Starting phenix.real_space_refine on Fri Mar 15 03:19:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/03_2024/7b6d_12052_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/03_2024/7b6d_12052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/03_2024/7b6d_12052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/03_2024/7b6d_12052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/03_2024/7b6d_12052_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/03_2024/7b6d_12052_neut.pdb" } resolution = 4.27 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6713 2.51 5 N 1749 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10470 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "B" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "C" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1204 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1741 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207} Chain: "E" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1177 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "F" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1333 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "G" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1363 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1089 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Time building chain proxies: 5.94, per 1000 atoms: 0.57 Number of scatterers: 10470 At special positions: 0 Unit cell: (167.232, 152.256, 79.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1958 8.00 N 1749 7.00 C 6713 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: 4.47 Conformation dependent library (CDL) restraints added in 1.8 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 43.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.567A pdb=" N GLY A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 63 removed outlier: 4.204A pdb=" N LEU A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 84 Processing helix chain 'A' and resid 126 through 140 removed outlier: 4.521A pdb=" N ALA A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 27 through 42 removed outlier: 4.352A pdb=" N GLU B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 107 through 114 removed outlier: 3.814A pdb=" N LYS B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 81 through 88 removed outlier: 3.635A pdb=" N ALA D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 165 through 182 removed outlier: 3.810A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 210 Processing helix chain 'E' and resid 26 through 55 removed outlier: 3.634A pdb=" N ASP E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 122 through 136 Processing helix chain 'F' and resid 32 through 50 Processing helix chain 'F' and resid 52 through 81 removed outlier: 3.573A pdb=" N LEU F 56 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 removed outlier: 3.898A pdb=" N TRP F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.285A pdb=" N PHE F 133 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 160 removed outlier: 3.691A pdb=" N PHE F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'G' and resid 14 through 33 Processing helix chain 'G' and resid 35 through 59 removed outlier: 3.703A pdb=" N VAL G 39 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU G 56 " --> pdb=" O MET G 52 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 85 removed outlier: 3.579A pdb=" N PHE G 81 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG G 82 " --> pdb=" O GLN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 3.539A pdb=" N THR G 121 " --> pdb=" O PRO G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 140 removed outlier: 3.940A pdb=" N SER G 130 " --> pdb=" O SER G 126 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG G 134 " --> pdb=" O SER G 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 