Starting phenix.real_space_refine on Sat Feb 17 10:56:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af5_11753/02_2024/7af5_11753_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af5_11753/02_2024/7af5_11753.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af5_11753/02_2024/7af5_11753_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af5_11753/02_2024/7af5_11753_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af5_11753/02_2024/7af5_11753_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af5_11753/02_2024/7af5_11753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af5_11753/02_2024/7af5_11753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af5_11753/02_2024/7af5_11753_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af5_11753/02_2024/7af5_11753_neut_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 52 5.21 5 S 28 5.16 5 C 9824 2.51 5 N 3444 2.21 5 O 4726 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 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 41": "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: 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': 35, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 170} Link IDs: {'rna2p': 71, 'rna3p': 384} 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: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1151 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Unusual residues: {' MG': 52} Classifications: {'undetermined': 52} Link IDs: {None: 51} 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: 9.95, per 1000 atoms: 0.54 Number of scatterers: 18531 At special positions: 0 Unit cell: (116.55, 151.2, 121.8, 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 52 11.99 O 4726 8.00 N 3444 7.00 C 9824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.02 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 9 sheets defined 42.4% alpha, 11.8% beta 138 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 9.93 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 removed outlier: 3.504A pdb=" N GLN B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) 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 26 through 46 removed outlier: 4.706A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 95 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 22 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 3.505A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.959A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (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 143 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 54 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 90 Processing helix chain 'I' and resid 92 through 100 removed outlier: 3.888A pdb=" N SER I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 88 removed outlier: 3.703A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 21 removed outlier: 4.134A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 36 Processing helix chain 'M' and resid 50 through 62 removed outlier: 3.676A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (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 removed outlier: 3.670A 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 removed outlier: 3.866A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 24 Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 71 through 74 Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.696A 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: 7.610A 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 103 through 105 removed outlier: 7.770A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 166 through 170 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 5 through 11 Processing sheet with id= G, first strand: chain 'J' and resid 97 through 101 removed outlier: 4.641A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) 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 33 369 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 556 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 9.57 Time building geometry restraints manager: 10.33 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: 3389 1.33 - 1.45: 7054 1.45 - 1.57: 8363 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19770 Sorted by residual: bond pdb=" N3 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.496 