Starting phenix.real_space_refine on Sat Feb 17 11:43:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/02_2024/7af3_11751_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/02_2024/7af3_11751.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/02_2024/7af3_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_11751/02_2024/7af3_11751_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/02_2024/7af3_11751_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/02_2024/7af3_11751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/02_2024/7af3_11751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/02_2024/7af3_11751_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af3_11751/02_2024/7af3_11751_neut_updated.pdb" } resolution = 2.82 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= 0.002 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-dev-5238/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: 10.68, per 1000 atoms: 0.57 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: 9.88 Conformation dependent library (CDL) restraints added in 1.7 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: 9.65 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: 9.41 Time building geometry restraints manager: 10.37 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: 11319 33.58 - 67.15: 1155 67.15 - 100.72: 132 100.72 - 134.30: 4 134.30 - 167.87: 2 Dihedral angle restraints: 12612 sinusoidal: 9433 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 12609 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: 3.080 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: 14.310 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 65.100 Find NCS groups from input model: 0.430 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:14.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.570 ------------------------------------------------------------------------------- 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 : 21.330 167.874 10554 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 % Allowed : 5.42 % Favored : 93.72 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 201 HIS 0.005 0.001 HIS B 170 PHE 0.010 0.002 PHE S 74 TYR 0.011 0.002 TYR B 213 ARG 0.007 0.001 ARG N 53 *********************** 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 : 1.224 Fit side-chains REVERT: C 211 MET cc_start: 0.6283 (mmm) cc_final: 0.5710 (mmt) REVERT: G 63 GLU cc_start: 0.7731 (mp0) cc_final: 0.7398 (mp0) REVERT: G 76 LYS cc_start: 0.4854 (ttpp) cc_final: 0.4501 (tmmm) REVERT: G 111 ARG cc_start: 0.7467 (tpt170) cc_final: 0.6901 (tpp80) REVERT: G 136 LYS cc_start: 0.7099 (mptt) cc_final: 0.6847 (mptt) REVERT: I 42 GLU cc_start: 0.7644 (tp30) cc_final: 0.7443 (mm-30) REVERT: J 80 THR cc_start: 0.8201 (p) cc_final: 0.7994 (p) REVERT: M 44 LYS cc_start: 0.9089 (mttt) cc_final: 0.8327 (mttt) REVERT: M 50 GLU cc_start: 0.7090 (tp30) cc_final: 0.6795 (tp30) REVERT: B 96 TRP cc_start: 0.7190 (t-100) cc_final: 0.6940 (t-100) outliers start: 8 outliers final: 4 residues processed: 298 average time/residue: 1.4028 time to fit residues: 464.6599 Evaluate side-chains 185 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain B residue 167 ASP 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: 0.9990 chunk 73 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8568 moved from start: 0.1867 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= 0.162 Angle : 0.650 15.583 28976 Z= 0.368 Chirality : 0.036 0.198 3601 Planarity : 0.006 0.122 2001 Dihedral : 22.298 168.468 8332 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.12 % Allowed : 18.31 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1095 helix: 0.79 (0.24), residues: 492 sheet: 0.07 (0.41), residues: 157 loop : -0.22 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.002 0.001 HIS S 14 PHE 0.012 0.001 PHE B 90 TYR 0.018 0.001 TYR I 90 ARG 0.006 0.000 ARG J 16 *********************** 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 249 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 211 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 211 MET cc_start: 0.6348 (mmm) cc_final: 0.5689 (mmt) REVERT: G 30 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7879 (pt) REVERT: G 111 ARG cc_start: 0.7451 (tpt170) cc_final: 0.6837 (tpp80) REVERT: G 137 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8058 (ttpt) REVERT: G 139 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6361 (pp20) REVERT: M 44 LYS cc_start: 0.9039 (mttt) cc_final: 0.8382 (mtpt) REVERT: M 47 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: M 50 GLU cc_start: 0.7265 (tp30) cc_final: 0.6993 (tp30) REVERT: B 10 LEU cc_start: 0.3379 (mt) cc_final: 0.3050 (pp) outliers start: 38 outliers final: 11 residues processed: 230 average time/residue: 1.2499 time to fit residues: 324.0261 Evaluate side-chains 202 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 I 110 GLN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19821 Z= 0.284 Angle : 0.650 12.909 28976 Z= 0.366 Chirality : 0.038 0.191 3601 Planarity : 0.006 0.128 2001 Dihedral : 22.163 168.734 8325 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.88 % Allowed : 22.21 % Favored : 72.91 % 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: 0.59 (0.25), residues: 1095 helix: 0.95 (0.24), residues: 493 sheet: 0.28 (0.40), residues: 161 loop : -0.05 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.002 0.001 HIS C 6 PHE 0.011 0.001 PHE I 20 TYR 0.020 0.002 TYR I 90 ARG 0.005 0.000 ARG J 89 *********************** 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 234 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: G 30 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7937 (pt) REVERT: G 111 ARG cc_start: 0.7556 (tpt170) cc_final: 0.6859 (tpp80) REVERT: G 139 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6281 (pp20) REVERT: I 72 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8705 (pp) REVERT: M 44 LYS cc_start: 0.9075 (mttt) cc_final: 0.8710 (mtpm) REVERT: M 50 GLU cc_start: 0.7416 (tp30) cc_final: 0.7178 (tp30) REVERT: B 10 LEU cc_start: 0.3428 (mt) cc_final: 0.3143 (pp) REVERT: B 175 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6240 (mt-10) REVERT: B 227 GLN cc_start: 0.3660 (OUTLIER) cc_final: 0.3355 (pp30) outliers start: 45 outliers final: 23 residues processed: 214 average time/residue: 1.2165 time to fit residues: 293.6590 Evaluate side-chains 202 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 227 GLN 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: 6.9990 chunk 66 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 M 105 ASN N 43 ASN B 18 HIS B 227 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 19821 Z= 0.421 Angle : 0.711 13.408 28976 Z= 0.394 Chirality : 0.042 0.198 3601 Planarity : 0.007 0.130 2001 Dihedral : 22.154 168.455 8325 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 5.74 % Allowed : 22.32 % Favored : 71.94 % 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: 0.44 (0.25), residues: 1095 helix: 0.88 (0.23), residues: 489 sheet: 0.16 (0.40), residues: 174 loop : -0.19 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 22 HIS 0.004 0.001 HIS M 12 PHE 0.014 0.002 PHE I 20 TYR 0.022 0.002 TYR I 90 ARG 0.006 0.001 ARG I 122 *********************** 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 254 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 201 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: G 30 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7979 (pt) REVERT: G 111 ARG cc_start: 0.7524 (tpt170) cc_final: 0.6903 (tpp80) REVERT: G 139 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6211 (pp20) REVERT: I 119 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7926 (mtp85) REVERT: M 3 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7675 (mmm-85) REVERT: M 27 LYS cc_start: 0.8696 (tptm) cc_final: 0.8385 (tppp) REVERT: M 44 LYS cc_start: 0.9124 (mttt) cc_final: 0.8584 (mtpt) REVERT: M 50 GLU cc_start: 0.7568 (tp30) cc_final: 0.7301 (tp30) REVERT: N 92 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: B 10 LEU cc_start: 0.3778 (mt) cc_final: 0.3365 (pp) REVERT: B 70 VAL cc_start: 0.7440 (t) cc_final: 0.7206 (t) REVERT: B 108 ARG cc_start: 0.8223 (mtp-110) cc_final: 0.7909 (ttp-110) REVERT: B 119 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8392 (t) REVERT: B 154 MET cc_start: 0.5624 (mtm) cc_final: 0.5367 (mtp) REVERT: B 223 GLU cc_start: 