48 Processing helix chain 'H' and resid 92 through 111 Processing helix chain 'H' and resid 123 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.223A pdb=" N PHE A 101 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 163 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A 160 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 143 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.172A pdb=" N TYR B 86 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.129A pdb=" N LEU C 62 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS D 154 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 5 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32 Processing sheet with id=AA5, first strand: chain 'D' and resid 41 through 43 removed outlier: 3.500A pdb=" N ASP D 41 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.616A pdb=" N VAL D 66 " --> pdb=" O MET D 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 15 through 21 removed outlier: 4.233A pdb=" N TYR E 17 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR E 4 " --> pdb=" O PHE E 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 110 through 113 Processing sheet with id=AA9, first strand: chain 'G' and resid 90 through 92 removed outlier: 7.053A pdb=" N GLU G 160 " --> pdb=" O VAL G 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 15 through 20 removed outlier: 3.740A pdb=" N LEU H 15 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA H 2 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP H 84 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS H 4 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL H 82 " --> pdb=" O CYS H 4 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL H 81 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS H 67 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS H 66 " --> pdb=" O THR H 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR H 61 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLY H 70 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU H 59 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL H 72 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU H 57 " --> pdb=" O VAL H 72 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3391 1.34 - 1.46: 2413 1.46 - 1.58: 4798 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 10683 Sorted by residual: bond pdb=" N GLY H 48 " pdb=" CA GLY H 48 " ideal model delta sigma weight residual 1.449 1.504 -0.055 1.45e-02 4.76e+03 1.44e+01 bond pdb=" C GLY H 48 " pdb=" O GLY H 48 " ideal model delta sigma weight residual 1.235 1.281 -0.046 1.35e-02 5.49e+03 1.16e+01 bond pdb=" C TYR H 30 " pdb=" O TYR H 30 " ideal model delta sigma weight residual 1.235 1.275 -0.039 1.26e-02 6.30e+03 9.74e+00 bond pdb=" N VAL H 39 " pdb=" CA VAL H 39 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.94e+00 bond pdb=" C CYS H 43 " pdb=" O CYS H 43 " ideal model delta sigma weight residual 1.237 1.269 -0.033 1.17e-02 7.31e+03 7.78e+00 ... (remaining 10678 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.74: 153 104.74 - 112.08: 5128 112.08 - 119.42: 3658 119.42 - 126.76: 5404 126.76 - 134.10: 107 Bond angle restraints: 14450 Sorted by residual: angle pdb=" CA LYS H 47 " pdb=" C LYS H 47 " pdb=" O LYS H 47 " ideal model delta sigma weight residual 120.42 115.36 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" C GLU F 109 " pdb=" N LYS F 110 " pdb=" CA LYS F 110 " ideal model delta sigma weight residual 122.37 114.56 7.81 1.72e+00 3.38e-01 2.06e+01 angle pdb=" N LYS H 47 " pdb=" CA LYS H 47 " pdb=" C LYS H 47 " ideal model delta sigma weight residual 111.36 116.29 -4.93 1.09e+00 8.42e-01 2.05e+01 angle pdb=" CA PRO C 138 " pdb=" C PRO C 138 " pdb=" N ILE C 139 " ideal model delta sigma weight residual 115.95 121.01 -5.06 1.12e+00 7.97e-01 2.04e+01 angle pdb=" C PHE