Starting phenix.real_space_refine on Sat Feb 17 11:06:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afn_11771/02_2024/7afn_11771_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afn_11771/02_2024/7afn_11771.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afn_11771/02_2024/7afn_11771_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afn_11771/02_2024/7afn_11771_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afn_11771/02_2024/7afn_11771_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afn_11771/02_2024/7afn_11771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afn_11771/02_2024/7afn_11771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afn_11771/02_2024/7afn_11771_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afn_11771/02_2024/7afn_11771_neut_updated.pdb" } resolution = 3.86 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 11 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 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 80": "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: 18520 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': 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 10.70, per 1000 atoms: 0.58 Number of scatterers: 18520 At special positions: 0 Unit cell: (121.52, 146.475, 125.86, 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 11 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: 11.73 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 " 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: 43 helices and 9 sheets defined 43.5% alpha, 12.5% beta 146 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 10.81 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: 3.673A 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 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 helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 26 through 50 removed outlier: 4.288A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.314A 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 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 'G' and resid 22 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 3.541A pdb=" N SER G 41 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 4.303A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 109 removed outlier: 4.195A pdb=" N ALA G 107 " --> pdb=" O TRP G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 Processing helix chain 'G' and resid 134 through 139 Processing helix chain 'G' and resid 141 through 147 removed outlier: 4.629A pdb=" N GLU G 146 " --> pdb=" O HIS G 142 " (cutoff:3.500A) 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 94 through 101 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 89 removed outlier: 3.710A 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 Processing helix chain 'M' and resid 66 through 82 Processing helix chain 'M' and resid 86 through 93 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 32 removed outlier: 3.849A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA N 22 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 50 removed outlier: 3.705A 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 90 Processing helix chain 'S' and resid 13 through 24 Processing helix chain 'S' and resid 71 through 74 No H-bonds generated for '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: 6.245A 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: 7.611A 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= 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: 6.124A 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: 6.677A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.305A 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 removed outlier: 6.674A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) 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 12 Processing sheet with id= G, first strand: chain 'J' and resid 70 through 76 Processing sheet with id= H, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= I, first strand: chain 'S' and resid 31 through 33 removed outlier: 4.213A pdb=" N LEU S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 578 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 8.33 Time building geometry restraints manager: 12.