1.345 0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N3 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.496 1.349 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C2 5MC 1 967 " pdb=" N3 5MC 1 967 " ideal model delta sigma weight residual 1.493 1.347 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" C2 2MG 1 966 " pdb=" N2 2MG 1 966 " ideal model delta sigma weight residual 1.475 1.341 0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C2 2MG 11207 " pdb=" N2 2MG 11207 " ideal model delta sigma weight residual 1.475 1.342 0.133 2.00e-02 2.50e+03 4.43e+01 ... (remaining 19765 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.42: 2764 106.42 - 113.81: 12156 113.81 - 121.20: 9032 121.20 - 128.59: 4356 128.59 - 135.97: 600 Bond angle restraints: 28908 Sorted by residual: angle pdb=" C THR B 125 " pdb=" CA THR B 125 " pdb=" CB THR B 125 " ideal model delta sigma weight residual 109.83 117.28 -7.45 9.90e-01 1.02e+00 5.67e+01 angle pdb=" C4' U 11211 " pdb=" C3' U 11211 " pdb=" O3' U 11211 " ideal model delta sigma weight residual 109.40 117.38 -7.98 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C8 2MG 11207 " ideal model delta sigma weight residual 110.07 125.31 -15.24 3.00e+00 1.11e-01 2.58e+01 angle pdb=" C GLU M 66 " pdb=" CA GLU M 66 " pdb=" CB GLU M 66 " ideal model delta sigma weight residual 116.63 110.87 5.76 1.16e+00 7.43e-01 2.47e+01 angle pdb=" O3' U 11211 " pdb=" C3' U 11211 " pdb=" C2' U 11211 " ideal model delta sigma weight residual 109.50 116.71 -7.21 1.50e+00 4.44e-01 2.31e+01 ... (remaining 28903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 11310 34.26 - 68.51: 1124 68.51 - 102.77: 140 102.77 - 137.02: 4 137.02 - 171.28: 4 Dihedral angle restraints: 12582 sinusoidal: 9424 harmonic: 3158 Sorted by residual: dihedral pdb=" C5' U 11211 " pdb=" C4' U 11211 " pdb=" C3' U 11211 " pdb=" O3' U 11211 " ideal model delta sinusoidal sigma weight residual 147.00 77.29 69.71 1 8.00e+00 1.56e-02 9.80e+01 dihedral pdb=" C4' U 11211 " pdb=" C3' U 11211 " pdb=" C2' U 11211 " pdb=" C1' U 11211 " ideal model delta sinusoidal sigma weight residual -35.00 30.40 -65.40 1 8.00e+00 1.56e-02 8.76e+01 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 29.46 170.54 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 12579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3454 0.103 - 0.206: 126 0.206 - 0.310: 11 0.310 - 0.413: 0 0.413 - 0.516: 2 Chirality restraints: 3593 Sorted by residual: chirality pdb=" C3' U 11211 " pdb=" C4' U 11211 " pdb=" O3' U 11211 " pdb=" C2' U 11211 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.52 2.00e-01 2.50e+01 6.66e+00 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 2.02 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CB VAL J 57 " pdb=" CA VAL J 57 " pdb=" CG1 VAL J 57 " pdb=" CG2 VAL J 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3590 not shown) Planarity restraints: 1993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11207 " -0.062 2.00e-02 2.50e+03 5.94e-01 7.94e+03 pdb=" C4' 2MG 11207 " -0.440 2.00e-02 2.50e+03 pdb=" O4' 2MG 11207 " -0.620 2.00e-02 2.50e+03 pdb=" C3' 2MG 11207 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG 11207 " 0.627 2.00e-02 2.50e+03 pdb=" C2' 2MG 11207 " 0.181 2.00e-02 2.50e+03 pdb=" O2' 2MG 11207 " -0.965 2.00e-02 2.50e+03 pdb=" C1' 2MG 11207 " -0.228 2.00e-02 2.50e+03 pdb=" N9 2MG 11207 " 0.911 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 966 " -0.005 2.00e-02 2.50e+03 5.25e-01 6.21e+03 pdb=" C4' 2MG 1 966 " 0.428 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 966 " 0.587 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 966 " -0.573 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 966 " -0.470 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 966 " -0.250 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 966 " 0.820 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 966 " 0.245 2.00e-02 2.50e+03 pdb=" N9 2MG 1 966 " -0.781 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 1 967 " 0.015 2.00e-02 2.50e+03 5.13e-01 5.92e+03 pdb=" C4' 5MC 1 967 " 0.417 2.00e-02 2.50e+03 pdb=" O4' 5MC 1 967 " 0.509 2.00e-02 2.50e+03 pdb=" C3' 5MC 1 967 " -0.576 2.00e-02 2.50e+03 pdb=" O3' 5MC 1 967 " -0.476 2.00e-02 2.50e+03 pdb=" C2' 5MC 1 967 " -0.240 2.00e-02 2.50e+03 pdb=" O2' 