Starting phenix.real_space_refine on Sun Mar 17 17:42:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/03_2024/7afk_11768_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/03_2024/7afk_11768.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/03_2024/7afk_11768_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/03_2024/7afk_11768_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/03_2024/7afk_11768_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/03_2024/7afk_11768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/03_2024/7afk_11768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/03_2024/7afk_11768_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afk_11768/03_2024/7afk_11768_neut_updated.pdb" } resolution = 4.9 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 12 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 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 39": "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" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18521 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: 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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 10.78, per 1000 atoms: 0.58 Number of scatterers: 18521 At special positions: 0 Unit cell: (118.265, 116.095, 159.495, 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 12 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: 13.38 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: 40 helices and 10 sheets defined 42.2% alpha, 11.9% beta 116 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 9.47 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.674A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 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 30 through 49 removed outlier: 5.977A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 95 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 114 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: 3.573A pdb=" N ALA G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 4.284A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.516A pdb=" N SER G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 147 removed outlier: 3.613A pdb=" N ALA G 145 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU G 146 " --> pdb=" O HIS G 142 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA G 147 " --> pdb=" O ARG G 143 " (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 72 through 91 Processing helix chain 'I' and resid 95 through 101 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 88 removed outlier: 4.240A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (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 62 removed outlier: 4.582A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 removed outlier: 4.405A pdb=" N LEU M 80 " --> pdb=" O SER M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 92 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 19 Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 40 through 50 Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.898A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 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: 6.246A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.069A 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: 6.319A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.928A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 54 through 58 Processing sheet with id= D, first strand: chain 'C' and resid 165 through 171 Processing sheet with id= E, first strand: chain 'G' and resid 73 through 75 Processing sheet with id= F, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= G, first strand: chain 'I' and resid 21 through 23 Processing sheet with id= H, first strand: chain 'J' and resid 70 through 76 Processing sheet with id= I, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= J, first strand: chain 'S' and resid 31 through 33 removed outlier: 4.056A pdb=" N LEU S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 13.