chain 'S' and resid 31 through 33 Processing sheet with id= H, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.697A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.928A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 576 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 9.92 Time building geometry restraints manager: 10.71 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: 3060 1.33 - 1.45: 7225 1.45 - 1.57: 8572 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19821 Sorted by residual: bond pdb=" N3 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.496 1.344 0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" N3 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.496 1.345 0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C2 5MC 1 967 " pdb=" N3 5MC 1 967 " ideal model delta sigma weight residual 1.493 1.345 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" C2 2MG 11207 " pdb=" N2 2MG 11207 " ideal model delta sigma weight residual 1.475 1.341 0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C2 2MG 1 966 " pdb=" N2 2MG 1 966 " ideal model delta sigma weight residual 1.475 1.341 0.134 2.00e-02 2.50e+03 4.47e+01 ... (remaining 19816 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.65: 2900 106.65 - 114.12: 12260 114.12 - 121.59: 9342 121.59 - 129.06: 4002 129.06 - 136.53: 472 Bond angle restraints: 28976 Sorted by residual: angle pdb=" C1' 2MG 1 966 " pdb=" N9 2MG 1 966 " pdb=" C8 2MG 1 966 " ideal model delta sigma weight residual 110.07 126.27 -16.20 3.00e+00 1.11e-01 2.92e+01 angle pdb=" N LYS M 103 " pdb=" CA LYS M 103 " pdb=" C LYS M 103 " ideal model delta sigma weight residual 111.82 105.67 6.15 1.16e+00 7.43e-01 2.81e+01 angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C8 2MG 11207 " ideal model delta sigma weight residual 110.07 125.12 -15.05 3.00e+00 1.11e-01 2.52e+01 angle pdb=" N VAL I 104 " pdb=" CA VAL I 104 " pdb=" C VAL I 104 " ideal model delta sigma weight residual 111.91 107.45 4.46 8.90e-01 1.26e+00 2.51e+01 angle pdb=" N ASP B 204 " pdb=" CA ASP B 204 " pdb=" C ASP B 204 " ideal model delta sigma weight residual 114.56 108.21 6.35 1.27e+00 6.20e-01 2.50e+01 ... (remaining 28971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.58: 10590 33.58 - 67.15: 375 67.15 - 100.72: 23 100.72 - 134.30: 4 134.30 - 167.87: 2 Dihedral angle restraints: 10994 sinusoidal: 7815 harmonic: 3179 Sorted by residual: dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 232.00 64.13 167.87 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" O4' U 11168 " pdb=" C1' U 11168 " pdb=" N1 U 11168 " pdb=" C2 U 11168 " ideal model delta sinusoidal sigma weight residual -128.00 35.77 -163.77 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 200.00 96.91 103.09 1 1.50e+01 4.44e-03 5.23e+01 ... (remaining 10991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3208 0.081 - 0.162: 327 0.162 - 0.243: 58 0.243 - 0.324: 7 0.324 - 0.405: 1 Chirality restraints: 3601 Sorted by residual: chirality pdb=" CA VAL J 57 " pdb=" N VAL J 57 " pdb=" C VAL J 57 " pdb=" CB VAL J 57 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB VAL J 57 " pdb=" CA VAL J 57 " pdb=" CG1 VAL J 57 " pdb=" CG2 VAL J 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA THR B 125 " pdb=" N THR B 125 " pdb=" C THR B 125 " pdb=" CB THR B 125 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3598 not shown) Planarity restraints: 2001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11207 " -0.055 2.00e-02 2.50e+03 5.80e-01 7.57e+03 pdb=" C4' 2MG 11207 " -0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG 11207 " -0.595 2.00e-02 2.50e+03 pdb=" C3' 2MG 11207 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 2MG 11207 " 0.606 2.00e-02 2.50e+03 pdb=" C2' 2MG 11207 " 0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG 11207 " -0.952 2.00e-02 2.50e+03 pdb=" C1' 2MG 11207 " -0.233 2.00e-02 2.50e+03 pdb=" N9 2MG 11207 " 0.875 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 966 " 0.020 2.00e-02 2.50e+03 5.60e-01 7.06e+03 pdb=" C4' 2MG 1 966 " 0.436 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 966 " 0.629 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 966 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 966 " -0.538 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 966 " -0.225 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 966 " 0.882 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 966 " 0.232 2.00e-02 2.50e+03 pdb=" N9 2MG 1 966 " -0.850 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 1 967 " -0.023 2.00e-02 2.50e+03 4.99e-01 5.60e+03 pdb=" C4' 5MC 1 967 " 0.416 2.00e-02 2.50e+03 pdb=" O4' 5MC 1 967 " 0.555 2.00e-02 2.50e+03 pdb=" C3' 5MC 1 967 " -0.567 2.00e-02 2.50e+03 pdb=" O3' 5MC 1 967 " -0.411 2.00e-02 2.50e+03 pdb=" C2' 5MC 1 967 " -0.268 2.00e-02 2.50e+03 pdb=" O2' 5MC 1 967 " 0.771 2.00e-02 2.50e+03 pdb=" C1' 5MC 1 967 " 0.258 2.00e-02 2.50e+03 pdb=" N1 5MC 1 967 " -0.732 2.00e-02 2.50e+03 ... (remaining 1998 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 106 2.49 - 3.09: 12659 3.09 - 3.69: 33337 3.69 - 4.30: 51537 4.30 - 4.90: 