5MC 1 967 " 0.841 2.00e-02 2.50e+03 pdb=" C1' 5MC 1 967 " 0.250 2.00e-02 2.50e+03 pdb=" N1 5MC 1 967 " -0.740 2.00e-02 2.50e+03 ... (remaining 1990 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 147 2.48 - 3.09: 12574 3.09 - 3.69: 34178 3.69 - 4.30: 51756 4.30 - 4.90: 71576 Nonbonded interactions: 170231 Sorted by model distance: nonbonded pdb=" OP2 C 11054 " pdb="MG MG 11622 " model vdw 1.876 2.170 nonbonded pdb=" O6 G 11178 " pdb="MG MG 11608 " model vdw 1.940 2.170 nonbonded pdb=" OP1 A 11197 " pdb="MG MG 11616 " model vdw 1.948 2.170 nonbonded pdb=" OP2 U 11095 " pdb="MG MG 11628 " model vdw 1.953 2.170 nonbonded pdb=" OP1 C 11303 " pdb="MG MG 11639 " model vdw 1.981 2.170 ... (remaining 170226 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: 0.010 Normalize map: mean=0, sd=1: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.350 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 63.840 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.008 0.151 19770 Z= 0.493 Angle : 0.739 15.241 28908 Z= 0.462 Chirality : 0.046 0.516 3593 Planarity : 0.022 0.594 1993 Dihedral : 21.843 171.281 10538 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.20 % 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: -1.98 (0.24), residues: 1088 helix: -0.55 (0.23), residues: 481 sheet: -1.83 (0.37), residues: 163 loop : -1.85 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.007 0.001 HIS N 71 PHE 0.009 0.002 PHE B 90 TYR 0.011 0.002 TYR C 42 ARG 0.007 0.001 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.333 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 9 MET cc_start: 0.1663 (mtt) cc_final: 0.0749 (pmm) REVERT: B 113 ARG cc_start: 0.7326 (tpt170) cc_final: 0.6984 (ttp-110) REVERT: B 138 THR cc_start: 0.8670 (m) cc_final: 0.8458 (p) REVERT: B 140 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7432 (mm-30) REVERT: B 152 LYS cc_start: 0.7512 (pttt) cc_final: 0.7139 (ptmt) REVERT: G 64 VAL cc_start: 0.8105 (t) cc_final: 0.7687 (t) REVERT: I 47 VAL cc_start: 0.9427 (p) cc_final: 0.9126 (p) REVERT: I 56 ASP cc_start: 0.8302 (t70) cc_final: 0.8096 (t0) REVERT: J 87 LEU cc_start: 0.9069 (pp) cc_final: 0.8792 (mt) REVERT: J 90 LEU cc_start: 0.7902 (tp) cc_final: 0.7670 (tt) REVERT: M 13 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7325 (ptpt) REVERT: M 69 LEU cc_start: 0.8912 (tp) cc_final: 0.8153 (tp) REVERT: M 82 ASP cc_start: 0.8466 (m-30) cc_final: 0.8220 (m-30) REVERT: S 16 LEU cc_start: 0.9325 (mt) cc_final: 0.9118 (mt) outliers start: 0 outliers final: 1 residues processed: 281 average time/residue: 1.5035 time to fit residues: 466.2214 Evaluate side-chains 198 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 119 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 138 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN C 8 ASN C 25 ASN C 123 GLN C 140 ASN G 148 ASN I 32 GLN I 126 GLN J 70 HIS ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19770 Z= 0.191 Angle : 0.673 13.343 28908 Z= 0.379 Chirality : 0.037 0.239 3593 Planarity : 0.006 0.122 1993 Dihedral : 22.609 178.146 8321 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.81 % Allowed : 20.02 % Favored : 76.17 % 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: -0.92 (0.24), residues: 1088 helix: 0.41 (0.23), residues: 482 sheet: -1.47 (0.39), residues: 162 loop : -1.32 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.002 0.001 HIS N 71 PHE 0.017 0.001 PHE B 90 TYR 0.012 0.001 TYR C 42 ARG 0.005 0.000 ARG M 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7239 (mm) REVERT: B 118 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: B 130 THR cc_start: 0.7102 (m) cc_final: 0.6844 (p) REVERT: M 13 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7329 (ptpt) REVERT: M 81 MET cc_start: 0.8898 (ttm) cc_final: 0.8569 (ttt) REVERT: M 82 ASP cc_start: 0.8421 (m-30) cc_final: 0.8169 (m-30) REVERT: S 65 GLU cc_start: 0.8349 (pm20) cc_final: 0.8124 (pm20) outliers start: 35 outliers final: 11 residues processed: 238 average time/residue: 1.3328 time to fit residues: 354.8470 Evaluate side-chains 190 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** C 140 ASN I 110 GLN I 126 GLN ** N 43 ASN ** 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: 0.8601 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19770 Z= 0.279 Angle : 