Starting phenix.real_space_refine on Fri Mar 15 03:09:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/03_2024/7b6x_12057.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/03_2024/7b6x_12057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/03_2024/7b6x_12057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/03_2024/7b6x_12057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/03_2024/7b6x_12057.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/03_2024/7b6x_12057.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 ARG 31": "NH1" <-> "NH2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ASP 167": "OD1" <-> "OD2" Residue "D PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "E TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E ASP 49": "OD1" <-> "OD2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "F ASP 62": "OD1" <-> "OD2" Residue "F ASP 66": "OD1" <-> "OD2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G ASP 57": "OD1" <-> "OD2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 119": "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: 5.99, per 1000 atoms: 0.57 Number of scatterers: 10470 At special positions: 0 Unit cell: (172.127, 148.255, 74.1276, 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: 4.30 Conformation dependent library (CDL) restraints added in 1.7 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: 38 helices and 10 sheets defined 43.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 16 through 33 removed outlier: 3.783A pdb=" N LEU A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 62 removed outlier: 4.250A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 126 through 140 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.318A pdb=" N PHE B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.699A pdb=" N ARG B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 removed outlier: 4.126A pdb=" N PHE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 104 through 121 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 166 through 182 Processing helix chain 'D' and resid 195 through 211 Processing helix chain 'E' and resid 26 through 55 removed outlier: 4.588A pdb=" N GLU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 110 removed outlier: 3.890A pdb=" N ASN E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'F' and resid 32 through 50 Processing helix chain 'F' and resid 52 through 78 removed outlier: 4.041A pdb=" N ARG F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.623A pdb=" N THR F 132 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 161 Processing helix chain 'F' and resid 181 through 191 Processing helix chain 'G' and resid 14 through 33 removed outlier: 3.554A pdb=" N LEU G 18 " --> pdb=" O ASN G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 62 removed outlier: 3.552A pdb=" N MET G 52 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU G 56 " --> pdb=" O MET G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 85 removed outlier: 3.605A pdb=" N THR G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 3.705A pdb=" N THR G 121 " --> pdb=" O PRO G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 127 through 140 Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.712A pdb=" N GLY G 155 " --> pdb=" O GLN G 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.884A pdb=" N VAL H 95 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.731A pdb=" N VAL A 163 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 103 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 161 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A 160 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 164 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 145 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 166 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A 143 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.597A 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: 6.908A pdb=" N ILE C 8 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR C 18 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 6 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN C 5 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 64 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR C 63 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU D 135 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 143 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 8 " --> pdb=" O ILE D 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32 removed outlier: 4.071A pdb=" N LYS D 30 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 96 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 65 