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2050 1.31 - 1.43: 7783 1.43 - 1.56: 9000 1.56 - 1.69: 914 1.69 - 1.82: 54 Bond restraints: 19801 Sorted by residual: bond pdb=" O3' G 1 963 " pdb=" P A 1 964 " ideal model delta sigma weight residual 1.607 1.738 -0.131 1.50e-02 4.44e+03 7.57e+01 bond pdb=" N3 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.496 1.340 0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" N3 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.496 1.352 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C2 5MC 1 967 " pdb=" N3 5MC 1 967 " ideal model delta sigma weight residual 1.493 1.351 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C2 2MG 11207 " pdb=" N2 2MG 11207 " ideal model delta sigma weight residual 1.475 1.338 0.137 2.00e-02 2.50e+03 4.71e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.99: 2563 105.99 - 113.56: 11946 113.56 - 121.13: 9379 121.13 - 128.70: 4498 128.70 - 136.27: 563 Bond angle restraints: 28949 Sorted by residual: angle pdb=" C3' G 1 963 " pdb=" O3' G 1 963 " pdb=" P A 1 964 " ideal model delta sigma weight residual 120.20 108.55 11.65 1.50e+00 4.44e-01 6.04e+01 angle pdb=" O3' U 11240 " pdb=" C3' U 11240 " pdb=" C2' U 11240 " ideal model delta sigma weight residual 109.50 119.53 -10.03 1.50e+00 4.44e-01 4.47e+01 angle pdb=" N ARG S 55 " pdb=" CA ARG S 55 " pdb=" C ARG S 55 " ideal model delta sigma weight residual 113.97 106.22 7.75 1.28e+00 6.10e-01 3.67e+01 angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C8 2MG 11207 " ideal model delta sigma weight residual 110.07 127.33 -17.26 3.00e+00 1.11e-01 3.31e+01 angle pdb=" CA GLY I 69 " pdb=" C GLY I 69 " pdb=" O GLY I 69 " ideal model delta sigma weight residual 122.29 117.69 4.60 8.10e-01 1.52e+00 3.22e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 11157 35.18 - 70.35: 1272 70.35 - 105.53: 156 105.53 - 140.70: 11 140.70 - 175.88: 4 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 -160.00 5.09 -165.09 1 1.50e+01 4.44e-03 8.39e+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 59.96 140.04 1 1.50e+01 4.44e-03 7.54e+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 232.00 56.12 175.88 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3235 0.119 - 0.237: 346 0.237 - 0.355: 15 0.355 - 0.474: 0 0.474 - 0.592: 1 Chirality restraints: 3597 Sorted by residual: chirality pdb=" CA ASN M 105 " pdb=" N ASN M 105 " pdb=" C ASN M 105 " pdb=" CB ASN M 105 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C3' A 1 964 " pdb=" C4' A 1 964 " pdb=" O3' A 1 964 " pdb=" C2' A 1 964 " both_signs ideal model delta sigma weight residual False -2.48 -2.80 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 3594 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11207 " 0.032 2.00e-02 2.50e+03 5.05e-01 5.75e+03 pdb=" C4' 2MG 11207 " 0.414 2.00e-02 2.50e+03 pdb=" O4' 2MG 11207 " 0.459 2.00e-02 2.50e+03 pdb=" C3' 2MG 11207 " -0.570 2.00e-02 2.50e+03 pdb=" O3' 2MG 11207 " -0.482 2.00e-02 2.50e+03 pdb=" C2' 2MG 11207 " -0.230 2.00e-02 2.50e+03 pdb=" O2' 2MG 11207 " 0.852 2.00e-02 2.50e+03 pdb=" C1' 2MG 11207 " 0.245 2.00e-02 2.50e+03 pdb=" N9 2MG 11207 " -0.721 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 966 " 0.260 2.00e-02 2.50e+03 4.07e-01 3.74e+03 pdb=" C4' 2MG 1 966 " -0.396 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 966 " -0.562 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 966 " 0.477 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 966 " 0.062 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 966 " 0.364 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 966 " -0.424 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 966 " -0.330 2.00e-02 2.50e+03 pdb=" N9 2MG 1 966 " 0.548 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 1 967 " -0.325 2.00e-02 2.50e+03 3.69e-01 3.07e+03 pdb=" C4' 5MC 1 967 " 0.358 2.00e-02 2.50e+03 pdb=" O4' 5MC 1 967 " 0.511 2.00e-02 2.50e+03 pdb=" C3' 5MC 1 967 " -0.443 2.00e-02 2.50e+03 pdb=" O3' 5MC 1 967 " 0.127 2.00e-02 2.50e+03 pdb=" C2' 5MC 1 967 " -0.418 2.00e-02 2.50e+03 pdb=" O2' 5MC 1 967 " 0.254 2.00e-02 2.50e+03 pdb=" C1' 5MC 1 967 " 0.341 2.00e-02 2.50e+03 pdb=" N1 5MC 1 967 " -0.405 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 150 2.38 - 3.01: 11586 3.01 - 3.64: 37210 3.64 - 4.27: 54141 4.27 - 4.90: 74324 Nonbonded interactions: 177411 Sorted by model distance: nonbonded pdb=" O5' C 11366 " pdb="MG MG 11606 " model vdw 1.755 2.170 nonbonded pdb=" O2' G 11242 " pdb="MG MG 11610 " model vdw 1.810 2.170 nonbonded pdb=" O3' G 11242 " pdb="MG MG 11610 " model vdw 1.823 2.170 nonbonded pdb=" O5' A 11238 " pdb="MG MG 11611 " model vdw 1.825 2.170 nonbonded pdb=" OP2 A 11238 " pdb="MG MG 11611 " model vdw 1.856 2.170 ... (remaining 177406 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 group one per residue 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: 4.000 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: 0.000 Extract box with map and model: 12.210 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 66.640 Find NCS groups from input model: 0.390 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 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 0.156 19801 Z= 0.555 Angle : 1.021 17.262 28949 Z= 0.689 Chirality : 0.068 0.592 3597 Planarity : 0.018 0.505 1998 Dihedral : 23.516 175.877 10548 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % 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: -1.93 (0.25), residues: 1092 helix: -0.85 (0.24), residues: 487 sheet: -1.11 (0.39), residues: 160 loop : -1.69 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 101 HIS 0.005 0.001 HIS B 170 PHE 0.025 0.002 PHE S 74 TYR 0.016 0.002 TYR M 23 ARG 0.008 0.001 ARG G 138 *********************** 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 282 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.426 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.9303 (mmm) cc_final: 0.8895 (tpp) REVERT: C 153 VAL cc_start: 0.9634 (m) cc_final: 0.9369 (m) REVERT: C 170 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8444 (tm-30) REVERT: C 183 ASP cc_start: 0.8491 (t0) cc_final: 0.8261 (t0) REVERT: G 31 MET cc_start: 0.8782 (ttp) cc_final: 0.8416 (ttp) REVERT: G 38 THR cc_start: 0.9231 (t) cc_final: 0.9028 (t) REVERT: G 101 MET cc_start: 0.9560 (mtm) cc_final: 0.9223 (mtp) REVERT: I 7 TYR cc_start: 0.7518 (p90) cc_final: 0.7304 (p90) REVERT: J 10 LEU cc_start: 0.9605 (mt) cc_final: 0.9391 (mm) REVERT: J 19 ASP cc_start: 0.9221 (m-30) cc_final: 0.8883 (m-30) REVERT: J 50 THR cc_start: 0.9396 (m) cc_final: 0.8328 (p) REVERT: J 63 ASP cc_start: 0.9308 (t0) cc_final: 0.8830 (t0) REVERT: M 23 TYR cc_start: 0.8794 (t80) cc_final: 0.8334 (t80) REVERT: M 75 MET cc_start: 0.9398 (mmp) cc_final: 0.9183 (mmm) REVERT: M 78 LYS cc_start: 0.9383 (tptp) cc_final: 0.9135 (tptp) REVERT: N 89 MET cc_start: 0.9440 (mmp) cc_final: 0.9162 (mmm) REVERT: S 66 MET cc_start: 0.9245 (mtp) cc_final: 0.8712 (mtp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3732 time to fit residues: 149.6109 Evaluate side-chains 142 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B 227 GLN C 32 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2666 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= 0.220 Angle : 0.717 14.508 28949 Z= 0.399 Chirality : 0.038 0.298 3597 Planarity : 0.006 0.116 1998 Dihedral : 24.279 170.826 8323 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.04 % Allowed : 18.89 % Favored : 78.07 % 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: -0.77 (0.25), residues: 1092 helix: -0.04 (0.22), residues: 501 sheet: -0.75 (0.39), residues: 170 loop : -0.80 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 201 HIS 0.005 0.001 HIS M 12 PHE 0.017 0.002 PHE S 74 TYR 0.028 0.002 TYR C 42 ARG 0.007 0.001 ARG B 139 *********************** 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 198 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.299 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 100 GLN cc_start: 0.7811 (tm-30) cc_final: 0.5641 (tm-30) REVERT: C 129 MET cc_start: 0.9255 (mmm) cc_final: 0.8807 (tpp) REVERT: C 142 MET cc_start: 0.9359 (mmm) cc_final: 0.8555 (mmm) REVERT: C 170 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8693 (tm-30) REVERT: C 211 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8263 (mmt) REVERT: G 31 MET cc_start: 0.8851 (ttp) cc_final: 0.8284 (ttp) REVERT: G 101 MET cc_start: 0.9631 (mtm) cc_final: 0.9266 (mtp) REVERT: I 118 LEU cc_start: 0.9438 (mt) cc_final: 0.9210 (mt) REVERT: J 19 ASP cc_start: 0.9257 (m-30) cc_final: 0.9030 (m-30) REVERT: J 46 LYS cc_start: 0.9299 (mptt) cc_final: 0.9080 (mmtm) REVERT: J 63 ASP cc_start: 0.9147 (t0) cc_final: 0.8699 (t0) REVERT: M 23 TYR cc_start: 0.8734 (t80) cc_final: 0.8112 (t80) REVERT: M 62 LYS cc_start: 0.9514 (mtpt) cc_final: 0.9254 (ptpt) REVERT: N 89 MET cc_start: 0.9414 (mmp) cc_final: 0.8927 (mmt) REVERT: S 41 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8684 (m-80) REVERT: S 66 MET cc_start: 0.9165 (mtp) cc_final: 0.8607 (mtp) outliers start: 28 outliers final: 16 residues processed: 183 average time/residue: 0.3129 time to fit residues: 87.2777 Evaluate side-chains 157 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain S residue 41 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3189 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= 0.210 Angle : 0.671 13.490 28949 Z= 0.377 Chirality : 0.035 0.287 3597 Planarity : 0.006 0.120 1998 Dihedral : 24.069 172.225 8323 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.58 % Allowed : 20.52 % Favored : 75.90 % 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: -0.18 (0.25), residues: 1092 helix: 0.61 (0.23), residues: 500 sheet: -0.65 (0.39), residues: 163 loop : -0.63 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 103 HIS 0.005 0.001 HIS S 14 PHE 0.042 0.002 PHE B 16 TYR 0.019 0.002 TYR C 168 ARG 0.018 0.001 ARG G 109 *********************** 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 182 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 1.260 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 ASN cc_start: 0.9434 (m-40) cc_final: 0.9130 (m-40) REVERT: C 129 MET cc_start: 0.9238 (mmm) cc_final: 0.8840 (tpp) REVERT: C 134 MET cc_start: 0.9619 (ptp) cc_final: 0.9209 (ppp) REVERT: C 142 MET cc_start: 0.9361 (mmm) cc_final: 0.8391 (mmp) REVERT: C 170 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8700 (tm-30) REVERT: G 31 MET cc_start: 0.8993 (ttp) cc_final: 0.8329 (ttp) REVERT: G 101 MET cc_start: 0.9637 (mtm) cc_final: 0.9220 (mtp) REVERT: G 103 TRP cc_start: 0.9695 (m-10) cc_final: 0.9348 (m100) REVERT: J 19 ASP cc_start: 0.9266 (m-30) cc_final: 0.9028 (m-30) REVERT: J 63 ASP cc_start: 0.9071 (t0) cc_final: 0.8593 (t70) REVERT: M 23 TYR cc_start: 0.8554 (t80) cc_final: 0.8139 (t80) REVERT: M 78 LYS cc_start: 0.9506 (tppt) cc_final: 0.9220 (tppt) REVERT: M 81 MET cc_start: 0.8864 (tpp) cc_final: 0.8205 (tpp) REVERT: N 82 ILE cc_start: 0.9369 (mt) cc_final: 0.9054 (mp) REVERT: N 86 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9119 (mp0) REVERT: N 89 MET cc_start: 0.9383 (mmp) cc_final: 0.8922 (mmt) REVERT: N 92 GLU cc_start: 0.9249 (mp0) cc_final: 0.9009 (mp0) REVERT: S 66 MET cc_start: 0.9041 (mtp) cc_final: 0.8613 (mtp) outliers start: 33 outliers final: 20 residues processed: 169 average time/residue: 0.3074 time to fit residues: 79.4920 Evaluate side-chains 155 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3795 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 : 0.641 13.173 28949 Z= 0.360 Chirality : 0.034 0.268 3597 Planarity : 0.006 0.118 1998 Dihedral : 23.826 172.291 8323 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.80 % Allowed : 20.09 % Favored : 76.11 % 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 (0.26), residues: 1092 helix: 1.06 (0.23), residues: 494 sheet: -0.42 (0.40), residues: 163 loop : -0.37 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 103 HIS 0.007 0.001 HIS B 15 PHE 0.016 0.002 PHE B 90 TYR 0.021 0.002 TYR C 168 ARG 0.005 0.000 ARG S 32 *********************** 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 189 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 1.462 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 6 MET cc_start: 0.5473 (mmt) cc_final: 0.5196 (mmt) REVERT: B 146 ASN cc_start: 