0.673 12.955 28908 Z= 0.375 Chirality : 0.037 0.222 3593 Planarity : 0.007 0.129 1993 Dihedral : 22.445 177.407 8319 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.57 % Allowed : 23.07 % Favored : 72.36 % 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: -0.41 (0.25), residues: 1088 helix: 0.80 (0.23), residues: 488 sheet: -1.23 (0.39), residues: 170 loop : -1.02 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.005 0.001 HIS N 71 PHE 0.014 0.001 PHE B 90 TYR 0.010 0.001 TYR C 42 ARG 0.010 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 185 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.1481 (mtt) cc_final: 0.0335 (pmm) REVERT: B 118 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: M 13 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7503 (ptpt) REVERT: M 69 LEU cc_start: 0.9133 (tp) cc_final: 0.8776 (tp) REVERT: M 81 MET cc_start: 0.8892 (ttm) cc_final: 0.8642 (ttt) REVERT: S 6 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8753 (ptmm) REVERT: S 65 GLU cc_start: 0.8342 (pm20) cc_final: 0.8075 (pm20) outliers start: 42 outliers final: 21 residues processed: 208 average time/residue: 1.3146 time to fit residues: 306.7876 Evaluate side-chains 201 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 138 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** C 140 ASN I 32 GLN I 126 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19770 Z= 0.190 Angle : 0.640 12.689 28908 Z= 0.360 Chirality : 0.035 0.210 3593 Planarity : 0.006 0.125 1993 Dihedral : 22.365 176.013 8319 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.46 % Allowed : 23.83 % Favored : 71.71 % 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: -0.09 (0.25), residues: 1088 helix: 1.16 (0.24), residues: 481 sheet: -1.02 (0.39), residues: 167 loop : -0.98 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.003 0.001 HIS N 71 PHE 0.013 0.001 PHE B 90 TYR 0.010 0.001 TYR C 42 ARG 0.013 0.000 ARG G 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: G 119 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7469 (mtt-85) REVERT: G 144 MET cc_start: 0.6318 (mmm) cc_final: 0.5677 (tmt) REVERT: M 13 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7524 (ptpt) REVERT: M 81 MET cc_start: 0.8819 (ttm) cc_final: 0.8494 (ttt) REVERT: S 6 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8684 (ptmm) outliers start: 41 outliers final: 19 residues processed: 207 average time/residue: 1.3525 time to fit residues: 313.0629 Evaluate side-chains 195 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN I 126 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 19770 Z= 0.419 Angle : 0.722 13.077 28908 Z= 0.396 Chirality : 0.040 0.245 3593 Planarity : 0.007 0.133 1993 Dihedral : 22.332 176.946 8319 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 5.66 % Allowed : 23.72 % Favored : 70.62 % 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: -0.12 (0.25), residues: 1088 helix: 1.10 (0.24), residues: 484 sheet: -0.97 (0.39), residues: 170 loop : -0.97 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 201 HIS 0.008 0.001 HIS N 71 PHE 0.014 0.001 PHE B 90 TYR 0.009 0.002 TYR C 42 ARG 0.007 0.001 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 177 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.0876 (mtt) cc_final: 0.0472 (mpp) REVERT: B 118 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: B 139 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7243 (mtt180) REVERT: G 119 ARG cc_start: 0.7843 (mtt90) cc_final: 0.7518 (mtt-85) REVERT: G 144 MET cc_start: 0.6341 (mmm) cc_final: 0.5677 (tmt) REVERT: I 59 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: I 105 THR cc_start: 0.8403 (t) cc_final: 0.8172 (m) REVERT: I 124 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8189 (mtp85) REVERT: M 13 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7379 (ptpt) REVERT: M 81 MET cc_start: 0.8890 (ttm) cc_final: 0.8638 (ttt) REVERT: M 82 ASP cc_start: 0.8370 (m-30) cc_final: 0.8168 (m-30) REVERT: N 66 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8448 (mp10) REVERT: S 6 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8724 (ptmm) outliers start: 52 outliers final: 24 residues processed: 210 average time/residue: 1.3576 time to fit residues: 319.6994 Evaluate side-chains 201 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 