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER D 99 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU D 63 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 71 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 40 through 43 Processing sheet with id=AA6, first strand: chain 'E' and resid 15 through 20 removed outlier: 3.583A pdb=" N TYR E 5 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 83 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS E 86 " --> pdb=" O PHE E 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 110 through 113 removed outlier: 3.509A pdb=" N ILE F 124 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 100 through 101 removed outlier: 3.505A pdb=" N PHE G 101 " --> pdb=" O VAL G 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 100 through 101 removed outlier: 3.505A pdb=" N PHE G 101 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU G 160 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLU G 143 " --> pdb=" O VAL G 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.677A pdb=" N TYR H 61 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY H 70 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU H 59 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL H 72 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU H 57 " --> pdb=" O VAL H 72 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1425 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: 2.65 Time building geometry restraints manager: 4.65 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: 3376 1.34 - 1.46: 2294 1.46 - 1.58: 4932 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 10683 Sorted by residual: bond pdb=" C GLU F 127 " pdb=" N PRO F 128 " ideal model delta sigma weight residual 1.334 1.292 0.042 1.11e-02 8.12e+03 1.41e+01 bond pdb=" C HIS D 61 " pdb=" N VAL D 62 " ideal model delta sigma weight residual 1.334 1.292 0.041 1.24e-02 6.50e+03 1.11e+01 bond pdb=" C TRP C 115 " pdb=" N THR C 116 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.47e-02 4.63e+03 1.09e+01 bond pdb=" CB PHE A 17 " pdb=" CG PHE A 17 " ideal model delta sigma weight residual 1.502 1.448 0.054 2.30e-02 1.89e+03 5.53e+00 bond pdb=" CB ARG D 100 " pdb=" CG ARG D 100 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.24e+00 ... (remaining 10678 not shown) Histogram of bond angle deviations from ideal: 97.09 - 104.48: 139 104.48 - 111.88: 4975 111.88 - 119.27: 3801 119.27 - 126.66: 5421 126.66 - 134.06: 114 Bond angle restraints: 14450 Sorted by residual: angle pdb=" CB LEU D 197 " pdb=" CG LEU D 197 " pdb=" CD1 LEU D 197 " ideal model delta sigma weight residual 110.70 125.27 -14.57 3.00e+00 1.11e-01 2.36e+01 angle pdb=" C PRO A 65 " pdb=" N ARG A 66 " pdb=" CA ARG A 66 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C ASN B 16 " pdb=" N TYR B 17 " pdb=" CA TYR B 17 " ideal model delta sigma weight residual 122.19 116.63 5.56 1.41e+00 5.03e-01 1.56e+01 angle pdb=" CB MET A 70 " pdb=" CG MET A 70 " pdb=" SD MET A 70 " ideal model delta sigma weight residual 112.70 123.46 -10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C VAL A 114 " pdb=" N GLU A 115 " pdb=" CA GLU A 115 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 ... (remaining 14445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5726 17.41 - 34.82: 628 34.82 - 52.23: 75 52.23 - 69.64: 11 69.64 - 87.05: 11 Dihedral angle restraints: 6451 sinusoidal: 2653 harmonic: 3798 Sorted by residual: dihedral pdb=" CA ILE D 214 " pdb=" C ILE D 214 " pdb=" N SER D 215 " pdb=" CA SER D 215 " ideal model delta harmonic sigma weight residual 180.00 140.32 39.68 0 5.00e+00 4.00e-02 6.30e+01 dihedral pdb=" CA ILE F 134 " pdb=" C ILE F 134 " pdb=" N SER F 135 " pdb=" CA SER F 135 " ideal model delta harmonic sigma weight residual -180.00 -141.08 -38.92 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA SER A 15 " pdb=" C SER A 15 " pdb=" N GLU A 16 " pdb=" CA GLU A 16 " ideal model delta harmonic sigma weight residual 180.00 153.27 26.73 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 6448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1414 0.083 - 0.166: 202 0.166 - 0.248: 9 0.248 - 0.331: 3 0.331 - 0.414: 3 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CB ILE F 134 " pdb=" CA ILE F 134 " pdb=" CG1 ILE F 134 " pdb=" CG2 ILE F 134 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CG LEU D 197 " pdb=" CB LEU D 197 " pdb=" CD1 LEU D 197 " pdb=" CD2 LEU D 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB ILE C 142 " pdb=" CA ILE C 142 " pdb=" CG1 ILE C 142 " pdb=" CG2 ILE C 142 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 1628 not shown) Planarity restraints: 