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2828 1.33 - 1.45: 7327 1.45 - 1.57: 8682 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19801 Sorted by residual: bond pdb=" N3 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.496 1.343 0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" N3 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.496 1.353 0.143 2.00e-02 2.50e+03 5.14e+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 5.02e+01 bond pdb=" C2 2MG 11207 " pdb=" N2 2MG 11207 " ideal model delta sigma weight residual 1.475 1.340 0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C2 2MG 1 966 " pdb=" N2 2MG 1 966 " ideal model delta sigma weight residual 1.475 1.349 0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.93: 2994 106.93 - 114.27: 12253 114.27 - 121.61: 9175 121.61 - 128.95: 3982 128.95 - 136.29: 545 Bond angle restraints: 28949 Sorted by residual: angle pdb=" N SER I 93 " pdb=" CA SER I 93 " pdb=" C SER I 93 " ideal model delta sigma weight residual 113.88 105.93 7.95 1.23e+00 6.61e-01 4.18e+01 angle pdb=" C1' 2MG 1 966 " pdb=" N9 2MG 1 966 " pdb=" C8 2MG 1 966 " ideal model delta sigma weight residual 110.07 126.12 -16.05 3.00e+00 1.11e-01 2.86e+01 angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C8 2MG 11207 " ideal model delta sigma weight residual 110.07 126.05 -15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O3' C 11103 " pdb=" C3' C 11103 " pdb=" C2' C 11103 " ideal model delta sigma weight residual 113.70 121.69 -7.99 1.50e+00 4.44e-01 2.83e+01 angle pdb=" O3' A 11157 " pdb=" C3' A 11157 " pdb=" C2' A 11157 " ideal model delta sigma weight residual 109.50 101.96 7.54 1.50e+00 4.44e-01 2.52e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 11123 35.78 - 71.56: 1300 71.56 - 107.34: 169 107.34 - 143.12: 4 143.12 - 178.90: 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 200.00 33.90 166.10 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual -128.00 50.90 -178.90 1 1.70e+01 3.46e-03 6.64e+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 232.00 54.69 177.31 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3181 0.077 - 0.154: 328 0.154 - 0.231: 77 0.231 - 0.308: 9 0.308 - 0.385: 2 Chirality restraints: 3597 Sorted by residual: chirality pdb=" C3' C 11103 " pdb=" C4' C 11103 " pdb=" O3' C 11103 " pdb=" C2' C 11103 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE J 49 " pdb=" N PHE J 49 " pdb=" C PHE J 49 " pdb=" CB PHE J 49 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' A 1 969 " pdb=" C4' A 1 969 " pdb=" O3' A 1 969 " pdb=" C2' A 1 969 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3594 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11207 " -0.060 2.00e-02 2.50e+03 6.06e-01 8.25e+03 pdb=" C4' 2MG 11207 " -0.456 2.00e-02 2.50e+03 pdb=" O4' 2MG 11207 " -0.652 2.00e-02 2.50e+03 pdb=" C3' 2MG 11207 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG 11207 " 0.645 2.00e-02 2.50e+03 pdb=" C2' 2MG 11207 " 0.178 2.00e-02 2.50e+03 pdb=" O2' 2MG 11207 " -0.967 2.00e-02 2.50e+03 pdb=" C1' 2MG 11207 " -0.219 2.00e-02 2.50e+03 pdb=" N9 2MG 11207 " 0.943 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 966 " -0.244 2.00e-02 2.50e+03 4.30e-01 4.16e+03 pdb=" C4' 2MG 1 966 " 0.408 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 966 " 0.602 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 966 " -0.481 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 966 " -0.131 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 966 " -0.346 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 966 " 0.478 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 966 " 0.324 2.00e-02 2.50e+03 pdb=" N9 2MG 1 966 " -0.610 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 1 967 " 0.297 2.00e-02 2.50e+03 3.72e-01 3.11e+03 pdb=" C4' 5MC 1 967 " -0.378 2.00e-02 2.50e+03 pdb=" O4' 5MC 1 967 " -0.499 2.00e-02 2.50e+03 pdb=" C3' 5MC 1 967 " 0.444 2.00e-02 2.50e+03 pdb=" O3' 5MC 1 967 " -0.056 2.00e-02 2.50e+03 pdb=" C2' 5MC 1 967 " 0.396 2.00e-02 2.50e+03 pdb=" O2' 5MC 1 967 " -0.315 2.00e-02 2.50e+03 pdb=" C1' 5MC 1 967 " -0.332 2.00e-02 2.50e+03 pdb=" N1 5MC 1 967 " 0.443 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 55 2.20 - 2.87: 7458 2.87 - 3.55: 35181 3.55 - 4.22: 60195 4.22 - 4.90: 80339 Nonbonded interactions: 183228 Sorted by model distance: nonbonded pdb=" O3' U 1 952 " pdb="MG MG 11608 " model vdw 1.519 2.170 nonbonded pdb=" OP1 A 11197 " pdb="MG MG 11610 " model vdw 1.629 2.170 nonbonded pdb=" OP1 A 1 964 " pdb="MG MG 11611 " model vdw 1.659 2.170 nonbonded pdb=" OP2 C 1 972 " pdb="MG MG 11607 " model vdw 1.697 2.170 nonbonded pdb=" OP1 C 11109 " pdb="MG MG 11604 " model vdw 1.732 2.170 ... (remaining 183223 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: 4.970 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: 0.010 Extract box with map and model: 14.030 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 66.350 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 0.153 19801 Z= 0.473 Angle : 0.888 16.051 28949 Z= 0.550 Chirality : 0.053 0.385 3597 Planarity : 0.019 0.606 1998 Dihedral : 23.957 178.902 10548 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 42.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.23), residues: 1092 helix: -1.23 (0.22), residues: 480 sheet: -2.30 (0.36), residues: 161 loop : -2.40 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 34 HIS 0.007 0.002 HIS M 12 PHE 0.019 0.002 PHE C 37 TYR 0.011 0.002 TYR N 20 ARG 0.008 0.001 ARG I 130 *********************** 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 241 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.342 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: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.9250 (mt) cc_final: 0.9009 (tp) REVERT: B 139 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7395 (mtt180) REVERT: C 102 ASN cc_start: 0.9455 (t0) cc_final: 0.9198 (m110) REVERT: C 129 MET cc_start: 0.8870 (mmm) cc_final: 0.8228 (tpp) REVERT: C 181 ASP cc_start: 0.9054 (t0) cc_final: 0.8352 (p0) REVERT: C 203 PHE cc_start: 0.9076 (t80) cc_final: 0.8699 (t80) REVERT: G 91 VAL cc_start: 0.7421 (p) cc_final: 0.7214 (p) REVERT: I 32 GLN cc_start: 0.8757 (mm110) cc_final: 0.8550 (mm-40) REVERT: I 57 MET cc_start: 0.9379 (ptm) cc_final: 0.9090 (mmm) REVERT: I 110 GLN cc_start: 0.9585 (pt0) cc_final: 0.8756 (pm20) REVERT: I 112 GLU cc_start: 0.8217 (tt0) cc_final: 0.7747 (mp0) REVERT: J 19 ASP cc_start: 0.9199 (m-30) cc_final: 0.8948 (m-30) REVERT: J 53 ILE cc_start: 0.9181 (pt) cc_final: 0.8954 (tt) REVERT: J 63 ASP cc_start: 0.8579 (t0) cc_final: 0.7683 (t0) REVERT: J 65 TYR cc_start: 0.8477 (m-80) cc_final: 0.8087 (m-80) REVERT: M 27 LYS cc_start: 0.9409 (tppt) cc_final: 0.8784 (tppt) REVERT: M 31 LYS cc_start: 0.9248 (pttm) cc_final: 0.8924 (pttp) REVERT: M 50 GLU cc_start: 0.9519 (pm20) cc_final: 0.9140 (tm-30) REVERT: M 68 ASP cc_start: 0.9530 (m-30) cc_final: 0.9002 (t0) REVERT: M 95 LEU cc_start: 0.8930 (mt) cc_final: 0.8357 (mt) REVERT: N 86 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8742 (mt-10) REVERT: N 101 TRP cc_start: 0.8402 (p90) cc_final: 0.6002 (p90) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3625 time to fit residues: 125.4415 Evaluate side-chains 156 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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: 1.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 0.0050 chunk 39 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 overall best weight: 2.7600 ------------------------------------------------------------------------------- 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 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 227 GLN C 140 ASN G 122 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19801 Z= 0.219 Angle : 0.717 13.691 28949 Z= 0.393 Chirality : 0.037 0.242 3597 Planarity : 0.007 0.122 1998 Dihedral : 24.891 179.319 8323 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 34.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.11 % Allowed : 5.86 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.24), residues: 1092 helix: -0.27 (0.23), residues: 483 sheet: -1.85 (0.36), residues: 155 loop : -1.79 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 96 HIS 0.006 0.001 HIS B 168 PHE 0.016 0.002 PHE C 37 TYR 0.011 0.002 TYR I 6 ARG 0.008 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.334 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: symmetry clash REVERT: B 50 PHE cc_start: 0.6658 (t80) cc_final: 0.6211 (t80) REVERT: C 102 ASN cc_start: 0.9508 (t0) cc_final: 0.9277 (m110) REVERT: C 129 MET cc_start: 0.8815 (mmm) cc_final: 0.8191 (tpp) REVERT: C 142 MET cc_start: 0.9201 (tpp) cc_final: 0.8968 (tpt) REVERT: C 150 LYS cc_start: 0.8666 (tttm) cc_final: 0.8251 (tmtt) REVERT: C 168 TYR cc_start: 0.7935 (t80) cc_final: 0.7273 (t80) REVERT: C 181 ASP cc_start: 0.9056 (t0) cc_final: 0.8369 (p0) REVERT: C 203 PHE cc_start: 0.9071 (t80) cc_final: 0.8603 (t80) REVERT: G 143 ARG cc_start: 0.6123 (ttt-90) cc_final: 0.5906 (mtt180) REVERT: I 32 GLN cc_start: 0.8772 (mm110) cc_final: 0.8554 (mm-40) REVERT: I 110 GLN cc_start: 0.9548 (pt0) cc_final: 0.8858 (pm20) REVERT: I 112 GLU cc_start: 0.8207 (tt0) cc_final: 0.7665 (mp0) REVERT: I 115 LYS cc_start: 0.9031 (mttt) cc_final: 0.8674 (mttt) REVERT: I 118 LEU cc_start: 0.9490 (mm) cc_final: 0.9259 (mt) REVERT: J 63 ASP cc_start: 0.7938 (t0) cc_final: 0.7476 (t0) REVERT: M 12 HIS cc_start: 0.8691 (p90) cc_final: 0.8339 (p-80) REVERT: M 27 LYS cc_start: 0.9305 (tppt) cc_final: 0.8665 (tppt) REVERT: M 31 LYS cc_start: 0.9175 (pttm) cc_final: 0.8887 (pttp) REVERT: M 47 GLU cc_start: 0.8948 (pt0) cc_final: 0.8619 (mp0) REVERT: M 50 GLU cc_start: 0.9510 (pm20) cc_final: 0.9125 (tm-30) REVERT: M 81 MET cc_start: 0.9090 (mtt) cc_final: 0.8888 (mtt) REVERT: N 86 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9106 (mt-10) REVERT: S 17 LYS cc_start: 0.9488 (mptt) cc_final: 0.9234 (mttt) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.3538 time to fit residues: 103.5109 Evaluate side-chains 150 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 111 optimal weight: 9.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19801 Z= 0.284 Angle : 0.727 13.134 28949 Z= 0.396 Chirality : 0.038 0.266 3597 Planarity : 0.007 0.124 1998 Dihedral : 24.897 179.316 8323 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 38.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % 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: -1.55 (0.24), residues: 1092 helix: -0.13 (0.22), residues: 483 sheet: -1.76 (0.37), residues: 161 loop : -1.64 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 104 HIS 0.007 0.001 HIS B 18 PHE 0.013 0.002 PHE C 37 TYR 0.016 0.002 TYR J 65 ARG 0.006 0.001 ARG I 49 *********************** 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 178 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.270 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: B 7 ARG cc_start: 0.8690 (ptt90) cc_final: 0.8204 (ptt90) REVERT: B 50 PHE cc_start: 0.6891 (t80) cc_final: 0.6432 (t80) REVERT: B 94 HIS cc_start: 0.7089 (t70) cc_final: 0.6840 (t70) REVERT: B 109 GLN cc_start: 0.8171 (tt0) cc_final: 0.7550 (tt0) REVERT: C 129 MET cc_start: 0.8737 (mmm) cc_final: 0.8190 (tpp) REVERT: C 142 MET cc_start: 0.9142 (tpp) cc_final: 0.8772 (tpt) REVERT: C 150 LYS cc_start: 0.8645 (tttm) cc_final: 0.8258 (tmtt) REVERT: C 168 TYR cc_start: 0.7882 (t80) cc_final: 0.7215 (t80) REVERT: C 181 ASP cc_start: 0.9058 (t0) cc_final: 0.8384 (p0) REVERT: I 110 GLN cc_start: 0.9527 (pt0) cc_final: 0.8890 (pm20) REVERT: J 19 ASP cc_start: 0.9145 (m-30) cc_final: 0.8856 (m-30) REVERT: J 63 ASP cc_start: 0.8471 (t0) cc_final: 0.8121 (t70) REVERT: M 27 LYS cc_start: 0.9355 (tppt) cc_final: 0.8774 (tppt) REVERT: M 31 LYS cc_start: 0.9167 (pttm) cc_final: 0.8918 (pttp) REVERT: N 74 LEU cc_start: 0.9392 (tp) cc_final: 0.9114 (tt) REVERT: N 86 GLU cc_start: 0.9538 (mt-10) cc_final: 0.9270 (mt-10) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3184 time to fit residues: 84.6960 Evaluate side-chains 138 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19801 Z= 0.200 Angle : 0.660 12.502 28949 Z= 0.366 Chirality : 0.036 0.264 3597 Planarity : 0.006 0.120 1998 Dihedral : 24.651 179.612 8323 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 32.