66 GLN Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** C 140 ASN I 32 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19770 Z= 0.209 Angle : 0.670 12.860 28908 Z= 0.373 Chirality : 0.036 0.217 3593 Planarity : 0.006 0.126 1993 Dihedral : 22.377 176.268 8319 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 4.46 % Allowed : 25.68 % Favored : 69.86 % 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: 0.04 (0.26), residues: 1088 helix: 1.20 (0.24), residues: 490 sheet: -0.87 (0.39), residues: 174 loop : -0.90 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.007 0.001 HIS B 39 PHE 0.016 0.001 PHE B 90 TYR 0.010 0.001 TYR M 86 ARG 0.006 0.000 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.1558 (ppp) cc_final: 0.1237 (mmp) REVERT: B 118 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: B 203 ASN cc_start: 0.2627 (t0) cc_final: 0.2393 (t0) REVERT: G 119 ARG cc_start: 0.7724 (mtt90) cc_final: 0.7503 (mtt-85) REVERT: G 144 MET cc_start: 0.6313 (mmm) cc_final: 0.5652 (tmt) REVERT: I 105 THR cc_start: 0.8364 (t) cc_final: 0.8131 (m) REVERT: I 124 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8122 (mtp85) REVERT: M 13 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7497 (ptpt) REVERT: N 66 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8421 (mp10) REVERT: S 6 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8676 (ptmm) outliers start: 41 outliers final: 28 residues processed: 214 average time/residue: 1.2594 time to fit residues: 303.4069 Evaluate side-chains 212 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 66 GLN Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 123 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.0980 ------------------------------------------------------------------------------- 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 51 ASN B 146 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19770 Z= 0.189 Angle : 0.658 12.575 28908 Z= 0.366 Chirality : 0.035 0.213 3593 Planarity : 0.006 0.125 1993 Dihedral : 22.321 175.762 8319 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 3.92 % Allowed : 27.64 % Favored : 68.44 % 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: 0.14 (0.26), residues: 1088 helix: 1.28 (0.24), residues: 481 sheet: -0.64 (0.40), residues: 172 loop : -0.89 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.003 0.001 HIS B 18 PHE 0.010 0.001 PHE S 74 TYR 0.010 0.001 TYR C 42 ARG 0.006 0.000 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.2848 (mmm) cc_final: 0.2574 (mtm) REVERT: B 127 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: B 203 ASN cc_start: 0.2640 (t0) cc_final: 0.2433 (t0) REVERT: G 119 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7373 (mtt-85) REVERT: G 144 MET cc_start: 0.6300 (mmm) cc_final: 0.5601 (tmt) REVERT: I 60 LYS cc_start: 0.8633 (mppt) cc_final: 0.8396 (mmtm) REVERT: I 105 THR cc_start: 0.8410 (t) cc_final: 0.8192 (m) REVERT: I 124 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8149 (mtp85) REVERT: M 13 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7372 (ptpt) REVERT: S 6 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8658 (ptmm) REVERT: S 17 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8826 (mmmm) outliers start: 36 outliers final: 23 residues processed: 205 average time/residue: 1.3200 time to fit residues: 303.1513 Evaluate side-chains 202 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 51 ASN B 146 ASN C 140 ASN I 32 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19770 Z= 0.211 Angle : 0.656 12.546 28908 Z= 0.366 Chirality : 0.035 0.224 3593 Planarity : 0.006 0.126 1993 Dihedral : 22.273 175.665 8319 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 3.48 % Allowed : 27.86 % Favored : 68.66 % 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: 0.22 (0.26), residues: 1088 helix: 1.34 (0.24), residues: 479 sheet: -0.57 (0.40), residues: 172 loop : -0.84 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.003 0.001 HIS N 71 PHE 0.017 0.001 PHE S 74 TYR 0.009 0.001 TYR M 86 ARG 0.004 0.000 ARG I 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.0536 (mmp) cc_final: -0.0150 (ppp) REVERT: B 127 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: G 144 MET cc_start: 0.6272 (mmm) cc_final: 0.5518 (tmt) REVERT: I 105 THR