1849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 117 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO A 118 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 136 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO F 137 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO F 137 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 137 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 16 " -0.020 2.00e-02 2.50e+03 1.63e-02 5.31e+00 pdb=" CG TYR H 16 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR H 16 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR H 16 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR H 16 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 16 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 16 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 16 " -0.003 2.00e-02 2.50e+03 ... (remaining 1846 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 269 2.61 - 3.18: 11331 3.18 - 3.75: 18377 3.75 - 4.33: 25203 4.33 - 4.90: 37379 Nonbonded interactions: 92559 Sorted by model distance: nonbonded pdb=" O PHE B 61 " pdb=" OG1 THR B 64 " model vdw 2.035 2.440 nonbonded pdb=" OD1 ASN C 67 " pdb=" OG SER D 132 " model vdw 2.056 2.440 nonbonded pdb=" OG SER G 102 " pdb=" NH1 ARG G 162 " model vdw 2.079 2.520 nonbonded pdb=" OG1 THR C 30 " pdb=" OE1 GLU C 33 " model vdw 2.082 2.440 nonbonded pdb=" NH2 ARG B 51 " pdb=" O LEU H 44 " model vdw 2.085 2.520 ... (remaining 92554 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: 3.180 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: 14.310 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 29.890 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 0.088 10683 Z= 0.492 Angle : 1.062 14.570 14450 Z= 0.575 Chirality : 0.058 0.414 1631 Planarity : 0.006 0.076 1849 Dihedral : 14.167 87.051 3985 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 44.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % 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: -2.77 (0.22), residues: 1274 helix: -1.11 (0.21), residues: 520 sheet: -1.58 (0.38), residues: 180 loop : -2.59 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 147 HIS 0.017 0.003 HIS F 113 PHE 0.037 0.004 PHE F 133 TYR 0.040 0.004 TYR H 16 ARG 0.038 0.002 ARG H 128 *********************** 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 141 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8539 (m-30) cc_final: 0.8142 (m-30) REVERT: B 59 MET cc_start: 0.8798 (pmm) cc_final: 0.8507 (pmm) REVERT: D 110 PHE cc_start: 0.8741 (t80) cc_final: 0.8416 (t80) REVERT: D 194 ARG cc_start: 0.7068 (mpp80) cc_final: 0.6651 (mpp80) REVERT: E 105 TYR cc_start: 0.8893 (t80) cc_final: 0.8421 (t80) REVERT: F 55 GLU cc_start: 0.8685 (pt0) cc_final: 0.8434 (tm-30) REVERT: F 177 MET cc_start: 0.7210 (tmm) cc_final: 0.6873 (tmm) REVERT: G 91 ILE cc_start: 0.3688 (mp) cc_final: 0.3208 (mt) REVERT: H 102 LEU cc_start: 0.8638 (tt) cc_final: 0.8157 (tp) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.2168 time to fit residues: 44.6434 Evaluate side-chains 104 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 112 optimal weight: 9.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 77 ASN B 146 HIS ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10683 Z= 0.222 Angle : 0.735 7.982 14450 Z= 0.386 Chirality : 0.047 0.233 1631 Planarity : 0.005 0.075 1849 Dihedral : 7.286 82.730 1408 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 29.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.11 % Allowed : 11.41 % Favored : 87.48 % 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: -2.13 (0.23), residues: 1274 helix: -0.42 (0.21), residues: 532 sheet: -1.31 (0.38), residues: 190 loop : -2.43 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 147 HIS 0.010 0.001 HIS F 113 PHE 0.024 0.002 PHE B 35 TYR 0.025 0.002 TYR C 69 ARG 0.014 0.001 ARG F 59 *********************** 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 147 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8506 (mppt) cc_final: 0.8289 (tptt) REVERT: A 99 ASP cc_start: 0.8366 (m-30) cc_final: 0.8105 (m-30) REVERT: A 113 PHE cc_start: 0.4354 (t80) cc_final: 0.4035 (t80) REVERT: C 73 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.7029 (t80) REVERT: D 110 PHE cc_start: 0.8781 (t80) cc_final: 0.8377 (t80) REVERT: E 5 TYR cc_start: 0.5761 (t80) cc_final: 0.5310 (t80) REVERT: E 101 MET cc_start: 0.8135 (mmm) cc_final: 0.7893 (mmm) REVERT: E 105 TYR cc_start: 0.8515 (t80) cc_final: 0.8154 (t80) REVERT: E 110 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6941 (mmp) REVERT: F 39 PHE cc_start: 0.7314 (t80) cc_final: 0.7053 (t80) REVERT: F 55 GLU cc_start: 0.8283 (pt0) cc_final: 0.7796 (tm-30) REVERT: G 91 ILE cc_start: 0.3568 (mp) cc_final: 0.3021 (mt) REVERT: H 102 LEU cc_start: 0.8544 (tt) cc_final: 0.8139 (tp) outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 0.2111 time to fit residues: 43.1541 Evaluate side-chains 117 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 130 VAL 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: 4.