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: -1.15 (0.25), residues: 1092 helix: 0.22 (0.23), residues: 486 sheet: -1.50 (0.38), residues: 164 loop : -1.50 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 101 HIS 0.014 0.001 HIS S 14 PHE 0.015 0.001 PHE B 91 TYR 0.008 0.001 TYR I 6 ARG 0.006 0.001 ARG B 7 *********************** 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 182 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.232 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 50 PHE cc_start: 0.6668 (t80) cc_final: 0.6334 (t80) REVERT: B 109 GLN cc_start: 0.8204 (tt0) cc_final: 0.7534 (tt0) REVERT: C 129 MET cc_start: 0.8717 (mmm) cc_final: 0.8129 (tpp) REVERT: C 134 MET cc_start: 0.8632 (ptm) cc_final: 0.8397 (ptm) REVERT: C 150 LYS cc_start: 0.8682 (tttm) cc_final: 0.8287 (tmtt) REVERT: C 168 TYR cc_start: 0.7718 (t80) cc_final: 0.7031 (t80) REVERT: C 181 ASP cc_start: 0.8912 (t0) cc_final: 0.8221 (p0) REVERT: C 203 PHE cc_start: 0.8933 (t80) cc_final: 0.8508 (t80) REVERT: C 211 MET cc_start: 0.7679 (tpp) cc_final: 0.7392 (tpp) REVERT: I 110 GLN cc_start: 0.9551 (pt0) cc_final: 0.8793 (pm20) REVERT: I 111 VAL cc_start: 0.9385 (p) cc_final: 0.8820 (p) REVERT: I 112 GLU cc_start: 0.8190 (tt0) cc_final: 0.7682 (mp0) REVERT: I 115 LYS cc_start: 0.8980 (mttt) cc_final: 0.8659 (mttt) REVERT: J 19 ASP cc_start: 0.9165 (m-30) cc_final: 0.8882 (m-30) REVERT: J 63 ASP cc_start: 0.8466 (t0) cc_final: 0.7539 (t0) REVERT: J 65 TYR cc_start: 0.8299 (m-80) cc_final: 0.7969 (m-80) REVERT: M 12 HIS cc_start: 0.8709 (p90) cc_final: 0.8349 (p-80) REVERT: M 27 LYS cc_start: 0.9328 (tppt) cc_final: 0.8949 (tppt) REVERT: M 50 GLU cc_start: 0.9486 (pm20) cc_final: 0.9215 (tm-30) REVERT: N 62 ASN cc_start: 0.8461 (m110) cc_final: 0.8102 (p0) REVERT: S 17 LYS cc_start: 0.9555 (mptt) cc_final: 0.9316 (mttt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3391 time to fit residues: 91.6009 Evaluate side-chains 138 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 61 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19801 Z= 0.318 Angle : 0.755 12.651 28949 Z= 0.406 Chirality : 0.039 0.255 3597 Planarity : 0.007 0.125 1998 Dihedral : 24.829 177.433 8323 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 43.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % 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: -1.39 (0.24), residues: 1092 helix: 0.05 (0.23), residues: 482 sheet: -1.52 (0.38), residues: 165 loop : -1.68 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 104 HIS 0.006 0.002 HIS S 14 PHE 0.025 0.002 PHE B 126 TYR 0.015 0.002 TYR I 6 ARG 0.009 0.001 ARG B 137 *********************** 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 157 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.224 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 50 PHE cc_start: 0.6865 (t80) cc_final: 0.6606 (t80) REVERT: B 109 GLN cc_start: 0.8063 (tt0) cc_final: 0.7785 (tt0) REVERT: C 129 MET cc_start: 0.8627 (mmm) cc_final: 0.8140 (tpp) REVERT: C 142 MET cc_start: 0.9348 (tpp) cc_final: 0.9073 (tpt) REVERT: C 150 LYS cc_start: 0.8647 (tttm) cc_final: 0.8235 (tptp) REVERT: C 168 TYR cc_start: 0.7821 (t80) cc_final: 0.7189 (t80) REVERT: C 181 ASP cc_start: 0.8938 (t0) cc_final: 0.8319 (p0) REVERT: G 78 ARG cc_start: 0.7747 (mpp-170) cc_final: 0.7174 (mmp-170) REVERT: I 42 GLU cc_start: 0.9082 (tp30) cc_final: 0.8825 (tp30) REVERT: I 46 MET cc_start: 0.9171 (mmp) cc_final: 0.8964 (mmm) REVERT: I 112 GLU cc_start: 0.8168 (tt0) cc_final: 0.7694 (mp0) REVERT: J 19 ASP cc_start: 0.9106 (m-30) cc_final: 0.8818 (m-30) REVERT: J 63 ASP cc_start: 0.8238 (t0) cc_final: 0.7968 (t70) REVERT: M 27 LYS cc_start: 0.9354 (tppt) cc_final: 