71335 Nonbonded interactions: 168974 Sorted by model distance: nonbonded pdb=" OP2 C 11054 " pdb="MG MG 11616 " model vdw 1.884 2.170 nonbonded pdb=" O6 G 11178 " pdb="MG MG 11611 " model vdw 1.918 2.170 nonbonded pdb=" OP1 G 1 945 " pdb="MG MG 11643 " model vdw 1.936 2.170 nonbonded pdb=" O6 G 11108 " pdb="MG MG 11635 " model vdw 1.936 2.170 nonbonded pdb=" OP1 G 1 993 " pdb="MG MG 11640 " model vdw 1.956 2.170 ... (remaining 168969 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: 3.020 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: 0.020 Extract box with map and model: 15.030 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 64.200 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.010 0.152 19821 Z= 0.594 Angle : 0.861 16.200 28976 Z= 0.584 Chirality : 0.054 0.405 3601 Planarity : 0.022 0.580 2001 Dihedral : 14.059 167.874 8936 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1095 helix: 0.20 (0.24), residues: 497 sheet: -0.54 (0.39), residues: 166 loop : -0.59 (0.28), residues: 432 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 292 time to evaluate : 1.438 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 298 average time/residue: 1.4412 time to fit residues: 477.6723 Evaluate side-chains 182 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1547 time to fit residues: 1.8279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.4980 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 4 ASN I 32 GLN J 3 ASN N 35 ASN B 51 ASN B 122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19821 Z= 0.164 Angle : 0.653 14.869 28976 Z= 0.369 Chirality : 0.036 0.201 3601 Planarity : 0.006 0.123 2001 Dihedral : 13.338 168.112 6707 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 4.01 % 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: 0.32 (0.25), residues: 1095 helix: 0.76 (0.24), residues: 492 sheet: 0.05 (0.41), residues: 157 loop : -0.20 (0.29), residues: 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 11 residues processed: 228 average time/residue: 1.2674 time to fit residues: 325.1901 Evaluate side-chains 196 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 185 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.8568 time to fit residues: 6.7826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 122 ASN I 32 GLN I 110 GLN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 ASN N 43 ASN B 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 19821 Z= 0.362 Angle : 0.690 13.231 28976 Z= 0.384 Chirality : 0.040 0.198 3601 Planarity : 0.007 0.129 2001 Dihedral : 13.409 168.213 6707 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 5.96 % 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: 0.43 (0.25), residues: 1095 helix: 0.78 (0.24), residues: 495 sheet: 0.20 (0.40), residues: 163 loop : -0.09 (0.30), residues: 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 185 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 26 residues processed: 216 average time/residue: 1.2898 time to fit residues: 314.3193 Evaluate side-chains 200 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 13 residues processed: 13 average time/residue: 0.7029 time to fit residues: 12.7464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 133 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN I 4 ASN I 32 GLN I 110 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 19821 Z= 0.268 Angle : 0.645 12.976 28976 Z= 0.364 Chirality : 0.038 0.194 3601 Planarity : 0.006 0.126 2001 Dihedral : 13.323 168.198 6707 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.28 % Favored : 97.63 % Rotamer Outliers : 5.20 % 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: 0.52 (0.25), residues: 1095 helix: 0.90 (0.23), residues: 496 sheet: 0.37 (0.40), residues: 162 loop : -0.15 (0.30), residues: 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 191 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 26 residues processed: 221 average time/residue: 1.2375 time to fit residues: 309.9466 Evaluate side-chains 211 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 15 residues processed: 11 average time/residue: 0.7298 time to fit residues: 11.5970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN I 110 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 19821 Z= 0.358 Angle : 0.683 13.261 28976 Z= 0.381 Chirality : 0.040 0.198 3601 Planarity : 0.007 0.128 2001 Dihedral : 13.361 168.302 6707 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer Outliers : 5.96 % 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: 0.42 (0.25), residues: 1095 helix: 0.80 (0.23), residues: 497 sheet: 0.31 (0.40), residues: 162 loop : -0.20 (0.30), residues: 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 203 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 29 residues processed: 236 average time/residue: 1.2441 time to fit residues: 332.2792 Evaluate side-chains 211 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 19 residues processed: 10 average time/residue: 0.3849 time to fit residues: 7.2868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN G 68 ASN I 4 ASN I 32 GLN I 110 