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 83 HIS ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 10683 Z= 0.289 Angle : 0.760 8.552 14450 Z= 0.397 Chirality : 0.046 0.186 1631 Planarity : 0.005 0.076 1849 Dihedral : 7.234 83.842 1408 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 33.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 3.43 % Allowed : 16.12 % Favored : 80.45 % 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: -2.08 (0.23), residues: 1274 helix: -0.31 (0.22), residues: 523 sheet: -1.27 (0.39), residues: 190 loop : -2.46 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 147 HIS 0.012 0.002 HIS F 113 PHE 0.021 0.002 PHE B 35 TYR 0.023 0.002 TYR C 69 ARG 0.018 0.001 ARG F 59 *********************** 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 156 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 116 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8313 (t0) cc_final: 0.7829 (t0) REVERT: C 73 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.7067 (t80) REVERT: D 110 PHE cc_start: 0.8818 (t80) cc_final: 0.8414 (t80) REVERT: E 5 TYR cc_start: 0.5936 (t80) cc_final: 0.5655 (t80) REVERT: E 50 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8664 (pm20) REVERT: E 94 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8260 (pt) REVERT: E 101 MET cc_start: 0.8122 (mmm) cc_final: 0.7865 (mmm) REVERT: E 105 TYR cc_start: 0.8677 (t80) cc_final: 0.8276 (t80) REVERT: F 39 PHE cc_start: 0.7328 (t80) cc_final: 0.7058 (t80) REVERT: F 55 GLU cc_start: 0.8403 (pt0) cc_final: 0.7770 (tm-30) REVERT: G 91 ILE cc_start: 0.3760 (mp) cc_final: 0.3226 (mt) REVERT: H 102 LEU cc_start: 0.8620 (tt) cc_final: 0.8295 (tp) outliers start: 40 outliers final: 26 residues processed: 143 average time/residue: 0.2045 time to fit residues: 43.5881 Evaluate side-chains 138 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 0.0030 chunk 119 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 32 optimal weight: 0.0070 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10683 Z= 0.187 Angle : 0.669 7.478 14450 Z= 0.349 Chirality : 0.044 0.175 1631 Planarity : 0.005 0.071 1849 Dihedral : 6.703 82.735 1408 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 25.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.26 % Allowed : 17.75 % Favored : 78.99 % 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: -1.65 (0.23), residues: 1274 helix: 0.07 (0.22), residues: 524 sheet: -1.26 (0.38), residues: 198 loop : -2.18 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 94 HIS 0.008 0.001 HIS F 113 PHE 0.034 0.002 PHE F 133 TYR 0.022 0.001 TYR C 69 ARG 0.009 0.000 ARG F 59 *********************** 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 171 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8317 (t0) cc_final: 0.7847 (t0) REVERT: D 110 PHE cc_start: 0.8796 (t80) cc_final: 0.8382 (t80) REVERT: E 5 TYR cc_start: 0.5734 (t80) cc_final: 0.5295 (t80) REVERT: E 50 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: E 94 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8098 (pt) REVERT: E 105 TYR cc_start: 0.8561 (t80) cc_final: 0.8284 (t80) REVERT: F 39 PHE cc_start: 0.7502 (t80) cc_final: 0.7241 (t80) REVERT: F 55 GLU cc_start: 0.8396 (pt0) cc_final: 0.7759 (tm-30) REVERT: F 74 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7174 (mt) REVERT: G 91 ILE cc_start: 0.3840 (mp) cc_final: 0.3297 (mt) REVERT: H 3 PHE cc_start: 0.7087 (m-10) cc_final: 0.6850 (m-10) outliers start: 38 outliers final: 19 residues processed: 162 average time/residue: 0.2039 time to fit residues: 48.8005 Evaluate side-chains 138 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.0370 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN B 152 ASN C 22 ASN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10683 Z= 0.181 Angle : 0.663 9.106 14450 Z= 0.344 Chirality : 0.044 0.163 1631 Planarity : 0.004 0.069 1849 Dihedral : 6.424 81.885 1408 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.03 % Allowed : 19.13 % Favored : 76.84 % 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: -1.46 (0.23), residues: 1274 helix: 0.30 (0.22), residues: 523 sheet: -1.14 (0.39), residues: 189 loop : -2.15 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 170 HIS 0.003 0.001 HIS B 108 PHE 0.026 0.002 PHE F 133 TYR 0.033 