0.8968 (tppt) REVERT: N 86 GLU cc_start: 0.9545 (mt-10) cc_final: 0.9273 (mt-10) REVERT: S 17 LYS cc_start: 0.9538 (mptt) cc_final: 0.9312 (mttt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3212 time to fit residues: 75.6978 Evaluate side-chains 123 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- 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 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 19801 Z= 0.467 Angle : 0.906 12.649 28949 Z= 0.476 Chirality : 0.044 0.249 3597 Planarity : 0.008 0.130 1998 Dihedral : 25.182 177.239 8323 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 55.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: -2.09 (0.23), residues: 1092 helix: -0.68 (0.22), residues: 473 sheet: -1.68 (0.37), residues: 164 loop : -1.92 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP N 101 HIS 0.012 0.002 HIS B 168 PHE 0.024 0.003 PHE B 30 TYR 0.016 0.002 TYR I 6 ARG 0.030 0.001 ARG S 3 *********************** 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 150 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.209 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 27 MET cc_start: 0.7979 (tpt) cc_final: 0.7495 (tpp) REVERT: B 28 LYS cc_start: 0.6545 (tptt) cc_final: 0.6209 (tptp) REVERT: B 109 GLN cc_start: 0.7858 (tt0) cc_final: 0.7573 (tt0) REVERT: C 129 MET cc_start: 0.8583 (mmm) cc_final: 0.8225 (tpp) REVERT: C 142 MET cc_start: 0.9260 (tpp) cc_final: 0.8936 (tpt) REVERT: C 181 ASP cc_start: 0.8980 (t0) cc_final: 0.8344 (p0) REVERT: G 110 LYS cc_start: 0.8393 (tttp) cc_final: 0.8169 (tptp) REVERT: I 112 GLU cc_start: 0.8248 (tt0) cc_final: 0.7757 (mp0) REVERT: J 19 ASP cc_start: 0.9234 (m-30) cc_final: 0.8959 (m-30) REVERT: J 63 ASP cc_start: 0.8073 (t0) cc_final: 0.7823 (t70) REVERT: M 27 LYS cc_start: 0.9341 (tppt) cc_final: 0.8960 (tppt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3078 time to fit residues: 70.4888 Evaluate side-chains 121 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN B 168 HIS G 130 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19801 Z= 0.171 Angle : 0.681 12.274 28949 Z= 0.375 Chirality : 0.036 0.268 3597 Planarity : 0.007 0.121 1998 Dihedral : 24.640 178.012 8323 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 29.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.11 % Allowed : 1.41 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1092 helix: 0.15 (0.24), residues: 473 sheet: -1.16 (0.39), residues: 167 loop : -1.52 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 103 HIS 0.005 0.001 HIS S 52 PHE 0.017 0.002 PHE C 37 TYR 0.008 0.001 TYR I 64 ARG 0.010 0.001 ARG S 3 *********************** 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 175 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.327 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: B 27 MET cc_start: 0.7898 (tpt) cc_final: 0.7052 (tpp) REVERT: B 28 LYS cc_start: 0.6515 (tptt) cc_final: 0.6138 (tptp) REVERT: B 67 ILE cc_start: 0.8067 (mm) cc_final: 0.7439 (mm) REVERT: B 109 GLN cc_start: 0.8161 (tt0) cc_final: 0.7825 (tt0) REVERT: C 129 MET cc_start: 0.8611 (mmm) cc_final: 0.8035 (tpp) REVERT: C 134 MET cc_start: 0.8639 (ptm) cc_final: 0.8400 (ptm) REVERT: C 181 ASP cc_start: 0.8902 (t0) cc_final: 0.8302 (p0) REVERT: C 203 PHE cc_start: 0.8964 (t80) cc_final: 0.8686 (t80) REVERT: C 211 MET cc_start: 0.7701 (tpp) cc_final: 0.7493 (tpp) REVERT: G 31 MET cc_start: 0.5003 (ptt) cc_final: 0.4774 (ptt) REVERT: G 110 LYS cc_start: 0.8167 (tttp) cc_final: 0.7960 (tmtt) REVERT: I 111 VAL cc_start: 0.9385 (p) cc_final: 0.8982 (p) REVERT: I 112 GLU cc_start: 0.8234 (tt0) cc_final: 0.7918 (mp0) REVERT: I 115 LYS cc_start: 0.8836 (mttt) cc_final: 0.8560 (mttt) REVERT: J 63 ASP cc_start: 0.8169 (t0) cc_final: 0.7598 (t70) REVERT: J 65 TYR cc_start: 0.8431 (m-80) cc_final: 0.7944 (m-80) REVERT: J 97 ASP cc_start: 0.8788 (t70) cc_final: 0.8549 (t0) REVERT: M 12 HIS cc_start: 0.8810 (p90) cc_final: 0.8578 (p-80) REVERT: M 27 LYS cc_start: 0.9296 (tppt) cc_final: 0.8965 (tppt) REVERT: M 50 GLU cc_start: 0.9475 (pm20) cc_final: 0.9213 (tm-30) REVERT: N 51 LEU cc_start: 0.9211 (tp) cc_final: 0.8999 (tt) REVERT: S 17 LYS cc_start: 0.9497 (mptt) cc_final: 0.9259 (mttt) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.3324 time to fit residues: 86.3195 Evaluate side-chains 135 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 7.9990 chunk 88 optimal weight: 0.2980 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19801 Z= 0.251 Angle : 0.705 12.095 28949 Z= 0.385 Chirality : 0.037 0.285 3597 Planarity : 0.007 0.124 1998 Dihedral : 24.685 179.183 8323 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 37.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1092 helix: 0.22 (0.24), residues: 475 sheet: -1.17 (0.39), residues: 169 loop : -1.50 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.004 0.001 HIS S 52 PHE 0.015 0.002 PHE C 37 TYR 0.016 0.002 TYR N 20 ARG 0.013 0.001 ARG S 3 *********************** 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 154 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.327 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 27 MET cc_start: 0.8014 (tpt) cc_final: 0.7279 (tpp) REVERT: B 28 LYS cc_start: 0.6559 (tptt) cc_final: 0.6205 (tptp) REVERT: B 90 PHE cc_start: 0.9356 (m-80) cc_final: 0.8914 (m-10) REVERT: B 109 GLN cc_start: 0.7993 (tt0) cc_final: 0.7751 (tt0) REVERT: C 129 MET cc_start: 0.8666 (mmm) cc_final: 0.8190 (tpp) REVERT: C 181 ASP cc_start: 0.8880 (t0) cc_final: 0.8275 (p0) REVERT: C 211 MET cc_start: 0.7718 (tpp) cc_final: 0.7381 (tpp) REVERT: G 110 LYS cc_start: 0.8237 (tttp) cc_final: 0.8009 (tptp) REVERT: G 116 MET cc_start: 0.6745 (ptp) cc_final: 0.6521 (mtt) REVERT: I 111 VAL cc_start: 0.9403 (p) cc_final: 0.8983 (p) REVERT: I 112 GLU cc_start: 0.8212 (tt0) cc_final: 0.7911 (mp0) REVERT: J 19 ASP cc_start: 0.9234 (m-30) cc_final: 0.8964 (m-30) REVERT: J 63 ASP cc_start: 0.8128 (t0) cc_final: 0.7871 (t70) REVERT: J 97 ASP cc_start: 0.8882 (t70) cc_final: 0.8663 (t0) REVERT: M 12 HIS cc_start: 0.8782 (p90) cc_final: 0.8506 (p-80) REVERT: M 27 LYS cc_start: 0.9293 (tppt) cc_final: 0.8963 (tppt) REVERT: M 50 GLU cc_start: 0.9510 (pm20) cc_final: 0.9222 (tm-30) REVERT: M 75 MET cc_start: 0.9548 (ptp) cc_final: 0.9342 (mpp) REVERT: M 81 MET cc_start: 0.9277 (mtt) cc_final: 0.9069 (mtt) REVERT: S 17 LYS cc_start: 0.9520 (mptt) cc_final: 0.9312 (mttt) REVERT: S 66 MET cc_start: 0.9157 (mtp) cc_final: 0.8920 (mtp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3152 time to fit residues: 74.5398 Evaluate side-chains 123 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 GLN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19801 Z= 0.175 Angle : 0.658 12.197 28949 Z= 0.364 Chirality : 0.036 0.261 3597 Planarity : 0.006 0.121 1998 Dihedral : 24.503 178.761 8323 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 30.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1092 helix: 0.26 (0.24), residues: 481 sheet: -0.99 (0.39), residues: 164 loop : -1.31 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 104 HIS 0.006 0.001 HIS S 52 PHE 0.014 0.002 PHE C 37 TYR 0.008 0.001 TYR B 213 ARG 0.010 0.001 ARG S 3 *********************** 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 163 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.422 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: B 27 MET cc_start: 0.8054 (tpt) cc_final: 0.7317 (tpp) REVERT: B 28 LYS cc_start: 0.6414 (tptt) cc_final: 0.6086 (tptp) REVERT: B 90 PHE cc_start: 0.9047 (m-80) cc_final: 0.8831 (m-80) REVERT: C 129 MET cc_start: 0.8635 (mmm) cc_final: 0.8122 (tpp) REVERT: C 181 ASP cc_start: 0.8873 (t0) cc_final: 0.8232 (p0) REVERT: C 203 PHE cc_start: 0.8879 (t80) cc_final: 0.8364 (t80) REVERT: C 211 MET cc_start: 0.7729 (tpp) cc_final: 0.7457 (tpp) REVERT: G 116 MET cc_start: 0.6717 (ptp) cc_final: 0.6504 (mtt) REVERT: I 111 VAL cc_start: 0.9341 (p) cc_final: 0.8955 (p) REVERT: I 112 GLU cc_start: 0.8121 (tt0) cc_final: 0.7882 (mp0) REVERT: I 118 LEU cc_start: 