Starting phenix.real_space_refine on Tue Nov 19 06:24:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/11_2024/7afd_11761_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/11_2024/7afd_11761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/11_2024/7afd_11761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/11_2024/7afd_11761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/11_2024/7afd_11761_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/11_2024/7afd_11761_neut.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 22 5.21 5 S 28 5.16 5 C 9845 2.51 5 N 3449 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18531 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 171} Link IDs: {'rna2p': 70, 'rna3p': 385} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 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: "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: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} 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: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Unusual residues: {' MG': 21} Classifications: {'undetermined': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.38, per 1000 atoms: 0.61 Number of scatterers: 18531 At special positions: 0 Unit cell: (116.095, 116.095, 160.58, 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 22 11.99 O 4730 8.00 N 3449 7.00 C 9845 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 - 3.00 Amino acid : True - 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: 4.74 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 49.5% alpha, 15.7% beta 131 base pairs and 218 stacking pairs defined. Time for finding SS restraints: 10.03 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.511A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.227A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.932A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 35 through 54 removed outlier: 4.209A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.141A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 133 through 145 removed outlier: 3.585A pdb=" N LYS G 137 " --> pdb=" O THR G 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 55 removed outlier: 3.932A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 57 through 59 No H-bonds generated for 'chain 'I' and resid 57 through 59' Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 88 removed outlier: 4.524A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.519A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 removed outlier: 4.503A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.506A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 51 removed outlier: 3.732A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 Proline residue: N 57 - end of helix Processing helix chain 'N' and resid 82 through 90 removed outlier: 3.679A pdb=" N GLU N 86 " --> pdb=" O ILE N 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 70 through 75 removed outlier: 3.541A pdb=" N GLU S 73 " --> pdb=" O LYS S 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.721A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.492A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 171 removed outlier: 6.413A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.591A pdb=" N TYR I 6 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 36 through 52 removed outlier: 5.925A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 36 through 52 removed outlier: 5.925A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS N 97 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.311A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 304 hydrogen bonds 398 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 218 stacking parallelities Total time for adding SS restraints: 9.13 Time building geometry restraints manager: 5.47 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: 3361 1.33 - 1.45: 7036 1.45 - 1.57: 8440 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19801 Sorted by residual: bond pdb=" N VAL S 58 " pdb=" CA VAL S 58 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.08e+01 bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.460 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" N VAL J 57 " pdb=" CA VAL J 57 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.30e+01 bond pdb=" N ILE M 9 " pdb=" CA ILE M 9 " ideal model delta sigma weight residual 1.460 1.493 -0.033 9.30e-03 1.16e+04 1.29e+01 bond pdb=" C6 2MG 11207 " pdb=" N1 2MG 11207 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 27864 2.13 - 4.26: 991 4.26 - 6.38: 70 6.38 - 8.51: 19 8.51 - 10.64: 5 Bond angle restraints: 28949 Sorted by residual: angle pdb=" N ASN S 53 " pdb=" CA ASN S 53 " pdb=" C ASN S 53 " ideal model delta sigma weight residual 110.53 101.70 8.83 1.32e+00 5.74e-01 4.48e+01 angle pdb=" CA GLY B 124 " pdb=" C GLY B 124 " pdb=" O GLY B 124 " ideal model delta sigma weight residual 121.30 116.92 4.38 9.80e-01 1.04e+00 2.00e+01 angle pdb=" C PHE I 20 " pdb=" CA PHE I 20 " pdb=" CB PHE I 20 " ideal model delta sigma weight residual 110.62 104.02 6.60 1.51e+00 4.39e-01 1.91e+01 angle pdb=" N LYS I 13 " pdb=" CA LYS I 13 " pdb=" C LYS I 13 " ideal model delta sigma weight residual 111.39 105.41 5.98 1.38e+00 5.25e-01 1.88e+01 angle pdb=" CA ASN I 25 " pdb=" C ASN I 25 " pdb=" O ASN I 25 " ideal model delta sigma weight residual 121.23 116.83 4.40 1.07e+00 8.73e-01 1.69e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 11296 35.20 - 70.40: 1196 70.40 - 105.60: 151 105.60 - 140.81: 5 140.81 - 176.01: 3 Dihedral angle restraints: 12651 sinusoidal: 9481 harmonic: 3170 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual 200.00 25.69 174.31 1 1.50e+01 4.44e-03 8.51e+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 73.83 126.17 1 1.50e+01 4.44e-03 6.79e+01 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 55.99 176.01 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3198 0.075 - 0.151: 328 0.151 - 0.226: 67 0.226 - 0.301: 13 0.301 - 0.376: 3 Chirality restraints: 3609 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 2.06 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA PHE I 20 " pdb=" N PHE I 20 " pdb=" C PHE I 20 " pdb=" CB PHE I 20 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA ARG J 37 " pdb=" N ARG J 37 " pdb=" C ARG J 37 " pdb=" CB ARG J 37 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 3606 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " -0.036 2.00e-02 2.50e+03 6.33e-02 1.30e+02 pdb=" N9 2MG 1 966 " -0.007 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " 0.029 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " 0.042 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " 0.013 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " 0.008 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " 0.033 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " -0.030 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " -0.062 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " -0.092 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " -0.055 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " -0.017 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " 0.023 2.00e-02 2.50e+03 3.02e-02 2.97e+01 pdb=" N9 2MG 11207 " -0.008 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " -0.014 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " -0.017 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " -0.002 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " -0.007 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " -0.016 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " 0.015 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " 0.030 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " 0.043 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " 0.025 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " 0.009 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 60 " -0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C LYS I 60 " 0.078 2.00e-02 2.50e+03 pdb=" O LYS I 60 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU I 61 " -0.027 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 293 2.46 - 3.07: 13717 3.07 - 3.68: 38280 3.68 - 4.29: 52570 4.29 - 4.90: 72519 Nonbonded interactions: 177379 Sorted by model distance: nonbonded pdb=" O6 G 11370 " pdb="MG MG 11603 " model vdw 1.850 2.170 nonbonded pdb=" OP1 C 1 972 " pdb="MG MG 11610 " model vdw 1.907 2.170 nonbonded pdb=" OP1 C 1 980 " pdb="MG MG 11602 " model vdw 1.930 2.170 nonbonded pdb=" OP1 A 11197 " pdb="MG MG 11613 " model vdw 2.002 2.170 nonbonded pdb=" OD1 ASN S 53 " pdb=" O GLN S 56 " model vdw 2.047 3.040 ... (remaining 177374 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.930 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 53.540 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 0.009 0.078 19801 Z= 0.534 Angle : 0.901 10.638 28949 Z= 0.547 Chirality : 0.053 0.376 3609 Planarity : 0.005 0.063 1995 Dihedral : 22.742 176.008 10599 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 29.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % 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: -2.70 (0.23), residues: 1092 helix: -1.32 (0.21), residues: 484 sheet: -2.19 (0.37), residues: 158 loop : -1.99 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 201 HIS 0.010 0.001 HIS S 14 PHE 0.013 0.002 PHE I 20 TYR 0.017 0.003 TYR I 90 ARG 0.011 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 LYS cc_start: 0.8855 (mttt) cc_final: 0.8546 (mmtm) REVERT: B 192 ASP cc_start: 0.8210 (t0) cc_final: 0.7339 (t0) REVERT: B 213 TYR cc_start: 0.7637 (m-80) cc_final: 0.7340 (m-80) REVERT: C 129 MET cc_start: 0.9126 (mmm) cc_final: 0.8880 (mmm) REVERT: C 181 ASP cc_start: 0.8994 (t70) cc_final: 0.8632 (p0) REVERT: G 103 TRP cc_start: 0.9254 (m-10) cc_final: 0.8962 (m-10) REVERT: G 116 MET cc_start: 0.8064 (pmm) cc_final: 0.7415 (tpt) REVERT: I 11 ARG cc_start: 0.4104 (pmt170) cc_final: 0.3653 (pmt170) REVERT: J 17 LEU cc_start: 0.9636 (mp) cc_final: 0.9424 (mm) REVERT: J 63 ASP cc_start: 0.8109 (t0) cc_final: 0.7827 (t70) REVERT: J 66 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7563 (tm-30) REVERT: J 67 ILE cc_start: 0.9500 (mm) cc_final: 0.9189 (mm) REVERT: M 16 VAL cc_start: 0.9353 (p) cc_final: 0.9102 (p) REVERT: N 89 MET cc_start: 0.9512 (mmt) cc_final: 0.9243 (mmm) REVERT: S 66 MET cc_start: 0.8865 (mtp) cc_final: 0.8549 (mtp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.4135 time to fit residues: 141.0703 Evaluate side-chains 142 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 120 GLN B 168 HIS B 227 GLN C 140 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19801 Z= 0.223 Angle : 0.683 7.816 28949 Z= 0.349 Chirality : 0.039 0.297 3609 Planarity : 0.005 0.041 1995 Dihedral : 23.625 177.898 8374 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.71 % Allowed : 18.35 % Favored : 78.94 % 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: -1.53 (0.24), residues: 1092 helix: -0.33 (0.22), residues: 503 sheet: -1.78 (0.38), residues: 156 loop : -1.38 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.006 0.001 HIS S 14 PHE 0.018 0.002 PHE B 184 TYR 0.012 0.002 TYR I 90 ARG 0.006 0.001 ARG N 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 SER cc_start: 0.9203 (m) cc_final: 0.8952 (p) REVERT: B 213 TYR cc_start: 0.7657 (m-80) cc_final: 0.7363 (m-80) REVERT: C 129 MET cc_start: 0.9040 (mmm) cc_final: 0.8685 (mmm) REVERT: G 116 MET cc_start: 0.8020 (pmm) cc_final: 0.7432 (tpt) REVERT: I 11 ARG cc_start: 0.3934 (pmt170) cc_final: 0.3513 (pmt170) REVERT: I 60 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8858 (mmmt) REVERT: I 118 LEU cc_start: 0.9254 (mt) cc_final: 0.8824 (mt) REVERT: J 17 LEU cc_start: 0.9619 (mp) cc_final: 0.9368 (mm) REVERT: J 19 ASP cc_start: 0.8845 (m-30) cc_final: 0.8461 (m-30) REVERT: J 63 ASP cc_start: 0.8346 (t0) cc_final: 0.7925 (t70) REVERT: M 75 MET cc_start: 0.8921 (mmm) cc_final: 0.8658 (mmp) REVERT: M 81 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8789 (mtt) REVERT: N 89 MET cc_start: 0.9519 (mmt) cc_final: 0.9284 (mmm) outliers start: 25 outliers final: 9 residues processed: 191 average time/residue: 0.3556 time to fit residues: 100.5553 Evaluate side-chains 146 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.0980 chunk 43 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS B 109 GLN ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS I 31 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3009 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: