Starting phenix.real_space_refine on Sat Feb 17 10:57:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/02_2024/7afd_11761_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/02_2024/7afd_11761.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/02_2024/7afd_11761_neut_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/02_2024/7afd_11761_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/02_2024/7afd_11761_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/02_2024/7afd_11761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/02_2024/7afd_11761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/02_2024/7afd_11761_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afd_11761/02_2024/7afd_11761_neut_updated.pdb" } 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 Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 74": "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: 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: 10.07, per 1000 atoms: 0.54 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 - 3.50 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: 12.13 Conformation dependent library (CDL) restraints added in 2.0 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... running ksdssp... Secondary structure from input PDB file: 45 helices and 10 sheets defined 42.8% alpha, 11.2% beta 131 base pairs and 218 stacking pairs defined. Time for finding SS restraints: 10.07 Creating SS restraints... 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 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.674A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 147 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 helix chain 'C' and resid 7 through 11 removed outlier: 3.932A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'C' and resid 29 through 49 removed outlier: 3.985A pdb=" N ALA C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 94 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 125 Processing helix chain 'C' and resid 130 through 144 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 16 through 18 No H-bonds generated for 'chain 'G' and resid 16 through 18' Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 4.209A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 4.141A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 134 through 144 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 42 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 95 through 101 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 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 15 through 20 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 61 removed outlier: 4.503A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 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 19 Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 40 through 50 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 83 through 89 Processing helix chain 'S' and resid 13 through 24 Processing helix chain 'S' and resid 71 through 74 Processing sheet with id= A, 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: 6.244A 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: 7.610A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, 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: 4.431A 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) Processing sheet with id= C, first strand: chain 'C' and resid 99 through 103 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= D, first strand: chain 'C' and resid 166 through 171 Processing sheet with id= E, first strand: chain 'G' and resid 73 through 75 Processing sheet with id= F, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.591A pdb=" N TYR I 6 " --> pdb=" O ILE I 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 28 through 30 removed outlier: 7.008A pdb=" N LEU I 63 " --> pdb=" O VAL I 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'J' and resid 97 through 101 removed outlier: 4.562A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= J, first strand: chain 'S' and resid 31 through 33 removed outlier: 3.629A pdb=" N LEU S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1047 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: 8.16 Time building geometry restraints manager: 12.39 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=" N3 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.496 1.336 0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" N3 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.496 1.339 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C2 5MC 1 967 " pdb=" N3 5MC 1 967 " ideal model delta sigma weight residual 1.493 1.341 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" C2 2MG 11207 " pdb=" N2 2MG 11207 " ideal model delta sigma weight residual 1.475 1.335 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C2 2MG 1 966 " pdb=" N2 2MG 1 966 " ideal model delta sigma weight residual 1.475 1.339 0.136 2.00e-02 2.50e+03 4.64e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.82: 2939 106.82 - 114.46: 12415 114.46 - 122.09: 9606 122.09 - 129.73: 3660 129.73 - 137.36: 329 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=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C8 2MG 11207 " ideal model delta sigma weight residual 110.07 128.18 -18.11 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 138.70 122.14 16.56 3.00e+00 1.11e-01 3.05e+01 angle pdb=" C1' 2MG 1 966 " pdb=" N9 2MG 1 966 " pdb=" C8 2MG 1 966 " ideal model delta sigma weight residual 110.07 126.26 -16.19 3.00e+00 1.11e-01 2.91e+01 angle pdb=" C1' 2MG 1 966 " pdb=" N9 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 138.70 124.63 14.07 3.00e+00 1.11e-01 2.20e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 11236 35.20 - 70.40: 1206 70.40 - 105.60: 150 105.60 - 140.81: 5 140.81 - 176.01: 3 Dihedral angle restraints: 12600 sinusoidal: 9430 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 12597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3186 0.075 - 0.151: 328 0.151 - 0.226: 67 0.226 - 0.301: 13 0.301 - 0.376: 3 Chirality restraints: 3597 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 3594 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 966 " 0.032 2.00e-02 2.50e+03 5.90e-01 7.83e+03 pdb=" C4' 2MG 1 966 " 0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 966 " 0.707 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 966 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 966 " -0.572 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 966 " -0.220 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 966 " 0.899 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 966 " 0.215 2.00e-02 2.50e+03 pdb=" N9 2MG 1 966 " -0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11207 " -0.058 2.00e-02 2.50e+03 5.84e-01 7.68e+03 pdb=" C4' 2MG 11207 " -0.432 2.00e-02 2.50e+03 pdb=" O4' 2MG 11207 " -0.576 2.00e-02 2.50e+03 pdb=" C3' 2MG 11207 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG 11207 " 0.623 2.00e-02 2.50e+03 pdb=" C2' 2MG 11207 " 0.175 2.00e-02 2.50e+03 pdb=" O2' 2MG 11207 " -0.971 2.00e-02 2.50e+03 pdb=" C1' 2MG 11207 " -0.238 2.00e-02 2.50e+03 pdb=" N9 2MG 11207 " 0.882 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 1 967 " 0.017 2.00e-02 2.50e+03 5.65e-01 7.19e+03 pdb=" C4' 5MC 1 967 " 0.437 2.00e-02 2.50e+03 pdb=" O4' 5MC 1 967 " 0.632 2.00e-02 2.50e+03 pdb=" C3' 5MC 1 967 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 5MC 1 967 " -0.549 2.00e-02 2.50e+03 pdb=" C2' 5MC 1 967 " -0.219 2.00e-02 2.50e+03 pdb=" O2' 5MC 1 967 " 0.896 2.00e-02 2.50e+03 pdb=" C1' 5MC 1 967 " 0.231 2.00e-02 2.50e+03 pdb=" N1 5MC 1 967 " -0.858 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 300 2.46 - 3.07: 13746 3.07 - 3.68: 38366 3.68 - 4.29: 52669 4.29 - 4.90: 72554 Nonbonded interactions: 177635 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 177630 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: 3.050 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: 12.550 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 64.880 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.310 ------------------------------------------------------------------------------- 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 