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 19821 Z= 0.277 Angle : 0.653 12.952 28976 Z= 0.368 Chirality : 0.038 0.196 3601 Planarity : 0.006 0.125 2001 Dihedral : 13.284 168.235 6707 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer Outliers : 4.98 % 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: 0.42 (0.25), residues: 1095 helix: 0.83 (0.23), residues: 495 sheet: 0.35 (0.40), residues: 163 loop : -0.24 (0.30), residues: 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 181 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 34 residues processed: 214 average time/residue: 1.1698 time to fit residues: 285.5151 Evaluate side-chains 207 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 22 residues processed: 13 average time/residue: 0.3982 time to fit residues: 8.6944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN I 32 GLN I 110 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 19821 Z= 0.236 Angle : 0.639 12.767 28976 Z= 0.362 Chirality : 0.036 0.194 3601 Planarity : 0.006 0.122 2001 Dihedral : 13.161 168.438 6707 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer Outliers : 4.66 % 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: 0.51 (0.26), residues: 1095 helix: 0.91 (0.23), residues: 495 sheet: 0.50 (0.41), residues: 163 loop : -0.26 (0.31), residues: 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 181 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 25 residues processed: 210 average time/residue: 1.1103 time to fit residues: 267.2142 Evaluate side-chains 198 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.5873 time to fit residues: 4.6155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 94 optimal weight: 0.0770 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 32 GLN I 110 GLN J 56 HIS S 57 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 19821 Z= 0.385 Angle : 0.698 13.323 28976 Z= 0.389 Chirality : 0.040 0.200 3601 Planarity : 0.007 0.125 2001 Dihedral : 13.251 168.419 6707 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer Outliers : 4.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1095 helix: 0.82 (0.23), residues: 495 sheet: 0.40 (0.41), residues: 163 loop : -0.34 (0.30), residues: 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 28 residues processed: 201 average time/residue: 1.2286 time to fit residues: 280.7341 Evaluate side-chains 194 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 7 average time/residue: 0.4357 time to fit residues: 5.8111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN I 4 ASN I 32 GLN I 110 GLN J 56 HIS B 24 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 19821 Z= 0.221 Angle : 0.643 12.770 28976 Z= 0.363 Chirality : 0.036 0.192 3601 Planarity : 0.006 0.122 2001 Dihedral : 13.108 168.258 6707 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer Outliers : 3.47 % 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: 0.47 (0.26), residues: 1095 helix: 0.97 (0.24), residues: 489 sheet: 0.46 (0.41), residues: 163 loop : -0.38 (0.30), residues: 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 22 residues processed: 209 average time/residue: 1.2199 time to fit residues: 290.0860 Evaluate side-chains 199 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.2221 time to fit residues: 2.0774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 101 optimal weight: 0.1980 chunk 153 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 32 GLN I 110 GLN N 35 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19821 Z= 0.160 Angle : 0.642 13.086 28976 Z= 0.363 Chirality : 0.035 0.191 3601 Planarity : 0.006 0.120 2001 Dihedral : 13.092 168.355 6707 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer Outliers : 2.93 % 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: 0.52 (0.26), residues: 1095 helix: 0.98 (0.24), residues: 489 sheet: 0.57 (0.41), residues: 162 loop : -0.35 (0.30), residues: 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 22 residues processed: 212 average time/residue: 1.2508 time to fit residues: 300.1708 Evaluate side-chains 202 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.1657 time to fit residues: 2.0053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 0.0270 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 32 GLN I 110 GLN J 56 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.082468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.058251 restraints weight = 46265.889| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.69 r_work: 0.2728 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 19821 Z= 0.253 Angle : 0.654 12.847 28976 Z= 0.367 Chirality : 0.036 0.196 3601 Planarity : 0.006 0.122 2001 Dihedral : 13.052 168.462 6707 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.71 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1095 helix: 0.98 (0.24), residues: 489 sheet: 0.52 (0.41), residues: 163 loop : -0.36 (0.30), residues: 443 =============================================================================== Job complete usr+sys time: 5660.99 seconds wall clock time: 102 minutes 48.28 seconds (6168.28 seconds total)