0.4414 (pt0) cc_final: 0.3430 (tp30) outliers start: 53 outliers final: 32 residues processed: 229 average time/residue: 1.2404 time to fit residues: 319.1701 Evaluate side-chains 230 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 3 ARG Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 32 GLN I 110 GLN S 57 HIS B 58 ASN B 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19821 Z= 0.268 Angle : 0.644 12.906 28976 Z= 0.365 Chirality : 0.037 0.195 3601 Planarity : 0.006 0.126 2001 Dihedral : 22.094 168.179 8325 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 5.42 % Allowed : 22.86 % Favored : 71.72 % 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: 0.63 (0.26), residues: 1095 helix: 1.02 (0.24), residues: 495 sheet: 0.41 (0.40), residues: 168 loop : -0.15 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.003 0.001 HIS C 6 PHE 0.010 0.001 PHE I 20 TYR 0.021 0.002 TYR I 90 ARG 0.003 0.000 ARG N 53 *********************** 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 248 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 198 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 30 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7946 (pt) REVERT: G 56 LYS cc_start: 0.7571 (tmtt) cc_final: 0.7267 (tmmt) REVERT: G 111 ARG cc_start: 0.7398 (tpt170) cc_final: 0.6668 (tpp80) REVERT: G 139 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6434 (pp20) REVERT: M 27 LYS cc_start: 0.8623 (tptm) cc_final: 0.8314 (tppp) REVERT: M 44 LYS cc_start: 0.8979 (mttt) cc_final: 0.8567 (mtpm) REVERT: M 50 GLU cc_start: 0.7597 (tp30) cc_final: 0.7305 (tp30) REVERT: N 92 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: B 10 LEU cc_start: 0.3476 (mt) cc_final: 0.3198 (pp) REVERT: B 70 VAL cc_start: 0.7616 (t) cc_final: 0.7363 (t) REVERT: B 154 MET cc_start: 0.5891 (mtm) cc_final: 0.5548 (mtp) REVERT: B 183 VAL cc_start: 0.4087 (OUTLIER) cc_final: 0.3783 (p) REVERT: B 186 ILE cc_start: 0.5334 (tp) cc_final: 0.4945 (pt) REVERT: B 223 GLU cc_start: 0.4417 (pt0) cc_final: 0.3414 (tp30) outliers start: 50 outliers final: 30 residues processed: 227 average time/residue: 1.2276 time to fit residues: 314.3029 Evaluate side-chains 217 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19821 Z= 0.252 Angle : 0.633 12.823 28976 Z= 0.359 Chirality : 0.036 0.195 3601 Planarity : 0.006 0.126 2001 Dihedral : 22.031 168.468 8325 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 5.53 % Allowed : 23.84 % Favored : 70.64 % 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: 0.70 (0.26), residues: 1095 helix: 1.08 (0.24), residues: 501 sheet: 0.53 (0.41), residues: 168 loop : -0.17 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.003 0.001 HIS C 6 PHE 0.010 0.001 PHE I 20 TYR 0.014 0.002 TYR I 90 ARG 0.003 0.000 ARG N 53 *********************** 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 243 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: G 30 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7910 (pt) REVERT: G 75 VAL cc_start: 0.6530 (OUTLIER) cc_final: 0.6234 (t) REVERT: G 139 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6481 (pp20) REVERT: I 119 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7863 (mtp85) REVERT: M 27 LYS cc_start: 0.8665 (tptm) cc_final: 0.8346 (tppp) REVERT: M 44 LYS cc_start: 0.9042 (mttt) cc_final: 0.8646 (mtpm) REVERT: M 50 GLU cc_start: 0.7671 (tp30) cc_final: 0.7328 (tp30) REVERT: N 92 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: S 13 LEU cc_start: 0.9329 (tp) cc_final: 0.9011 (tp) REVERT: B 10 LEU cc_start: 0.3507 (mt) cc_final: 0.3239 (pp) REVERT: B 70 VAL cc_start: 0.7775 (t) cc_final: 0.7546 (t) REVERT: B 183 VAL cc_start: 0.4510 (OUTLIER) cc_final: 0.4238 (p) REVERT: B 223 GLU cc_start: 0.4679 (pt0) cc_final: 0.3553 (tp30) outliers start: 51 outliers final: 29 residues processed: 220 average time/residue: 1.2251 time to fit residues: 304.7489 Evaluate side-chains 223 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19821 Z= 0.160 Angle : 0.609 12.959 28976 Z= 0.347 Chirality : 0.034 0.192 3601 Planarity : 0.006 0.123 2001 Dihedral : 22.022 169.047 8325 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 4.12 % Allowed : 25.57 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1095 helix: 1.28 (0.24), residues: 488 sheet: 0.79 (0.41), residues: 162 loop : -0.26 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.002 0.000 HIS C 6 PHE 0.008 0.001 PHE S 74 TYR 0.013 0.001 TYR I 6 ARG 0.005 0.000 ARG B 225 *********************** 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 238 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: G 75 VAL cc_start: 0.6505 (OUTLIER) cc_final: 0.6208 (t) REVERT: G 111 ARG cc_start: 0.7405 (tpt-90) cc_final: 0.6506 (tpp80) REVERT: G 129 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7044 (mp0) REVERT: G 139 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6562 (pp20) REVERT: J 27 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7834 (pp20) REVERT: M 27 LYS cc_start: 0.8624 (tptm) cc_final: 0.8313 (tppp) REVERT: M 44 LYS cc_start: 0.9004 (mttt) cc_final: 0.8613 (mtpm) REVERT: M 50 GLU cc_start: 0.7705 (tp30) cc_final: 0.7396 (tp30) REVERT: B 10 LEU cc_start: 0.3560 (mt) cc_final: 0.3356 (pp) REVERT: B 70 VAL cc_start: 0.7890 (t) cc_final: 0.7649 (t) REVERT: B 105 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7295 (pttt) REVERT: B 183 VAL cc_start: 0.4652 (OUTLIER) cc_final: 0.4425 (p) REVERT: B 223 GLU cc_start: 0.4700 (pt0) cc_final: 0.3614 (tp30) outliers start: 38 outliers final: 19 residues processed: 221 average time/residue: 1.3192 time to fit residues: 328.6564 Evaluate side-chains 213 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 183 VAL 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: 6.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 32 GLN I 110 GLN J 56 HIS B 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 19821 Z= 0.473 Angle : 0.733 13.503 28976 Z= 0.403 Chirality : 0.043 0.201 3601 Planarity : 0.007 0.130 2001 Dihedral : 22.031 168.780 8325 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 5.20 % Allowed : 25.35 % Favored : 69.45 % 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: 0.53 (0.25), residues: 1095 helix: 0.98 (0.23), residues: 490 sheet: 0.63 (0.41), residues: 162 loop : -0.37 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 22 HIS 0.005 0.001 HIS B 168 PHE 0.020 0.002 PHE I 127 TYR 0.015 0.002 TYR C 184 ARG 0.006 0.001 ARG I 122 *********************** 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 227 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 179 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: G 75 VAL cc_start: 0.6559 (OUTLIER) cc_final: 0.6244 (t) REVERT: G 111 ARG cc_start: 0.7143 (tpt-90) cc_final: 0.6096 (tpp80) REVERT: G 129 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6987 (mp0) REVERT: G 139 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6398 (pp20) REVERT: I 119 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7857 (mtp85) REVERT: M 27 LYS cc_start: 0.8733 (tptm) cc_final: 0.8415 (tppp) REVERT: M 44 LYS cc_start: 0.9171 (mttt) cc_final: 0.8719 (mtpt) REVERT: M 50 GLU cc_start: 0.7710 (tp30) cc_final: 0.7410 (tp30) REVERT: B 10 LEU cc_start: 0.3747 (mt) cc_final: 0.3364 (pp) REVERT: B 70 VAL cc_start: 0.8029 (t) cc_final: 0.7822 (t) REVERT: B 105 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7323 (pttt) REVERT: B 108 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7830 (ttp-110) REVERT: B 183 VAL cc_start: 0.5068 (OUTLIER) cc_final: 0.4867 (p) outliers start: 48 outliers final: 30 residues processed: 212 average time/residue: 1.2420 time to fit residues: 296.6857 Evaluate side-chains 207 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL 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: 0.3980 chunk 138 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.0142 ------------------------------------------------------------------------------- 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3071 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= 0.170 Angle : 0.628 12.904 28976 Z= 0.355 Chirality : 0.035 0.190 3601 Planarity : 0.006 0.123 2001 Dihedral : 22.001 168.455 8325 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 3.68 % Allowed : 27.19 % Favored : 69.12 % 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: 0.80 (0.26), residues: 1095 helix: 1.19 (0.24), residues: 487 sheet: 1.00 (0.41), residues: 152 loop : -0.28 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.003 0.001 HIS J 56 PHE 0.014 0.001 PHE B 91 TYR 0.014 0.002 TYR I 6 ARG 0.005 0.000 ARG B 113 *********************** 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 226 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: G 75 VAL cc_start: 0.6489 (OUTLIER) cc_final: 0.6184 (t) REVERT: G 111 ARG cc_start: 0.7267 (tpt-90) cc_final: 0.6296 (tpp80) REVERT: G 129 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7019 (mp0) REVERT: G 139 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6611 (pp20) REVERT: M 27 LYS cc_start: 0.8625 (tptm) cc_final: 0.8310 (tppp) REVERT: M 50 GLU cc_start: 0.7704 (tp30) cc_final: 0.7387 (tp30) REVERT: B 10 LEU cc_start: 0.3937 (mt) cc_final: 0.3550 (pp) REVERT: B 70 VAL cc_start: 0.8102 (t) cc_final: 0.7887 (t) REVERT: B 105 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7290 (pttt) REVERT: B 118 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7088 (tm-30) REVERT: B 223 GLU cc_start: 0.4802 (pt0) cc_final: 0.3631 (tp30) outliers start: 34 outliers final: 24 residues processed: 212 average time/residue: 1.3239 time to fit residues: 315.8112 Evaluate side-chains 213 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 167 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 86 GLN I 32 GLN I 110 GLN J 56 HIS N 35 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 19821 Z= 0.464 Angle : 0.739 13.461 28976 Z= 0.406 Chirality : 0.042 0.205 3601 Planarity : 0.007 0.130 2001 Dihedral : 22.024 168.653 8325 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 3.68 % Allowed : 26.87 % Favored : 69.45 % 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: 0.91 (0.23), residues: 487 sheet: 0.44 (0.40), residues: 164 loop : -0.38 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 22 HIS 0.004 0.001 HIS M 12 PHE 0.015 0.002 PHE I 20 TYR 0.016 0.002 TYR C 184 ARG 0.009 0.001 ARG B 113 ********************** 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 212 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: G 21 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: G 75 VAL cc_start: 0.6567 (OUTLIER) cc_final: 0.6250 (t) REVERT: G 111 ARG cc_start: 0.7081 (tpt-90) cc_final: 0.5992 (tpp80) REVERT: G 126 ASP cc_start: 0.7483 (m-30) cc_final: 0.7118 (m-30) REVERT: G 129 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7031 (mp0) REVERT: G 139 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6304 (pp20) REVERT: I 107 ASP cc_start: 0.8867 (p0) cc_final: 0.8585 (p0) REVERT: I 119 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7856 (mtp85) REVERT: M 27 LYS cc_start: 0.8739 (tptm) cc_final: 0.8402 (tppp) REVERT: M 50 GLU cc_start: 0.7767 (tp30) cc_final: 0.7484 (tp30) REVERT: B 70 VAL cc_start: 0.8220 (t) cc_final: 0.8012 (t) REVERT: B 78 GLU cc_start: 0.6232 (tp30) cc_final: 0.5913 (pm20) REVERT: B 105 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7463 (pttt) outliers start: 34 outliers final: 23 residues processed: 201 average time/residue: 1.3437 time to fit residues: 302.5705 Evaluate side-chains 198 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 119 ARG Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 84 VAL Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 86 GLN I 32 GLN I 110 GLN J 56 HIS B 24 ASN B 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.059314 restraints weight = 46739.975| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.74 r_work: 0.2775 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19821 Z= 0.193 Angle : 0.660 13.000 28976 Z= 0.369 Chirality : 0.036 0.196 3601 Planarity : 0.006 0.124 2001 Dihedral : 22.055 167.895 8325 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 3.03 % Allowed : 28.82 % Favored : 68.15 % 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: 0.55 (0.25), residues: 1095 helix: 1.01 (0.24), residues: 485 sheet: 0.57 (0.40), residues: 162 loop : -0.33 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.003 0.001 HIS J 56 PHE 0.011 0.001 PHE S 74 TYR 0.012 0.001 TYR C 184 ARG 0.007 0.001 ARG B 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5899.87 seconds wall clock time: 106 minutes 12.26 seconds (6372.26 seconds total)