G 165 " pdb=" N VAL G 166 " pdb=" CA VAL G 166 " ideal model delta sigma weight residual 123.08 118.78 4.30 1.01e+00 9.80e-01 1.81e+01 ... (remaining 14445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5792 17.84 - 35.68: 553 35.68 - 53.52: 79 53.52 - 71.36: 16 71.36 - 89.20: 11 Dihedral angle restraints: 6451 sinusoidal: 2653 harmonic: 3798 Sorted by residual: dihedral pdb=" CA ASN D 216 " pdb=" C ASN D 216 " pdb=" N ILE D 217 " pdb=" CA ILE D 217 " ideal model delta harmonic sigma weight residual -180.00 -122.18 -57.82 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA PRO D 35 " pdb=" C PRO D 35 " pdb=" N LEU D 36 " pdb=" CA LEU D 36 " ideal model delta harmonic sigma weight residual 180.00 -142.52 -37.48 0 5.00e+00 4.00e-02 5.62e+01 dihedral pdb=" CA ASP C 87 " pdb=" C ASP C 87 " pdb=" N THR C 88 " pdb=" CA THR C 88 " ideal model delta harmonic sigma weight residual -180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 6448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1367 0.068 - 0.137: 231 0.137 - 0.205: 27 0.205 - 0.274: 4 0.274 - 0.342: 2 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CA LYS H 47 " pdb=" N LYS H 47 " pdb=" C LYS H 47 " pdb=" CB LYS H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE F 123 " pdb=" CA ILE F 123 " pdb=" CG1 ILE F 123 " pdb=" CG2 ILE F 123 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE F 72 " pdb=" CA ILE F 72 " pdb=" CG1 ILE F 72 " pdb=" CG2 ILE F 72 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1628 not shown) Planarity restraints: 1849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 48 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLY H 48 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY H 48 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA H 49 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 116 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO A 117 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 117 " 0.051 5.00e-02 4.00e+02 7.80e-02 9.75e+00 pdb=" N PRO A 118 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.043 5.00e-02 4.00e+02 ... (remaining 1846 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 216 2.62 - 3.19: 10941 3.19 - 3.76: 18086 3.76 - 4.33: 25073 4.33 - 4.90: 36828 Nonbonded interactions: 91144 Sorted by model distance: nonbonded pdb=" OH TYR E 102 " pdb=" OD1 ASP F 73 " model vdw 2.049 2.440 nonbonded pdb=" OG SER G 102 " pdb=" NH1 ARG G 162 " model vdw 2.085 2.520 nonbonded pdb=" O GLU A 69 " pdb=" OG1 THR A 73 " model vdw 2.112 2.440 nonbonded pdb=" OD1 ASP A 38 " pdb=" NZ LYS A 41 " model vdw 2.145 2.520 nonbonded pdb=" O TYR F 45 " pdb=" OG SER F 48 " model vdw 2.161 2.440 ... (remaining 91139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'G' and resid 10 through 174) } 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.190 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.130 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.005 0.088 10683 Z= 0.295 Angle : 0.875 11.392 14450 Z= 0.521 Chirality : 0.053 0.342 1631 Planarity : 0.006 0.082 1849 Dihedral : 14.401 89.202 3985 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 32.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.20 % Favored : 89.72 % Rotamer: Outliers : 0.43 % Allowed : 0.69 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.46 (0.22), residues: 1274 helix: -0.82 (0.22), residues: 505 sheet: -1.36 (0.35), residues: 208 loop : -2.48 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP F 100 HIS 0.008 0.001 HIS B 11 PHE 0.032 0.003 PHE C 82 TYR 0.021 0.002 TYR F 75 ARG 0.011 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8503 (mmp) cc_final: 0.8065 (mmm) REVERT: A 50 MET cc_start: 0.8292 (tmm) cc_final: 0.7942 (tmm) REVERT: A 70 MET cc_start: 0.8530 (tpp) cc_final: 0.8264 (tpp) REVERT: B 68 MET cc_start: 0.8528 (mmm) cc_final: 0.8277 (mmm) REVERT: C 56 ASP cc_start: 0.7077 (m-30) cc_final: 0.6637 (t70) REVERT: E 18 GLU cc_start: 0.8481 (pp20) cc_final: 0.8147 (pp20) REVERT: E 42 HIS cc_start: 0.8747 (m-70) cc_final: 0.8439 (t70) REVERT: E 83 ILE cc_start: 0.9205 (mm) cc_final: 0.8792 (tp) REVERT: E 110 MET cc_start: 0.8913 (mpp) cc_final: 0.8580 (mpp) REVERT: E 130 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8449 (tm-30) REVERT: F 124 ILE cc_start: 0.7148 (tt) cc_final: 0.6915 (tp) REVERT: G 148 PHE cc_start: 0.8853 (m-80) cc_final: 0.8511 (m-80) REVERT: H 1 MET cc_start: 0.0673 (mmm) cc_final: 0.0281 (tpt) REVERT: H 16 TYR cc_start: 0.8345 (p90) cc_final: 0.7859 (p90) REVERT: H 102 LEU cc_start: 0.9569 (tp) cc_final: 0.9341 (tt) REVERT: H 122 THR cc_start: 0.6134 (p) cc_final: 0.5795 (t) outliers start: 5 outliers final: 0 residues processed: 135 average time/residue: 0.2108 time to fit residues: 41.3143 Evaluate side-chains 90 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.0170 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10683 Z= 0.216 Angle : 0.698 8.973 14450 Z= 0.373 Chirality : 0.046 0.199 1631 Planarity : 0.005 0.052 1849 Dihedral : 7.331 71.804 1405 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 0.34 % Allowed : 7.80 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.07 (0.23), residues: 1274 helix: -0.33 (0.22), residues: 516 sheet: -1.50 (0.34), residues: 214 loop : -2.32 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 100 HIS 0.009 0.001 HIS E 51 PHE 0.022 0.002 PHE B 35 TYR 0.024 0.002 TYR B 17 ARG 0.011 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.371 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: A 29 MET cc_start: 0.8294 (mmp) cc_final: 0.8049 (mmm) REVERT: A 70 MET cc_start: 0.8556 (tpp) cc_final: 0.8112 (tpp) REVERT: C 41 MET cc_start: 0.8699 (mmm) cc_final: 0.8397 (mtp) REVERT: C 56 ASP cc_start: 0.7100 (m-30) cc_final: 0.6728 (t70) REVERT: E 18 GLU cc_start: 0.8426 (pp20) cc_final: 0.8097 (pp20) REVERT: E 42 HIS cc_start: 0.8661 (m90) cc_final: 0.8383 (m170) REVERT: E 83 ILE cc_start: 0.9302 (mm) cc_final: 0.8958 (tp) REVERT: E 97 PHE cc_start: 0.8370 (t80) cc_final: 0.8108 (t80) REVERT: F 147 ASN cc_start: 0.8370 (t0) cc_final: 0.8075 (t0) REVERT: F 177 MET cc_start: 0.8187 (tmm) cc_final: 0.7716 (tmm) REVERT: G 43 LEU cc_start: 0.9145 (tt) cc_final: 0.8815 (pp) REVERT: G 148 PHE cc_start: 0.8773 (m-80) cc_final: 0.8408 (m-80) REVERT: H 1 MET cc_start: 0.0465 (mmm) cc_final: -0.0228 (tpt) REVERT: H 16 TYR cc_start: 0.8251 (p90) cc_final: 0.7796 (p90) outliers start: 4 outliers final: 2 residues processed: 128 average time/residue: 0.2216 time to fit residues: 41.2459 Evaluate side-chains 87 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 0.1980 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10683 Z= 0.208 Angle : 0.673 8.269 14450 Z= 0.361 Chirality : 0.045 0.255 1631 Planarity : 0.005 0.043 1849 Dihedral : 7.050 72.722 1405 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 27.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 0.26 % Allowed : 4.29 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1274 helix: -0.19 (0.22), residues: 520 sheet: -1.30 (0.35), residues: 209 loop : -2.34 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 147 HIS 0.008 0.001 HIS E 51 PHE 0.026 0.002 PHE B 35 TYR 0.026 0.002 TYR B 32 ARG 0.007 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8579 (tpp) cc_final: 0.8077 (tpp) REVERT: B 32 TYR cc_start: 0.8025 (m-80) cc_final: 0.7738 (m-80) REVERT: C 41 MET cc_start: 0.8613 (mmm) cc_final: 0.8321 (mtp) REVERT: C 56 ASP cc_start: 0.7132 (m-30) cc_final: 0.6732 (t70) REVERT: D 69 MET cc_start: 0.7794 (pmm) cc_final: 0.7427 (pmm) REVERT: D 97 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8230 (mmmm) REVERT: E 1 MET cc_start: 0.5781 (ppp) cc_final: 0.5515 (ppp) REVERT: E 18 