0.160 19801 Z= 0.561 Angle : 0.899 18.112 28949 Z= 0.547 Chirality : 0.053 0.376 3597 Planarity : 0.023 0.590 1998 Dihedral : 22.832 176.008 10548 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 fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.417 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: 0.4110 time to fit residues: 140.1818 Evaluate side-chains 142 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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: 0.9990 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 177 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19801 Z= 0.187 Angle : 0.714 14.072 28949 Z= 0.391 Chirality : 0.037 0.287 3597 Planarity : 0.006 0.120 1998 Dihedral : 23.734 177.672 8323 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.71 % Allowed : 18.13 % Favored : 79.15 % 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: -1.43 (0.24), residues: 1092 helix: -0.20 (0.23), residues: 483 sheet: -1.82 (0.38), residues: 163 loop : -1.30 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.006 0.001 HIS B 168 PHE 0.017 0.002 PHE B 90 TYR 0.014 0.002 TYR I 90 ARG 0.005 0.000 ARG I 119 *********************** 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 202 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.373 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 192 ASP cc_start: 0.7722 (t0) cc_final: 0.7308 (t0) REVERT: B 213 TYR cc_start: 0.7602 (m-80) cc_final: 0.7297 (m-80) REVERT: C 36 ASP cc_start: 0.8732 (p0) cc_final: 0.8510 (p0) REVERT: C 129 MET cc_start: 0.9007 (mmm) cc_final: 0.8729 (mmm) REVERT: G 15 ASP cc_start: 0.7585 (t0) cc_final: 0.7351 (t0) REVERT: G 116 MET cc_start: 0.8131 (pmm) cc_final: 0.7512 (tpt) REVERT: I 60 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8914 (mmmt) REVERT: I 118 LEU cc_start: 0.9199 (mt) cc_final: 0.8767 (mt) REVERT: J 19 ASP cc_start: 0.8790 (m-30) cc_final: 0.8494 (p0) REVERT: J 63 ASP cc_start: 0.8391 (t0) cc_final: 0.8062 (t0) REVERT: M 75 MET cc_start: 0.8796 (mmm) cc_final: 0.8583 (mmm) REVERT: M 81 MET cc_start: 0.9145 (mtm) cc_final: 0.8818 (mtt) REVERT: N 89 MET cc_start: 0.9411 (mmt) cc_final: 0.9210 (mmm) REVERT: S 66 MET cc_start: 0.8655 (mtp) cc_final: 0.8350 (mtp) outliers start: 25 outliers final: 11 residues processed: 193 average time/residue: 0.3255 time to fit residues: 93.4646 Evaluate side-chains 152 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 79 LEU 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: 5.9990 chunk 43 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 168 HIS B 227 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19801 Z= 0.211 Angle : 0.673 12.729 28949 Z= 0.372 Chirality : 0.036 0.225 3597 Planarity : 0.006 0.125 1998 Dihedral : 23.544 179.255 8323 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.80 % Allowed : 19.54 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1092 helix: 0.16 (0.23), residues: 478 sheet: -1.52 (0.38), residues: 160 loop : -1.05 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 103 HIS 0.011 0.001 HIS B 168 PHE 0.015 0.001 PHE B 184 TYR 0.012 0.002 TYR I 90 ARG 0.006 0.001 ARG G 10 *********************** REFINEMENT MACRO_CYCLE 3 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 195 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.328 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: B 50 PHE cc_start: 0.7933 (t80) cc_final: 0.7717 (t80) REVERT: B 213 TYR cc_start: 0.7541 (m-80) cc_final: 0.7234 (m-80) REVERT: G 10 ARG cc_start: 0.5773 (OUTLIER) cc_final: 0.5560 (ptp90) REVERT: G 15 ASP cc_start: 0.7541 (t0) cc_final: 0.7209 (t0) REVERT: G 111 ARG cc_start: 0.7516 (ttt90) cc_final: 0.7217 (ttm-80) REVERT: G 116 MET cc_start: 0.8166 (pmm) cc_final: 0.7427 (tpt) REVERT: I 53 GLU cc_start: 0.9246 (pp20) cc_final: 0.8998 (pp20) REVERT: I 60 LYS cc_start: 0.9364 (mmmt) cc_final: 0.9138 (mmmt) REVERT: I 118 LEU cc_start: 0.9257 (mt) cc_final: 0.8822 (mt) REVERT: J 19 ASP cc_start: 0.8821 (m-30) cc_final: 0.8571 (p0) REVERT: J 63 ASP cc_start: 0.8332 (t0) cc_final: 0.8010 (t70) REVERT: M 72 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8648 (mm-30) REVERT: M 81 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8807 (mtt) REVERT: S 6 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8553 (ptpp) REVERT: S 66 MET cc_start: 0.8639 (mtp) cc_final: 0.8304 (mtp) outliers start: 35 outliers final: 13 residues processed: 182 average time/residue: 0.3108 time to fit residues: 85.0245 Evaluate side-chains 158 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 42 ASP 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 44 MET Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS B 19 GLN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19801 Z= 0.305 Angle : 0.710 13.127 28949 Z= 0.389 Chirality : 0.038 0.222 3597 Planarity : 0.007 0.124 1998 Dihedral : 23.568 177.041 8323 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 27.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 4.67 % Allowed : 19.98 % Favored : 75.35 % 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: -0.96 (0.24), residues: 1092 helix: 0.08 (0.23), residues: 485 sheet: -1.40 (0.38), residues: 161 loop : -1.00 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 103 HIS 0.011 0.001 HIS B 168 PHE 0.011 0.002 PHE B 184 TYR 0.012 0.002 TYR I 38 ARG 0.006 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 4 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 188 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.323 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: B 213 TYR cc_start: 0.7565 (m-80) cc_final: 0.7214 (m-80) REVERT: C 139 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8655 (tm-30) REVERT: G 15 ASP cc_start: 0.7848 (t0) cc_final: 0.7495 (t0) REVERT: G 116 MET cc_start: 0.8224 (pmm) cc_final: 0.7672 (tpt) REVERT: I 46 MET cc_start: 0.9086 (mmm) cc_final: 0.8695 (tmm) REVERT: I 118 LEU cc_start: 0.9426 (mt) cc_final: 0.9033 (mt) REVERT: J 63 ASP cc_start: 0.8346 (t0) cc_final: 0.7987 (t70) REVERT: M 78 LYS cc_start: 0.9444 (tptm) cc_final: 0.9225 (tptm) REVERT: M 81 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8903 (ttm) REVERT: S 6 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8519 (ptpp) REVERT: S 66 MET cc_start: 0.8584 (mtp) cc_final: 0.8340 (mtp) outliers start: 43 outliers final: 23 residues processed: 173 average time/residue: 0.3130 time to fit residues: 82.5195 Evaluate side-chains 159 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 19801 Z= 0.416 Angle : 0.786 13.114 28949 Z= 0.422 Chirality : 0.041 0.228 3597 Planarity : 0.007 0.124 1998 Dihedral : 23.632 175.415 8323 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 31.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 4.34 % Allowed : 21.61 % Favored : 74.05 % 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: -1.17 (0.24), residues: 1092 helix: -0.10 (0.23), residues: 480 sheet: -1.40 (0.37), residues: 167 loop : -1.13 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 103 HIS 0.017 0.002 HIS B 168 PHE 0.014 0.002 PHE G 26 TYR 0.011 0.002 TYR I 90 ARG 0.008 0.001 ARG G 138 *********************** REFINEMENT MACRO_CYCLE 5 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 176 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 1.421 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: B 213 TYR cc_start: 0.7686 (m-80) cc_final: 0.7306 (m-80) REVERT: G 15 ASP cc_start: 0.7969 (t0) cc_final: 0.7613 (t0) REVERT: G 116 MET cc_start: 0.8222 (pmm) cc_final: 0.7611 (tpt) REVERT: I 118 LEU cc_start: 0.9423 (mt) cc_final: 0.9030 (mt) REVERT: J 19 ASP cc_start: 0.8863 (m-30) cc_final: 0.8531 (m-30) REVERT: J 47 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: J 63 ASP cc_start: 0.8245 (t0) cc_final: 0.7838 (t70) REVERT: M 75 MET cc_start: 0.8978 (mmp) cc_final: 0.8765 (mmp) REVERT: M 78 LYS cc_start: 0.9500 (tptm) cc_final: 0.9253 (tptm) REVERT: M 81 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8816 (mtt) REVERT: S 66 MET cc_start: 0.8535 (mtp) cc_final: 0.8312 (mtp) outliers start: 40 outliers final: 24 residues processed: 162 average time/residue: 0.3035 time to fit residues: 75.7831 Evaluate side-chains 149 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER 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 39 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS C 140 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19801 Z= 0.269 Angle : 0.701 13.179 28949 Z= 0.385 Chirality : 0.037 0.227 3597 Planarity : 0.006 0.121 1998 Dihedral : 23.488 175.131 8323 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 4.23 % Allowed : 24.00 % Favored : 71.77 % 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: -0.86 (0.25), residues: 1092 helix: 0.10 (0.23), residues: 484 sheet: -1.11 (0.40), residues: 156 loop : -0.96 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 103 HIS 0.010 0.001 HIS B 168 PHE 0.015 0.001 PHE B 184 TYR 0.014 0.002 TYR I 38 ARG 0.005 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 6 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 179 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 1.443 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: B 213 TYR cc_start: 0.7708 (m-80) cc_final: 0.7363 (m-80) REVERT: C 139 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8574 (tm-30) REVERT: G 15 ASP cc_start: 0.7944 (t0) cc_final: 0.7532 (t0) REVERT: G 116 MET cc_start: 0.8246 (pmm) cc_final: 0.7582 (tpt) REVERT: I 118 LEU cc_start: 0.9416 (mt) cc_final: 0.8998 (mt) REVERT: J 19 ASP cc_start: 0.8868 (m-30) cc_final: 0.8585 (p0) REVERT: J 47 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: J 63 ASP cc_start: 0.8327 (t0) cc_final: 0.7907 (t70) REVERT: M 78 LYS cc_start: 0.9469 (tptm) cc_final: 0.9242 (tptm) REVERT: M 81 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8897 (ttm) REVERT: S 6 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8484 (ptpp) REVERT: S 66 MET cc_start: 0.8511 (mtp) cc_final: 0.8282 (mtp) outliers start: 39 outliers final: 25 residues processed: 168 average time/residue: 0.2918 time to fit residues: 77.8831 Evaluate side-chains 154 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** I 75 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19801 Z= 0.167 Angle : 0.665 13.331 28949 Z= 0.368 Chirality : 0.035 0.218 3597 Planarity : 0.006 0.119 1998 Dihedral : 23.326 175.448 8323 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 4.23 % Allowed : 24.10 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1092 helix: 0.32 (0.23), residues: 479 sheet: -1.08 (0.42), residues: 149 loop : -0.88 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 103 HIS 0.039 0.002 HIS B 168 PHE 0.014 0.001 PHE B 184 TYR 0.012 0.002 TYR I 38 ARG 0.003 0.000 ARG G 138 *********************** REFINEMENT MACRO_CYCLE 7 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 190 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.337 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: B 213 TYR cc_start: 0.7659 (m-80) cc_final: 0.7377 (m-80) REVERT: C 139 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8511 (tm-30) REVERT: G 10 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6123 (ptp-170) REVERT: G 15 ASP cc_start: 0.7888 (t0) cc_final: 0.7532 (t0) REVERT: G 52 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8835 (pp30) REVERT: G 101 MET cc_start: 0.9427 (mtm) cc_final: 0.9062 (ptm) REVERT: G 106 GLU cc_start: 0.9137 (pp20) cc_final: 0.8843 (pp20) REVERT: G 116 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7514 (tpt) REVERT: I 64 TYR cc_start: 0.6908 (t80) cc_final: 0.6475 (t80) REVERT: I 98 LEU cc_start: 0.9475 (mt) cc_final: 0.9246 (mt) REVERT: I 118 LEU cc_start: 0.9327 (mt) cc_final: 0.8873 (mt) REVERT: J 47 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: J 63 ASP cc_start: 0.8400 (t0) cc_final: 0.7996 (t70) REVERT: M 27 LYS cc_start: 0.9209 (tppt) cc_final: 0.8958 (tppt) REVERT: M 78 LYS cc_start: 0.9422 (tptm) cc_final: 0.9158 (tptm) REVERT: M 81 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8881 (ttm) REVERT: S 6 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8543 (ptpp) outliers start: 39 outliers final: 21 residues processed: 178 average time/residue: 0.3090 time to fit residues: 84.0288 Evaluate side-chains 160 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 88 ASP 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 B residue 227 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 0.2980 chunk 100 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 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** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19801 Z= 0.202 Angle : 0.687 13.276 28949 Z= 0.375 Chirality : 0.035 0.234 3597 Planarity : 0.006 0.119 1998 Dihedral : 23.284 175.730 8323 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 3.80 % Allowed : 25.19 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1092 helix: 0.30 (0.23), residues: 481 sheet: -1.04 (0.40), residues: 161 loop : -0.97 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 103 HIS 0.011 0.001 HIS B 168 PHE 0.018 0.001 PHE B 184 TYR 0.010 0.001 TYR B 213 ARG 0.003 0.000 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 8 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 168 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 1.513 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 167 ASP cc_start: 0.6874 (p0) cc_final: 0.6545 (p0) REVERT: B 213 TYR cc_start: 0.7696 (m-80) cc_final: 0.7430 (m-80) REVERT: C 139 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8565 (tm-30) REVERT: G 10 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.6316 (ptp-170) REVERT: G 15 ASP cc_start: 0.8024 (t0) cc_final: 0.7774 (t0) REVERT: G 52 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8809 (pp30) REVERT: G 103 TRP cc_start: 0.9399 (m-10) cc_final: 0.9188 (m-10) REVERT: G 106 GLU cc_start: 0.9121 (pp20) cc_final: 0.8816 (pp20) REVERT: G 116 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7519 (tpt) REVERT: I 64 TYR cc_start: 0.6778 (t80) cc_final: 0.6377 (t80) REVERT: I 118 LEU cc_start: 0.9333 (mt) cc_final: 0.8890 (mt) REVERT: J 47 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: J 63 ASP cc_start: 0.8416 (t0) cc_final: 0.7990 (t70) REVERT: J 64 GLN cc_start: 0.8500 (mt0) cc_final: 0.8296 (mm-40) REVERT: M 27 LYS cc_start: 0.9212 (tppt) cc_final: 0.8988 (tppt) REVERT: M 81 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8834 (mtt) outliers start: 35 outliers final: 26 residues processed: 160 average time/residue: 0.3096 time to fit residues: 79.4573 Evaluate side-chains 160 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 88 ASP 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 B residue 227 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 81 MET Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 141 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 124 optimal weight: 0.0030 chunk 129 optimal weight: 0.0770 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19801 Z= 0.153 Angle : 0.661 13.105 28949 Z= 0.365 Chirality : 0.034 0.223 3597 Planarity : 0.006 0.118 1998 Dihedral : 23.134 175.055 8323 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 3.15 % Allowed : 25.73 % Favored : 71.12 % 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: -0.63 (0.25), residues: 1092 helix: 0.39 (0.23), residues: 467 sheet: -1.05 (0.42), residues: 149 loop : -0.92 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 103 HIS 0.013 0.001 HIS B 168 PHE 0.018 0.001 PHE B 162 TYR 0.013 0.002 TYR B 213 ARG 0.003 0.000 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 9 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 176 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.295 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: B 22 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5589 (m-80) REVERT: B 27 MET cc_start: 0.3958 (ttt) cc_final: 0.3702 (ttm) REVERT: B 192 ASP cc_start: 0.7811 (t0) cc_final: 0.7455 (t0) REVERT: B 213 TYR cc_start: 0.7678 (m-80) cc_final: 0.7413 (m-80) REVERT: C 123 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8858 (mm-40) REVERT: C 129 MET cc_start: 0.8787 (tpp) cc_final: 0.8554 (mmm) REVERT: C 139 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8603 (tm-30) REVERT: G 10 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.6106 (ptp-170) REVERT: G 21 GLU cc_start: 0.9363 (pp20) cc_final: 0.8865 (tm-30) REVERT: G 52 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8767 (pp30) REVERT: G 103 TRP cc_start: 0.9430 (m-10) cc_final: 0.9218 (m-10) REVERT: G 106 GLU cc_start: 0.9098 (pp20) cc_final: 0.8805 (pp20) REVERT: G 116 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7266 (tpt) REVERT: I 98 LEU cc_start: 0.9443 (mt) cc_final: 0.9194 (mt) REVERT: I 118 LEU cc_start: 0.9262 (mt) cc_final: 0.8811 (mt) REVERT: J 63 ASP cc_start: 0.8476 (t0) cc_final: 0.7703 (t70) REVERT: J 64 GLN cc_start: 0.8365 (mt0) cc_final: 0.8095 (mm-40) REVERT: M 11 ASP cc_start: 0.8438 (m-30) cc_final: 0.8013 (p0) REVERT: M 27 LYS cc_start: 0.9216 (tppt) cc_final: 0.8990 (tppt) REVERT: M 81 MET cc_start: 0.9189 (mtm) cc_final: 0.8897 (ttm) outliers start: 29 outliers final: 21 residues processed: 168 average time/residue: 0.2883 time to fit residues: 74.6054 Evaluate side-chains 160 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 152 optimal weight: 0.0030 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 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** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19801 Z= 0.170 Angle : 0.683 13.280 28949 Z= 0.373 Chirality : 0.034 0.217 3597 Planarity : 0.006 0.118 1998 Dihedral : 23.112 175.254 8323 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 2.82 % Allowed : 26.93 % Favored : 70.25 % 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: -0.62 (0.25), residues: 1092 helix: 0.31 (0.23), residues: 472 sheet: -0.84 (0.42), residues: 148 loop : -0.90 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 103 HIS 0.010 0.001 HIS B 168 PHE 0.017 0.001 PHE B 184 TYR 0.013 0.001 TYR B 213 ARG 0.005 0.000 ARG C 143 ********************** REFINEMENT MACRO_CYCLE 10 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 170 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.258 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: B 27 MET cc_start: 0.3810 (ttt) cc_final: 0.3558 (ttm) REVERT: B 213 TYR cc_start: 0.7720 (m-80) cc_final: 0.7435 (m-80) REVERT: C 123 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8840 (mm-40) REVERT: C 129 MET cc_start: 0.8787 (tpp) cc_final: 0.8561 (mmm) REVERT: G 21 GLU cc_start: 0.9335 (pp20) cc_final: 0.8922 (tm-30) REVERT: G 52 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8812 (pp30) REVERT: G 116 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7309 (tpt) REVERT: I 98 LEU cc_start: 0.9422 (mt) cc_final: 0.9191 (mt) REVERT: I 118 LEU cc_start: 0.9274 (mt) cc_final: 0.8834 (mt) REVERT: J 19 ASP cc_start: 0.8819 (m-30) cc_final: 0.8439 (m-30) REVERT: J 63 ASP cc_start: 0.8411 (t0) cc_final: 0.7655 (t70) REVERT: J 64 GLN cc_start: 0.8351 (mt0) cc_final: 0.8135 (mm-40) REVERT: M 11 ASP cc_start: 0.8437 (m-30) cc_final: 0.8024 (p0) REVERT: M 27 LYS cc_start: 0.9223 (tppt) cc_final: 0.8994 (tppt) REVERT: M 81 MET cc_start: 0.9153 (mtm) cc_final: 0.8892 (ttm) outliers start: 26 outliers final: 21 residues processed: 162 average time/residue: 0.3014 time to fit residues: 75.4420 Evaluate side-chains 157 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 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** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.037114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.029627 restraints weight = 159296.424| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.19 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19801 Z= 0.169 Angle : 0.685 12.998 28949 Z= 0.374 Chirality : 0.034 0.212 3597 Planarity : 0.006 0.117 1998 Dihedral : 23.098 174.727 8323 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.67 % Favored : 95.24 % Rotamer: Outliers : 2.82 % Allowed : 27.47 % Favored : 69.71 % 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 (0.25), residues: 1092 helix: 0.29 (0.23), residues: 472 sheet: -0.80 (0.42), residues: 148 loop : -0.90 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 103 HIS 0.012 0.001 HIS B 168 PHE 0.017 0.001 PHE B 184 TYR 0.013 0.002 TYR B 213 ARG 0.003 0.000 ARG C 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3071.38 seconds wall clock time: 57 minutes 52.69 seconds (3472.69 seconds total)