cc_start: 0.8434 (t) cc_final: 0.8221 (m) REVERT: I 124 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8152 (mtp85) REVERT: J 99 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7760 (mm110) REVERT: M 13 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7352 (ptpt) REVERT: S 6 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8665 (ptmm) outliers start: 32 outliers final: 23 residues processed: 200 average time/residue: 1.3546 time to fit residues: 303.3057 Evaluate side-chains 202 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 51 ASN B 146 ASN B 177 ASN C 140 ASN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19770 Z= 0.203 Angle : 0.660 12.552 28908 Z= 0.367 Chirality : 0.035 0.216 3593 Planarity : 0.006 0.126 1993 Dihedral : 22.252 175.501 8319 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 3.48 % Allowed : 28.51 % Favored : 68.01 % 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: 0.24 (0.26), residues: 1088 helix: 1.35 (0.24), residues: 479 sheet: -0.55 (0.40), residues: 172 loop : -0.82 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.003 0.001 HIS N 71 PHE 0.018 0.001 PHE S 74 TYR 0.011 0.001 TYR M 86 ARG 0.007 0.000 ARG J 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: G 119 ARG cc_start: 0.7793 (mtt90) cc_final: 0.7556 (mtt90) REVERT: G 144 MET cc_start: 0.6339 (mmm) cc_final: 0.5442 (tmt) REVERT: I 46 MET cc_start: 0.7529 (tmm) cc_final: 0.7288 (ppp) REVERT: I 105 THR cc_start: 0.8431 (t) cc_final: 0.8224 (m) REVERT: J 99 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7704 (mm110) REVERT: M 13 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7382 (ptpt) REVERT: S 6 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8675 (ptmm) outliers start: 32 outliers final: 22 residues processed: 198 average time/residue: 1.2746 time to fit residues: 283.4058 Evaluate side-chains 198 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 139 optimal weight: 0.0970 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN B 146 ASN B 177 ASN B 190 ASN C 140 ASN I 32 GLN J 4 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19770 Z= 0.219 Angle : 0.666 12.507 28908 Z= 0.370 Chirality : 0.035 0.219 3593 Planarity : 0.006 0.126 1993 Dihedral : 22.222 175.542 8319 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 3.26 % Allowed : 28.84 % Favored : 67.90 % 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: 0.23 (0.26), residues: 1088 helix: 1.29 (0.24), residues: 484 sheet: -0.56 (0.40), residues: 171 loop : -0.78 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 96 HIS 0.003 0.001 HIS N 71 PHE 0.019 0.001 PHE S 74 TYR 0.012 0.001 TYR M 86 ARG 0.009 0.000 ARG I 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7219 (m-30) REVERT: G 119 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7772 (mtt90) REVERT: G 144 MET cc_start: 0.6334 (mmm) cc_final: 0.5442 (tmt) REVERT: I 46 MET cc_start: 0.7510 (tmm) cc_final: 0.7276 (ppp) REVERT: M 13 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7370 (ptpt) REVERT: S 6 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8681 (ptmm) REVERT: S 17 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8841 (mmmm) outliers start: 30 outliers final: 25 residues processed: 195 average time/residue: 1.3348 time to fit residues: 292.9037 Evaluate side-chains 202 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 51 ASN B 146 ASN B 177 ASN C 140 ASN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.076584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.052447 restraints weight = 52682.888| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.49 r_work: 0.2640 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19770 Z= 0.341 Angle : 0.712 12.803 28908 Z= 0.391 Chirality : 0.039 0.238 3593 Planarity : 0.007 0.130 1993 Dihedral : 22.233 176.187 8319 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 3.59 % Allowed : 28.84 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1088 helix: 1.26 (0.24), residues: 488 sheet: -0.61 (0.41), residues: 163 loop : -0.76 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 96 HIS 0.006 0.001 HIS N 71 PHE 0.015 0.001 PHE S 74 TYR 0.018 0.002 TYR M 86 ARG 0.009 0.001 ARG I 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6000.93 seconds wall clock time: 108 minutes 15.80 seconds (6495.80 seconds total)