GLU cc_start: 0.8430 (pp20) cc_final: 0.8115 (pp20) REVERT: E 83 ILE cc_start: 0.9263 (mm) cc_final: 0.8929 (tp) REVERT: E 134 ARG cc_start: 0.7632 (mpp-170) cc_final: 0.6602 (mmp80) REVERT: E 138 LEU cc_start: 0.7492 (tp) cc_final: 0.6198 (tp) REVERT: F 147 ASN cc_start: 0.8381 (t0) cc_final: 0.8046 (t0) REVERT: G 52 MET cc_start: 0.8559 (mtm) cc_final: 0.7509 (mmm) REVERT: G 105 PHE cc_start: 0.7607 (m-80) cc_final: 0.7200 (m-80) REVERT: G 139 MET cc_start: 0.7445 (tpp) cc_final: 0.7072 (tpp) REVERT: G 148 PHE cc_start: 0.8766 (m-80) cc_final: 0.8231 (m-10) REVERT: H 1 MET cc_start: 0.0924 (mmm) cc_final: 0.0080 (tpt) REVERT: H 16 TYR cc_start: 0.8198 (p90) cc_final: 0.7763 (p90) REVERT: H 134 MET cc_start: 0.6423 (tpt) cc_final: 0.5771 (tpp) outliers start: 3 outliers final: 0 residues processed: 130 average time/residue: 0.2120 time to fit residues: 40.0475 Evaluate side-chains 90 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10683 Z= 0.230 Angle : 0.676 6.504 14450 Z= 0.365 Chirality : 0.045 0.191 1631 Planarity : 0.005 0.040 1849 Dihedral : 6.965 75.190 1405 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 29.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 0.26 % Allowed : 6.35 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.95 (0.23), residues: 1274 helix: -0.23 (0.22), residues: 518 sheet: -1.22 (0.35), residues: 209 loop : -2.36 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 94 HIS 0.012 0.001 HIS B 11 PHE 0.023 0.002 PHE B 112 TYR 0.024 0.002 TYR B 17 ARG 0.004 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8504 (mmm) cc_final: 0.7931 (mmm) REVERT: A 70 MET cc_start: 0.8344 (tpp) cc_final: 0.7896 (tpp) REVERT: B 32 TYR cc_start: 0.7998 (m-80) cc_final: 0.7763 (m-80) REVERT: C 41 MET cc_start: 0.8607 (mmm) cc_final: 0.8384 (mtp) REVERT: C 56 ASP cc_start: 0.7222 (m-30) cc_final: 0.6815 (t70) REVERT: D 97 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8340 (mmmm) REVERT: E 18 GLU cc_start: 0.8432 (pp20) cc_final: 0.8109 (pp20) REVERT: E 83 ILE cc_start: 0.9321 (mm) cc_final: 0.9017 (tp) REVERT: E 130 GLU cc_start: 0.8893 (tp30) cc_final: 0.8606 (mt-10) REVERT: F 147 ASN cc_start: 0.8180 (t0) cc_final: 0.7921 (t0) REVERT: G 52 MET cc_start: 0.8447 (mtm) cc_final: 0.8217 (ptp) REVERT: G 105 PHE cc_start: 0.7624 (m-80) cc_final: 0.7183 (m-80) REVERT: G 148 PHE cc_start: 0.8774 (m-80) cc_final: 0.8234 (m-10) REVERT: H 16 TYR cc_start: 0.8217 (p90) cc_final: 0.7817 (p90) outliers start: 3 outliers final: 0 residues processed: 123 average time/residue: 0.2267 time to fit residues: 40.7130 Evaluate side-chains 86 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10683 Z= 0.176 Angle : 0.660 8.213 14450 Z= 0.350 Chirality : 0.045 0.258 1631 Planarity : 0.004 0.043 1849 Dihedral : 6.540 74.599 1405 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.74 (0.23), residues: 1274 helix: 0.01 (0.22), residues: 521 sheet: -1.09 (0.35), residues: 207 loop : -2.33 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 147 HIS 0.007 0.001 HIS B 11 PHE 0.014 0.002 PHE G 105 TYR 0.022 0.002 TYR E 102 ARG 0.004 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8629 (mmm) cc_final: 0.8241 (mmm) REVERT: A 70 MET cc_start: 0.8329 (tpp) cc_final: 0.7867 (tpp) REVERT: C 41 MET cc_start: 0.8603 (mmm) cc_final: 0.8328 (mtp) REVERT: C 56 ASP cc_start: 0.7021 (m-30) cc_final: 0.6460 (t70) REVERT: D 97 LYS cc_start: 0.8343 (mmmt) cc_final: 0.8096 (mmmm) REVERT: E 1 MET cc_start: 0.5656 (ppp) cc_final: 0.5425 (ppp) REVERT: E 18 GLU cc_start: 0.8391 (pp20) cc_final: 0.8175 (pp20) REVERT: E 83 ILE cc_start: 0.9238 (mm) cc_final: 0.8922 (tp) REVERT: F 113 HIS cc_start: 0.8538 (p-80) cc_final: 0.8284 (p-80) REVERT: F 147 ASN cc_start: 0.8120 (t0) cc_final: 0.7873 (t0) REVERT: F 163 PRO cc_start: 0.8117 (Cg_exo) cc_final: 0.7822 (Cg_endo) REVERT: G 29 MET cc_start: 