0.8927 (m110) cc_final: 0.8553 (p0) REVERT: C 25 ASN cc_start: 0.9412 (m-40) cc_final: 0.9121 (m-40) REVERT: C 129 MET cc_start: 0.9199 (mmm) cc_final: 0.8793 (tpp) REVERT: C 134 MET cc_start: 0.9598 (ptp) cc_final: 0.9188 (ppp) REVERT: C 142 MET cc_start: 0.9366 (mmm) cc_final: 0.8367 (mmp) REVERT: C 170 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8764 (tm-30) REVERT: G 31 MET cc_start: 0.9124 (ttp) cc_final: 0.8353 (ttp) REVERT: G 103 TRP cc_start: 0.9655 (m-10) cc_final: 0.9376 (m100) REVERT: G 144 MET cc_start: 0.9417 (mpp) cc_final: 0.9202 (mmt) REVERT: I 42 GLU cc_start: 0.8577 (pp20) cc_final: 0.8137 (pp20) REVERT: I 46 MET cc_start: 0.8932 (mmm) cc_final: 0.8384 (mmm) REVERT: I 57 MET cc_start: 0.9080 (ttm) cc_final: 0.8872 (mmm) REVERT: I 118 LEU cc_start: 0.9473 (mt) cc_final: 0.9240 (mt) REVERT: J 63 ASP cc_start: 0.9131 (t0) cc_final: 0.8611 (t0) REVERT: M 78 LYS cc_start: 0.9628 (tppt) cc_final: 0.9379 (tppt) REVERT: M 81 MET cc_start: 0.8937 (tpp) cc_final: 0.8408 (tpp) REVERT: N 62 ASN cc_start: 0.8777 (m110) cc_final: 0.8192 (p0) REVERT: N 82 ILE cc_start: 0.9267 (mt) cc_final: 0.8924 (mp) REVERT: N 86 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9101 (mp0) REVERT: N 89 MET cc_start: 0.9385 (mmp) cc_final: 0.9058 (mmt) REVERT: S 66 MET cc_start: 0.9138 (mtp) cc_final: 0.8710 (mtp) outliers start: 35 outliers final: 22 residues processed: 176 average time/residue: 0.3052 time to fit residues: 82.1985 Evaluate side-chains 145 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain S residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19801 Z= 0.340 Angle : 0.740 13.192 28949 Z= 0.406 Chirality : 0.038 0.287 3597 Planarity : 0.007 0.122 1998 Dihedral : 24.003 173.940 8323 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 30.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.99 % Allowed : 20.63 % Favored : 74.38 % 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: 0.19 (0.25), residues: 1092 helix: 0.89 (0.23), residues: 497 sheet: -0.65 (0.38), residues: 170 loop : -0.29 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 104 HIS 0.008 0.002 HIS S 14 PHE 0.028 0.002 PHE B 16 TYR 0.025 0.002 TYR C 168 ARG 0.008 0.001 ARG M 3 *********************** 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 173 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 1.251 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: C 25 ASN cc_start: 0.9398 (m-40) cc_final: 0.9140 (m-40) REVERT: C 129 MET cc_start: 0.9275 (mmm) cc_final: 0.8776 (tpp) REVERT: C 142 MET cc_start: 0.9277 (mmm) cc_final: 0.8842 (mmt) REVERT: C 170 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8722 (tm-30) REVERT: G 31 MET cc_start: 0.9161 (ttp) cc_final: 0.8439 (ttp) REVERT: G 144 MET cc_start: 0.9389 (mpp) cc_final: 0.9174 (mmt) REVERT: I 42 GLU cc_start: 0.8719 (pp20) cc_final: 0.8366 (pp20) REVERT: I 57 MET cc_start: 0.9180 (ttm) cc_final: 0.8749 (mmm) REVERT: I 88 MET cc_start: 0.9085 (ttt) cc_final: 0.8757 (ttt) REVERT: J 63 ASP cc_start: 0.8976 (t0) cc_final: 0.8440 (t70) REVERT: M 12 HIS cc_start: 0.8290 (p90) cc_final: 0.8026 (p90) REVERT: M 27 LYS cc_start: 0.9485 (tptt) cc_final: 0.9264 (tptt) REVERT: M 78 LYS cc_start: 0.9632 (tppt) cc_final: 0.9388 (tppt) REVERT: M 81 MET cc_start: 0.8926 (tpp) cc_final: 0.8480 (tpp) REVERT: N 6 MET cc_start: 0.8975 (mmt) cc_final: 0.8751 (mmp) REVERT: N 82 ILE cc_start: 0.9360 (mt) cc_final: 0.9047 (mp) REVERT: N 86 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9140 (mp0) REVERT: N 89 MET cc_start: 0.9393 (mmp) cc_final: 0.9008 (mmt) REVERT: S 66 MET cc_start: 0.9230 (mtp) cc_final: 0.8801 (mtp) outliers start: 46 outliers final: 37 residues processed: 157 average time/residue: 0.3266 time to fit residues: 79.9563 Evaluate side-chains 157 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.0270 chunk 29 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4208 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= 0.203 Angle : 0.666 12.913 28949 Z= 0.372 Chirality : 0.035 0.277 3597 Planarity : 0.006 0.120 1998 Dihedral : 23.892 172.397 8323 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.26 % Allowed : 23.78 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1092 helix: 1.00 (0.23), residues: 498 sheet: -0.44 (0.38), residues: 168 loop : -0.20 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP G 103 HIS 0.008 0.001 HIS B 168 PHE 0.022 0.002 PHE B 16 TYR 0.025 0.002 TYR C 168 ARG 0.006 0.000 ARG J 16 *********************** 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 156 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.528 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: symmetry clash REVERT: C 25 ASN cc_start: 0.9402 (m-40) cc_final: 0.9139 (m-40) REVERT: C 129 MET cc_start: 0.9252 (mmm) cc_final: 0.8788 (tpp) REVERT: C 134 MET cc_start: 0.9592 (ptp) cc_final: 0.9156 (ppp) REVERT: C 142 MET cc_start: 0.9287 (mmm) cc_final: 0.8461 (mmp) REVERT: C 170 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8785 (tm-30) REVERT: G 31 MET cc_start: 0.9145 (ttp) cc_final: 0.8404 (ttp) REVERT: G 103 TRP cc_start: 0.9641 (m-10) cc_final: 0.9340 (m100) REVERT: G 144 MET cc_start: 0.9406 (mpp) cc_final: 0.9172 (mmt) REVERT: I 42 GLU cc_start: 0.8668 (pp20) cc_final: 0.8398 (pp20) REVERT: I 57 MET cc_start: 0.9142 (ttm) cc_final: 0.8834 (mmm) REVERT: I 112 GLU cc_start: 0.8840 (tp30) cc_final: 0.7926 (tp30) REVERT: I 118 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8756 (tp) REVERT: J 46 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8501 (mmtm) REVERT: J 63 ASP cc_start: 0.9064 (t0) cc_final: 0.8430 (t0) REVERT: M 27 LYS cc_start: 0.9491 (tptt) cc_final: 0.9268 (tptt) REVERT: M 34 LEU cc_start: 0.9321 (tp) cc_final: 0.8935 (tp) REVERT: M 78 LYS cc_start: 0.9633 (tppt) cc_final: 0.9362 (tppt) REVERT: M 81 MET cc_start: 0.8842 (tpp) cc_final: 0.8483 (tpp) REVERT: N 6 MET cc_start: 0.8984 (mmt) cc_final: 0.8772 (mmp) REVERT: N 62 ASN cc_start: 0.8837 (m110) cc_final: 0.8234 (p0) REVERT: N 82 ILE cc_start: 0.9356 (mt) cc_final: 0.9074 (mp) REVERT: N 86 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9061 (mp0) REVERT: N 89 MET cc_start: 0.9363 (mmp) cc_final: 0.9003 (mmt) REVERT: S 15 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9386 (mm) REVERT: S 66 MET cc_start: 0.9203 (mtp) cc_final: 0.8728 (mtp) outliers start: 30 outliers final: 23 residues processed: 143 average time/residue: 0.2984 time to fit residues: 66.5052 Evaluate side-chains 145 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 65 GLU 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: 8.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19801 Z= 0.222 Angle : 0.668 12.852 28949 Z= 0.373 Chirality : 0.035 0.287 3597 Planarity : 0.006 0.120 1998 Dihedral : 23.839 173.029 8323 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.13 % Allowed : 24.00 % Favored : 71.88 % 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: 0.30 (0.25), residues: 1092 helix: 0.92 (0.23), residues: 501 sheet: -0.42 (0.38), residues: 168 loop : -0.25 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 103 HIS 0.006 0.001 HIS S 14 PHE 0.019 0.002 PHE B 16 TYR 0.024 0.002 TYR C 168 ARG 0.010 0.001 ARG C 131 *********************** 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 161 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 2.072 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: symmetry clash revert: symmetry clash REVERT: B 68 LEU cc_start: 0.8989 (tp) cc_final: 0.8740 (mm) REVERT: C 25 ASN cc_start: 0.9395 (m-40) cc_final: 0.9131 (m-40) REVERT: C 142 MET cc_start: 0.9276 (mmm) cc_final: 0.8472 (mmp) REVERT: C 170 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8786 (tm-30) REVERT: G 31 MET cc_start: 0.9075 (ttp) cc_final: 0.8324 (ttp) REVERT: G 103 TRP cc_start: 0.9672 (m-10) cc_final: 0.9380 (m100) REVERT: G 144 MET cc_start: 0.9424 (mpp) cc_final: 0.9193 (mmt) REVERT: I 42 GLU cc_start: 0.8705 (pp20) cc_final: 0.8484 (pp20) REVERT: I 118 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8558 (tp) REVERT: J 63 ASP cc_start: 0.9121 (t0) cc_final: 0.8518 (t0) REVERT: M 27 LYS cc_start: 0.9484 (tptt) cc_final: 0.9275 (tptt) REVERT: M 34 LEU cc_start: 0.9359 (tp) cc_final: 0.8965 (tp) REVERT: M 78 LYS cc_start: 0.9638 (tppt) cc_final: 0.9429 (tppt) REVERT: M 81 MET cc_start: 0.8766 (tpp) cc_final: 0.8487 (tpp) REVERT: N 6 MET cc_start: 0.9002 (mmt) cc_final: 0.8786 (mmp) REVERT: N 62 ASN cc_start: 0.8835 (m110) cc_final: 0.8241 (p0) REVERT: N 82 ILE cc_start: 0.9332 (mt) cc_final: 0.9036 (mp) REVERT: N 86 GLU cc_start: 0.9340 (mt-10) cc_final: 0.9082 (mp0) REVERT: N 89 MET cc_start: 0.9408 (mmp) cc_final: 0.9032 (mmt) REVERT: S 16 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9540 (mm) REVERT: S 66 MET cc_start: 0.9225 (mtp) cc_final: 0.8855 (mtp) outliers start: 38 outliers final: 29 residues processed: 148 average time/residue: 0.3113 time to fit residues: 72.8506 Evaluate side-chains 150 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 19801 Z= 0.377 Angle : 0.777 12.765 28949 Z= 0.421 Chirality : 0.039 0.292 3597 Planarity : 0.007 0.123 1998 Dihedral : 24.076 174.015 8323 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 35.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.45 % Allowed : 23.67 % Favored : 71.88 % 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: -0.03 (0.25), residues: 1092 helix: 0.65 (0.23), residues: 491 sheet: -0.67 (0.37), residues: 166 loop : -0.36 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 103 HIS 0.014 0.002 HIS B 168 PHE 0.018 0.002 PHE B 16 TYR 0.035 0.003 TYR C 168 ARG 0.012 0.001 ARG C 131 *********************** 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 161 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 1.500 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: symmetry clash REVERT: C 142 MET cc_start: 0.9201 (mmm) cc_final: 0.8767 (mmt) REVERT: C 170 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8597 (tm-30) REVERT: G 31 MET cc_start: 0.9117 (ttp) cc_final: 0.8392 (ttp) REVERT: G 103 TRP cc_start: 0.9645 (m-10) cc_final: 0.9415 (m100) REVERT: I 36 GLU cc_start: 0.9453 (pm20) cc_final: 0.9253 (pm20) REVERT: I 118 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8564 (tp) REVERT: J 63 ASP cc_start: 0.9046 (t0) cc_final: 0.8522 (t0) REVERT: M 27 LYS cc_start: 0.9454 (tptt) cc_final: 0.9183 (tptt) REVERT: M 34 LEU cc_start: 0.9448 (tp) cc_final: 0.9154 (tt) REVERT: N 6 MET cc_start: 0.9005 (mmt) cc_final: 0.8793 (mmp) REVERT: N 82 ILE cc_start: 0.9380 (mt) cc_final: 0.9080 (mp) REVERT: N 86 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9127 (mp0) REVERT: N 89 MET cc_start: 0.9435 (mmp) cc_final: 0.9021 (mmt) REVERT: S 66 MET cc_start: 0.9270 (mtp) cc_final: 0.8878 (mtp) outliers start: 41 outliers final: 34 residues processed: 147 average time/residue: 0.2900 time to fit residues: 67.7566 Evaluate side-chains 149 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 127 PHE Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN J 56 HIS ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4753 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= 0.176 Angle : 0.682 12.869 28949 Z= 0.378 Chirality : 0.035 0.305 3597 Planarity : 0.006 0.119 1998 Dihedral : 23.834 171.437 8323 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.58 % Allowed : 25.52 % Favored : 70.90 % 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: 0.29 (0.26), residues: 1092 helix: 1.00 (0.24), residues: 485 sheet: -0.36 (0.38), residues: 166 loop : -0.36 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 103 HIS 0.007 0.001 HIS B 168 PHE 0.015 0.001 PHE B 16 TYR 0.027 0.002 TYR C 168 ARG 0.008 0.000 ARG C 131 *********************** 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 160 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.386 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 27 MET cc_start: 0.5809 (mtp) cc_final: 0.5507 (mtt) REVERT: C 142 MET cc_start: 0.9243 (mmm) cc_final: 0.8417 (mmp) REVERT: C 170 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8848 (tm-30) REVERT: G 31 MET cc_start: 0.9100 (ttp) cc_final: 0.8321 (ttp) REVERT: G 103 TRP cc_start: 0.9644 (m-10) cc_final: 0.9375 (m100) REVERT: I 57 MET cc_start: 0.8940 (ttm) cc_final: 0.8714 (tpp) REVERT: I 61 LEU cc_start: 0.9322 (mt) cc_final: 0.8814 (mt) REVERT: I 118 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8529 (tp) REVERT: J 63 ASP cc_start: 0.9171 (t0) cc_final: 0.8561 (t0) REVERT: M 27 LYS cc_start: 0.9437 (tptt) cc_final: 0.8453 (tptt) REVERT: M 31 LYS cc_start: 0.9481 (pttm) cc_final: 0.8874 (pttm) REVERT: M 34 LEU cc_start: 0.9460 (tp) cc_final: 0.9094 (tp) REVERT: N 6 MET cc_start: 0.9033 (mmt) cc_final: 0.8800 (mmp) REVERT: N 62 ASN cc_start: 0.8768 (m110) cc_final: 0.8167 (p0) REVERT: N 82 ILE cc_start: 0.9351 (mt) cc_final: 0.9065 (mp) REVERT: N 86 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9031 (mp0) REVERT: N 89 MET cc_start: 0.9389 (mmp) cc_final: 0.9037 (mmt) REVERT: S 5 LEU cc_start: 0.9469 (mt) cc_final: 0.9234 (mt) REVERT: S 66 MET cc_start: 0.9259 (mtp) cc_final: 0.8857 (mtp) outliers start: 33 outliers final: 27 residues processed: 148 average time/residue: 0.2963 time to fit residues: 68.2825 Evaluate side-chains 146 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 0.0670 chunk 96 optimal weight: 0.6980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN I 110 GLN J 70 HIS ** N 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 19801 Z= 0.157 Angle : 0.688 12.840 28949 Z= 0.378 Chirality : 0.034 0.316 3597 Planarity : 0.006 0.118 1998 Dihedral : 23.544 171.581 8323 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.61 % Allowed : 27.14 % 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: 0.31 (0.25), residues: 1092 helix: 0.83 (0.24), residues: 490 sheet: 0.22 (0.41), residues: 161 loop : -0.40 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 103 HIS 0.004 0.001 HIS S 14 PHE 0.013 0.001 PHE I 127 TYR 0.026 0.002 TYR C 168 ARG 0.016 0.001 ARG I 109 ********************** 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 162 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.355 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: symmetry clash REVERT: C 142 MET cc_start: 0.9275 (mmm) cc_final: 0.8418 (mmp) REVERT: G 31 MET cc_start: 0.9087 (ttp) cc_final: 0.8292 (ttp) REVERT: G 103 TRP cc_start: 0.9642 (m-10) cc_final: 0.9361 (m100) REVERT: I 112 GLU cc_start: 0.8748 (tp30) cc_final: 0.8000 (mp0) REVERT: I 118 LEU cc_start: 0.8949 (mt) cc_final: 0.8386 (tp) REVERT: J 11 LYS cc_start: 0.9210 (mmmm) cc_final: 0.8727 (mmmt) REVERT: J 63 ASP cc_start: 0.9259 (t0) cc_final: 0.8627 (t0) REVERT: J 66 GLU cc_start: 0.7511 (tp30) cc_final: 0.7166 (tp30) REVERT: M 34 LEU cc_start: 0.9418 (tp) cc_final: 0.9054 (tp) REVERT: N 62 ASN cc_start: 0.8786 (m110) cc_final: 0.8311 (p0) REVERT: N 82 ILE cc_start: 0.9288 (mt) cc_final: 0.8994 (mp) REVERT: N 86 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9045 (mp0) REVERT: N 89 MET cc_start: 0.9365 (mmp) cc_final: 0.9005 (mmt) REVERT: S 5 LEU cc_start: 0.9479 (mt) cc_final: 0.9243 (mt) REVERT: S 66 MET cc_start: 0.9225 (mtp) cc_final: 0.8872 (mtp) outliers start: 24 outliers final: 19 residues processed: 152 average time/residue: 0.3244 time to fit residues: 74.1425 Evaluate side-chains 145 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 111 optimal weight: 0.0170 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 4.8028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.026827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.021291 restraints weight = 236194.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.021992 restraints weight = 102833.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.022385 restraints weight = 63307.354| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19801 Z= 0.344 Angle : 0.765 13.404 28949 Z= 0.415 Chirality : 0.038 0.287 3597 Planarity : 0.007 0.122 1998 Dihedral : 23.796 174.445 8323 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 31.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.04 % Allowed : 28.01 % Favored : 68.95 % 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: 0.17 (0.25), residues: 1092 helix: 0.72 (0.24), residues: 489 sheet: -0.23 (0.39), residues: 167 loop : -0.29 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 103 HIS 0.009 0.002 HIS J 70 PHE 0.016 0.002 PHE B 16 TYR 0.030 0.003 TYR C 168 ARG 0.011 0.001 ARG S 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.45 seconds wall clock time: 56 minutes 25.03 seconds (3385.03 seconds total)