0.9349 (mt) cc_final: 0.9131 (mt) REVERT: J 63 ASP cc_start: 0.8146 (t0) cc_final: 0.7858 (t70) REVERT: J 97 ASP cc_start: 0.8898 (t70) cc_final: 0.8677 (t0) REVERT: M 12 HIS cc_start: 0.8774 (p90) cc_final: 0.8563 (p-80) REVERT: M 27 LYS cc_start: 0.9287 (tppt) cc_final: 0.8991 (tppt) REVERT: M 50 GLU cc_start: 0.9504 (pm20) cc_final: 0.9157 (tp30) REVERT: M 81 MET cc_start: 0.9248 (mtt) cc_final: 0.9027 (mtt) REVERT: N 51 LEU cc_start: 0.9210 (tp) cc_final: 0.8991 (tt) REVERT: N 62 ASN cc_start: 0.8399 (m110) cc_final: 0.7803 (p0) REVERT: S 66 MET cc_start: 0.9064 (mtp) cc_final: 0.8860 (mtp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.3108 time to fit residues: 77.2030 Evaluate side-chains 130 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 140 optimal weight: 0.0470 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 0.0270 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 40.0000 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19801 Z= 0.145 Angle : 0.650 12.535 28949 Z= 0.361 Chirality : 0.035 0.256 3597 Planarity : 0.007 0.119 1998 Dihedral : 24.204 178.142 8323 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.71 (0.25), residues: 1092 helix: 0.38 (0.24), residues: 481 sheet: -0.70 (0.40), residues: 164 loop : -1.24 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP S 34 HIS 0.005 0.001 HIS S 52 PHE 0.015 0.001 PHE B 50 TYR 0.017 0.001 TYR N 20 ARG 0.011 0.001 ARG B 63 ********************** 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 168 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.293 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: B 27 MET cc_start: 0.7941 (tpt) cc_final: 0.7425 (tpp) REVERT: B 109 GLN cc_start: 0.8380 (tt0) cc_final: 0.8095 (tt0) REVERT: B 158 PRO cc_start: 0.7545 (Cg_exo) cc_final: 0.7327 (Cg_endo) REVERT: C 129 MET cc_start: 0.8574 (mmm) cc_final: 0.8116 (tpp) REVERT: C 134 MET cc_start: 0.8540 (ptm) cc_final: 0.8209 (ptm) REVERT: C 142 MET cc_start: 0.9116 (mmm) cc_final: 0.8634 (mmm) REVERT: C 181 ASP cc_start: 0.8924 (t0) cc_final: 0.8420 (p0) REVERT: C 203 PHE cc_start: 0.8858 (t80) cc_final: 0.8319 (t80) REVERT: C 211 MET cc_start: 0.7684 (tpp) cc_final: 0.7374 (tpp) REVERT: G 21 GLU cc_start: 0.9171 (mp0) cc_final: 0.8657 (tp30) REVERT: G 143 ARG cc_start: 0.5808 (ttt-90) cc_final: 0.5565 (mtt180) REVERT: I 110 GLN cc_start: 0.9489 (pt0) cc_final: 0.8952 (pm20) REVERT: J 63 ASP cc_start: 0.8269 (t0) cc_final: 0.8003 (t70) REVERT: M 27 LYS cc_start: 0.9224 (tppt) cc_final: 0.8605 (tppt) REVERT: M 50 GLU cc_start: 0.9477 (pm20) cc_final: 0.9045 (tp30) REVERT: M 81 MET cc_start: 0.9199 (mtt) cc_final: 0.8961 (tpp) REVERT: N 51 LEU cc_start: 0.9255 (tp) cc_final: 0.9050 (tt) REVERT: N 62 ASN cc_start: 0.8580 (m110) cc_final: 0.7956 (p0) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3031 time to fit residues: 77.9809 Evaluate side-chains 141 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 97 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** M 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.033066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.024237 restraints weight = 245484.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.025048 restraints weight = 130936.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.025509 restraints weight = 88915.858| |-----------------------------------------------------------------------------| r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19801 Z= 0.150 Angle : 0.628 12.396 28949 Z= 0.351 Chirality : 0.034 0.254 3597 Planarity : 0.006 0.120 1998 Dihedral : 24.206 179.556 8323 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1092 helix: 0.50 (0.24), residues: 483 sheet: -0.45 (0.41), residues: 161 loop : -1.13 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 34 HIS 0.003 0.001 HIS M 12 PHE 0.011 0.001 PHE S 74 TYR 0.012 0.001 TYR G 44 ARG 0.009 0.001 ARG S 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.04 seconds wall clock time: 56 minutes 57.59 seconds (3417.59 seconds total)