0.8636 (mmp) cc_final: 0.8391 (mmp) REVERT: G 43 LEU cc_start: 0.9177 (tt) cc_final: 0.8789 (pp) REVERT: G 52 MET cc_start: 0.8623 (mtm) cc_final: 0.7702 (mmm) REVERT: G 105 PHE cc_start: 0.7610 (m-80) cc_final: 0.7128 (m-80) REVERT: G 129 LEU cc_start: 0.8710 (mm) cc_final: 0.8434 (mp) REVERT: G 139 MET cc_start: 0.7101 (tpp) cc_final: 0.6744 (tpp) REVERT: G 148 PHE cc_start: 0.8725 (m-80) cc_final: 0.8072 (m-10) REVERT: H 16 TYR cc_start: 0.8205 (p90) cc_final: 0.7825 (p90) REVERT: H 134 MET cc_start: 0.6482 (tpt) cc_final: 0.5747 (tpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2227 time to fit residues: 39.9262 Evaluate side-chains 86 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10683 Z= 0.186 Angle : 0.649 7.354 14450 Z= 0.344 Chirality : 0.045 0.214 1631 Planarity : 0.004 0.041 1849 Dihedral : 6.380 73.876 1405 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.60 (0.23), residues: 1274 helix: 0.13 (0.23), residues: 520 sheet: -0.97 (0.35), residues: 209 loop : -2.28 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 94 HIS 0.009 0.001 HIS B 11 PHE 0.011 0.002 PHE G 105 TYR 0.025 0.002 TYR B 17 ARG 0.007 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8684 (mmm) cc_final: 0.8333 (mmm) REVERT: A 70 MET cc_start: 0.8335 (tpp) cc_final: 0.7928 (tpp) REVERT: C 41 MET cc_start: 0.8681 (mmm) cc_final: 0.8414 (mtp) REVERT: C 56 ASP cc_start: 0.7014 (m-30) cc_final: 0.6477 (t70) REVERT: D 97 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8177 (mmmm) REVERT: E 1 MET cc_start: 0.5672 (ppp) cc_final: 0.5425 (ppp) REVERT: E 18 GLU cc_start: 0.8414 (pp20) cc_final: 0.8199 (pp20) REVERT: E 83 ILE cc_start: 0.9205 (mm) cc_final: 0.8896 (tp) REVERT: E 130 GLU cc_start: 0.8781 (tp30) cc_final: 0.8500 (mt-10) REVERT: F 113 HIS cc_start: 0.8532 (p-80) cc_final: 0.8273 (p-80) REVERT: F 147 ASN cc_start: 0.8205 (t0) cc_final: 0.7961 (t0) REVERT: F 163 PRO cc_start: 0.8112 (Cg_exo) cc_final: 0.7824 (Cg_endo) REVERT: F 182 ASP cc_start: 0.9017 (t0) cc_final: 0.8735 (t0) REVERT: G 52 MET cc_start: 0.8606 (mtm) cc_final: 0.7703 (mmm) REVERT: G 105 PHE cc_start: 0.7615 (m-80) cc_final: 0.7143 (m-80) REVERT: G 129 LEU cc_start: 0.8741 (mm) cc_final: 0.8480 (mp) REVERT: G 139 MET cc_start: 0.7318 (tpp) cc_final: 0.7014 (tpp) REVERT: G 148 PHE cc_start: 0.8743 (m-80) cc_final: 0.8121 (m-10) REVERT: H 16 TYR cc_start: 0.8211 (p90) cc_final: 0.7817 (p90) REVERT: H 134 MET cc_start: 0.6453 (tpt) cc_final: 0.5785 (tpp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2254 time to fit residues: 39.3542 Evaluate side-chains 84 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10683 Z= 0.188 Angle : 0.658 7.504 14450 Z= 0.345 Chirality : 0.045 0.246 1631 Planarity : 0.004 0.039 1849 Dihedral : 6.305 71.081 1405 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.49 (0.23), residues: 1274 helix: 0.21 (0.23), residues: 520 sheet: -0.98 (0.35), residues: 211 loop : -2.18 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 94 HIS 0.007 0.001 HIS B 11 PHE 0.014 0.002 PHE C 140 TYR 0.034 0.002 TYR B 32 ARG 0.009 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8771 (mmm) cc_final: 0.8475 (mmm) REVERT: A 70 MET cc_start: 0.8346 (tpp) cc_final: 0.7938 (tpp) REVERT: B 66 PHE cc_start: 0.8349 (t80) cc_final: 0.7833 (t80) REVERT: C 41 MET cc_start: 0.8580 (mmm) cc_final: 0.8327 (mtp) REVERT: C 56 ASP cc_start: 0.7022 (m-30) cc_final: 0.6471 (t70) REVERT: D 97 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8177 (mmmm) REVERT: E 1 MET cc_start: 0.5663 (ppp) cc_final: 0.5409 (ppp) REVERT: E 18 GLU cc_start: 0.8424 (pp20) cc_final: 0.8215 (pp20) REVERT: E 83 ILE cc_start: 0.9191 (mm) cc_final: 0.8891 (tp) REVERT: F 113 HIS cc_start: 0.8537 (p-80) cc_final: 0.8277 (p-80) REVERT: F 147 ASN cc_start: 0.8427 (t0) cc_final: 0.8100 (t0) REVERT: F 163 PRO cc_start: 0.8137 (Cg_exo) cc_final: 0.7847 (Cg_endo) REVERT: F 182 ASP cc_start: 0.9028 (t0) cc_final: 0.8704 (t0) REVERT: G 52 MET cc_start: 0.8619 (mtm) cc_final: 0.7660 (mmm) REVERT: G 105 PHE cc_start: 0.7614 (m-80) cc_final: 0.7185 (m-80) REVERT: G 148 PHE cc_start: 0.8787 (m-80) cc_final: 0.8488 (m-80) REVERT: H 16 TYR cc_start: 0.8211 (p90) cc_final: 0.7819 (p90) REVERT: H 134 MET cc_start: 0.6446 (tpt) cc_final: 0.5783 (tpp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2129 time to fit residues: 36.9088 Evaluate side-chains 85 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.3980 chunk 47 optimal weight: 0.0570 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 0.0570 chunk 23 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS E 35 HIS ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10683 Z= 0.209 Angle : 0.682 8.036 14450 Z= 0.363 Chirality : 0.046 0.199 1631 Planarity : 0.004 0.043 1849 Dihedral : 6.224 70.968 1405 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.58 (0.23), residues: 1274 helix: 0.04 (0.22), residues: 524 sheet: -0.95 (0.35), residues: 209 loop : -2.18 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 100 HIS 0.008 0.001 HIS B 11 PHE 0.020 0.002 PHE D 186 TYR 0.022 0.002 TYR F 45 ARG 0.005 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.354 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: A 50 MET cc_start: 0.8496 (tmm) cc_final: 0.8281 (tmm) REVERT: A 52 MET cc_start: 0.6966 (mmt) cc_final: 0.6751 (mmt) REVERT: A 70 MET cc_start: 0.8250 (tpp) cc_final: 0.7830 (tpp) REVERT: C 41 MET cc_start: 0.8601 (mmm) cc_final: 0.8365 (mtp) REVERT: C 56 ASP cc_start: 0.6943 (m-30) cc_final: 0.6449 (t70) REVERT: D 97 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8261 (mmmm) REVERT: E 1 MET cc_start: 0.5494 (ppp) cc_final: 0.5221 (ppp) REVERT: E 18 GLU cc_start: 0.8358 (pp20) cc_final: 0.8061 (pp20) REVERT: E 83 ILE cc_start: 0.9211 (mm) cc_final: 0.8902 (tp) REVERT: E 138 LEU cc_start: 0.7659 (tp) cc_final: 0.7446 (mt) REVERT: F 113 HIS cc_start: 0.8531 (p-80) cc_final: 0.8280 (p-80) REVERT: F 147 ASN cc_start: 0.8437 (t0) cc_final: 0.8172 (t0) REVERT: F 163 PRO cc_start: 0.8180 (Cg_exo) cc_final: 0.7877 (Cg_endo) REVERT: F 182 ASP cc_start: 0.9035 (t0) cc_final: 0.8704 (t0) REVERT: G 43 LEU cc_start: 0.9253 (tt) cc_final: 0.8822 (pp) REVERT: G 52 MET cc_start: 0.8488 (mtm) cc_final: 0.7599 (mmm) REVERT: G 105 PHE cc_start: 0.7581 (m-80) cc_final: 0.6982 (m-80) REVERT: G 148 PHE cc_start: 0.8812 (m-80) cc_final: 0.8189 (m-80) REVERT: H 1 MET cc_start: -0.0318 (tpt) cc_final: -0.0943 (tpt) REVERT: H 16 TYR cc_start: 0.8206 (p90) cc_final: 0.7991 (p90) REVERT: H 124 LYS cc_start: 0.8639 (tmtt) cc_final: 0.8437 (tptt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2289 time to fit residues: 38.3328 Evaluate side-chains 83 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 0.1980 chunk 87 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10683 Z= 0.182 Angle : 0.671 7.956 14450 Z= 0.354 Chirality : 0.046 0.232 1631 Planarity : 0.004 0.047 1849 Dihedral : 6.028 70.274 1405 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.23), residues: 1274 helix: 0.24 (0.23), residues: 516 sheet: -0.87 (0.34), residues: 209 loop : -2.07 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 94 HIS 0.005 0.001 HIS B 11 PHE 0.018 0.002 PHE D 186 TYR 0.033 0.002 TYR B 32 ARG 0.006 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8818 (mmm) cc_final: 0.8463 (mmm) REVERT: A 70 MET cc_start: 0.8395 (tpp) cc_final: 0.7948 (tpp) REVERT: A 150 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8066 (tp-100) REVERT: C 41 MET cc_start: 0.8589 (mmm) cc_final: 0.8363 (mtp) REVERT: C 56 ASP cc_start: 0.6963 (m-30) cc_final: 0.6459 (t70) REVERT: D 69 MET cc_start: 0.6956 (pmm) cc_final: 0.6609 (pmm) REVERT: D 97 LYS cc_start: 0.8403 (mmmt) cc_final: 0.8155 (mmmm) REVERT: E 1 MET cc_start: 0.5417 (ppp) cc_final: 0.5142 (ppp) REVERT: E 83 ILE cc_start: 0.9184 (mm) cc_final: 0.8925 (tp) REVERT: E 134 ARG cc_start: 0.7765 (mpp-170) cc_final: 0.7514 (mmp80) REVERT: E 138 LEU cc_start: 0.7533 (tp) cc_final: 0.7016 (mt) REVERT: F 113 HIS cc_start: 0.8470 (p-80) cc_final: 0.8220 (p-80) REVERT: F 147 ASN cc_start: 0.8419 (t0) cc_final: 0.8176 (t0) REVERT: F 163 PRO cc_start: 0.8039 (Cg_exo) cc_final: 0.7736 (Cg_endo) REVERT: F 182 ASP cc_start: 0.9009 (t0) cc_final: 0.8635 (t0) REVERT: G 52 MET cc_start: 0.8490 (mtm) cc_final: 0.7654 (mmm) REVERT: H 16 TYR cc_start: 0.8184 (p90) cc_final: 0.7979 (p90) REVERT: H 124 LYS cc_start: 0.8619 (tmtt) cc_final: 0.8405 (tptt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2186 time to fit residues: 38.2705 Evaluate side-chains 86 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10683 Z= 0.187 Angle : 0.676 8.108 14450 Z= 0.357 Chirality : 0.046 0.231 1631 Planarity : 0.004 0.083 1849 Dihedral : 5.998 73.645 1405 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.35 (0.23), residues: 1274 helix: 0.25 (0.23), residues: 525 sheet: -0.78 (0.35), residues: 209 loop : -2.09 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 94 HIS 0.006 0.001 HIS B 11 PHE 0.030 0.002 PHE G 105 TYR 0.028 0.002 TYR F 75 ARG 0.007 0.000 ARG E 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8819 (mmm) cc_final: 0.8493 (mmm) REVERT: A 70 MET cc_start: 0.8225 (tpp) cc_final: 0.7805 (tpp) REVERT: A 150 GLN cc_start: 0.8416 (tp-100) cc_final: 0.8149 (tp-100) REVERT: C 41 MET cc_start: 0.8597 (mmm) cc_final: 0.8372 (mtp) REVERT: C 56 ASP cc_start: 0.7005 (m-30) cc_final: 0.6615 (t70) REVERT: D 69 MET cc_start: 0.6980 (pmm) cc_final: 0.6695 (pmm) REVERT: D 97 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8128 (mmmm) REVERT: E 1 MET cc_start: 0.5367 (ppp) cc_final: 0.5084 (ppp) REVERT: E 18 GLU cc_start: 0.8511 (pp20) cc_final: 0.8263 (pp20) REVERT: E 83 ILE cc_start: 0.9179 (mm) cc_final: 0.8921 (tp) REVERT: E 134 ARG cc_start: 0.7767 (mpp-170) cc_final: 0.7349 (mmp80) REVERT: E 138 LEU cc_start: 0.7524 (tp) cc_final: 0.7214 (tp) REVERT: F 113 HIS cc_start: 0.8481 (p-80) cc_final: 0.8204 (p-80) REVERT: F 147 ASN cc_start: 0.8425 (t0) cc_final: 0.8187 (t0) REVERT: F 163 PRO cc_start: 0.8012 (Cg_exo) cc_final: 0.7700 (Cg_endo) REVERT: F 182 ASP cc_start: 0.9000 (t0) cc_final: 0.8608 (t0) REVERT: G 52 MET cc_start: 0.8469 (mtm) cc_final: 0.7651 (mmm) REVERT: G 70 MET cc_start: 0.6976 (mmt) cc_final: 0.6723 (mmm) REVERT: G 121 THR cc_start: 0.7921 (m) cc_final: 0.7682 (m) REVERT: G 129 LEU cc_start: 0.8406 (mt) cc_final: 0.8189 (mp) REVERT: H 16 TYR cc_start: 0.8259 (p90) cc_final: 0.8045 (p90) REVERT: H 124 LYS cc_start: 0.8626 (tmtt) cc_final: 0.8418 (tptt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2252 time to fit residues: 38.1032 Evaluate side-chains 88 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.041926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.034228 restraints weight = 113791.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.035089 restraints weight = 86865.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.035756 restraints weight = 69950.813| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10683 Z= 0.186 Angle : 0.670 7.995 14450 Z= 0.355 Chirality : 0.045 0.209 1631 Planarity : 0.004 0.080 1849 Dihedral : 5.985 76.686 1405 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.33 (0.23), residues: 1274 helix: 0.25 (0.23), residues: 526 sheet: -0.77 (0.36), residues: 200 loop : -2.05 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 94 HIS 0.006 0.001 HIS B 11 PHE 0.019 0.001 PHE B 115 TYR 0.035 0.002 TYR B 32 ARG 0.006 0.000 ARG E 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2099.47 seconds wall clock time: 39 minutes 8.48 seconds (2348.48 seconds total)