0.002 TYR F 75 ARG 0.011 0.000 ARG F 59 *********************** 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 177 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8278 (t0) cc_final: 0.7766 (t0) REVERT: A 106 ASP cc_start: 0.7628 (t70) cc_final: 0.7278 (m-30) REVERT: D 110 PHE cc_start: 0.8751 (t80) cc_final: 0.8338 (t80) REVERT: E 5 TYR cc_start: 0.5680 (t80) cc_final: 0.5277 (t80) REVERT: E 50 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: E 94 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8041 (pt) REVERT: E 101 MET cc_start: 0.8236 (mmm) cc_final: 0.8016 (mmm) REVERT: E 105 TYR cc_start: 0.8574 (t80) cc_final: 0.8322 (t80) REVERT: F 39 PHE cc_start: 0.7206 (t80) cc_final: 0.6964 (t80) REVERT: F 55 GLU cc_start: 0.8401 (pt0) cc_final: 0.7744 (tm-30) REVERT: F 74 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7066 (mt) REVERT: F 177 MET cc_start: 0.7020 (tmm) cc_final: 0.6678 (tmm) REVERT: G 91 ILE cc_start: 0.3894 (mp) cc_final: 0.3349 (mt) outliers start: 47 outliers final: 27 residues processed: 166 average time/residue: 0.1976 time to fit residues: 48.1105 Evaluate side-chains 148 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2853 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= 0.195 Angle : 0.668 8.940 14450 Z= 0.345 Chirality : 0.044 0.185 1631 Planarity : 0.004 0.069 1849 Dihedral : 6.328 81.918 1405 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.86 % Allowed : 20.24 % Favored : 75.90 % 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 (0.24), residues: 1274 helix: 0.37 (0.23), residues: 523 sheet: -1.20 (0.38), residues: 193 loop : -2.07 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.004 0.001 HIS B 108 PHE 0.035 0.002 PHE F 133 TYR 0.025 0.002 TYR F 75 ARG 0.004 0.000 ARG B 151 *********************** 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 166 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8237 (t0) cc_final: 0.7712 (t0) REVERT: D 110 PHE cc_start: 0.8753 (t80) cc_final: 0.8347 (t80) REVERT: D 153 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8411 (mm) REVERT: E 5 TYR cc_start: 0.5722 (t80) cc_final: 0.5341 (t80) REVERT: E 50 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: E 94 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8049 (pt) REVERT: E 101 MET cc_start: 0.8163 (mmm) cc_final: 0.7937 (mmm) REVERT: E 105 TYR cc_start: 0.8630 (t80) cc_final: 0.8321 (t80) REVERT: E 110 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6748 (mmp) REVERT: F 55 GLU cc_start: 0.8398 (pt0) cc_final: 0.7774 (tm-30) REVERT: F 177 MET cc_start: 0.6909 (tmm) cc_final: 0.6471 (tmm) REVERT: G 91 ILE cc_start: 0.3815 (mp) cc_final: 0.3313 (mt) outliers start: 45 outliers final: 31 residues processed: 155 average time/residue: 0.1786 time to fit residues: 41.4635 Evaluate side-chains 152 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.2980 chunk 13 optimal weight: 0.0570 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 55 optimal weight: 7.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10683 Z= 0.175 Angle : 0.652 8.829 14450 Z= 0.334 Chirality : 0.043 0.176 1631 Planarity : 0.004 0.071 1849 Dihedral : 6.149 80.642 1405 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.46 % Allowed : 20.67 % Favored : 74.87 % 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: -1.27 (0.24), residues: 1274 helix: 0.47 (0.22), residues: 525 sheet: -1.10 (0.38), residues: 193 loop : -2.06 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.003 0.001 HIS B 108 PHE 0.032 0.002 PHE F 39 TYR 0.022 0.001 TYR F 75 ARG 0.010 0.000 ARG B 151 *********************** 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 177 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 125 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.7255 (mmt) cc_final: 0.7042 (mmt) REVERT: A 35 ASN cc_start: 0.8391 (t0) cc_final: 0.7892 (t0) REVERT: A 106 ASP cc_start: 0.7648 (t70) cc_final: 0.7324 (m-30) REVERT: A 113 PHE cc_start: 0.4186 (t80) cc_final: 0.3706 (t80) REVERT: D 110 PHE cc_start: 0.8744 (t80) cc_final: 0.8344 (t80) REVERT: D 153 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8363 (mm) REVERT: E 5 TYR cc_start: 0.5551 (t80) cc_final: 0.5176 (t80) REVERT: E 50 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8601 (pm20) REVERT: E 94 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.7993 (pt) REVERT: E 101 MET cc_start: 0.8209 (mmm) cc_final: 0.7990 (mmm) REVERT: E 105 TYR cc_start: 0.8594 (t80) cc_final: 0.8283 (t80) REVERT: E 110 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6919 (mmp) REVERT: F 55 GLU cc_start: 0.8351 (pt0) cc_final: 0.7715 (tm-30) REVERT: F 73 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.4883 (t0) REVERT: F 191 MET cc_start: 0.6739 (mtm) cc_final: 0.6506 (mtt) REVERT: G 91 ILE cc_start: 0.3851 (mp) cc_final: 0.3356 (mt) outliers start: 52 outliers final: 37 residues processed: 162 average time/residue: 0.1795 time to fit residues: 43.7066 Evaluate side-chains 160 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 118 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 0.0070 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10683 Z= 0.177 Angle : 0.652 9.359 14450 Z= 0.335 Chirality : 0.043 0.180 1631 Planarity : 0.004 0.070 1849 Dihedral : 5.996 78.709 1405 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.37 % Allowed : 20.93 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.13 (0.24), residues: 1274 helix: 0.59 (0.23), residues: 523 sheet: -1.00 (0.38), residues: 198 loop : -1.97 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.012 0.001 HIS F 113 PHE 0.029 0.002 PHE F 133 TYR 0.021 0.002 TYR F 75 ARG 0.003 0.000 ARG G 76 *********************** 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 181 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 130 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7231 (mmt) cc_final: 0.6891 (mmt) REVERT: A 35 ASN cc_start: 0.8285 (t0) cc_final: 0.7742 (t0) REVERT: A 106 ASP cc_start: 0.7645 (t70) cc_final: 0.7324 (m-30) REVERT: A 113 PHE cc_start: 0.4296 (t80) cc_final: 0.3997 (t80) REVERT: A 142 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6947 (mt) REVERT: D 110 PHE cc_start: 0.8745 (t80) cc_final: 0.8352 (t80) REVERT: D 153 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8375 (mm) REVERT: E 5 TYR cc_start: 0.5544 (t80) cc_final: 0.5189 (t80) REVERT: E 94 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.7977 (pt) REVERT: E 101 MET cc_start: 0.8248 (mmm) cc_final: 0.8034 (mmm) REVERT: E 105 TYR cc_start: 0.8593 (t80) cc_final: 0.8280 (t80) REVERT: F 55 GLU cc_start: 0.8376 (pt0) cc_final: 0.7655 (tm-30) REVERT: F 73 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.4676 (t0) REVERT: F 74 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7175 (mt) REVERT: F 145 CYS cc_start: 0.6587 (t) cc_final: 0.6211 (t) REVERT: G 91 ILE cc_start: 0.3837 (mp) cc_final: 0.3358 (mt) outliers start: 51 outliers final: 36 residues processed: 170 average time/residue: 0.2063 time to fit residues: 51.6000 Evaluate side-chains 161 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 48 optimal weight: 0.0010 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10683 Z= 0.178 Angle : 0.678 9.444 14450 Z= 0.346 Chirality : 0.044 0.258 1631 Planarity : 0.004 0.072 1849 Dihedral : 5.950 78.156 1405 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.37 % Allowed : 21.27 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.04 (0.24), residues: 1274 helix: 0.68 (0.23), residues: 519 sheet: -1.00 (0.38), residues: 198 loop : -1.90 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 147 HIS 0.014 0.001 HIS F 113 PHE 0.031 0.002 PHE F 39 TYR 0.037 0.002 TYR F 75 ARG 0.003 0.000 ARG F 119 *********************** 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 180 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 129 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8365 (t0) cc_final: 0.7878 (t0) REVERT: A 106 ASP cc_start: 0.7638 (t70) cc_final: 0.7329 (m-30) REVERT: A 142 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6949 (mt) REVERT: D 110 PHE cc_start: 0.8747 (t80) cc_final: 0.8351 (t80) REVERT: D 153 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8454 (mm) REVERT: E 5 TYR cc_start: 0.5407 (t80) cc_final: 0.5054 (t80) REVERT: E 94 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.7949 (pt) REVERT: E 105 TYR cc_start: 0.8634 (t80) cc_final: 0.8300 (t80) REVERT: F 55 GLU cc_start: 0.8422 (pt0) cc_final: 0.7792 (tm-30) REVERT: F 73 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.4431 (t0) REVERT: F 177 MET cc_start: 0.6118 (tmm) cc_final: 0.5839 (tmm) REVERT: F 191 MET cc_start: 0.6891 (mtm) cc_final: 0.6614 (mtt) REVERT: G 91 ILE cc_start: 0.4005 (mp) cc_final: 0.3443 (mt) outliers start: 51 outliers final: 41 residues processed: 168 average time/residue: 0.1885 time to fit residues: 47.0629 Evaluate side-chains 166 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.0570 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 0.0030 chunk 75 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10683 Z= 0.175 Angle : 0.685 9.874 14450 Z= 0.351 Chirality : 0.045 0.252 1631 Planarity : 0.004 0.057 1849 Dihedral : 5.844 76.956 1405 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.77 % Allowed : 22.21 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.00 (0.24), residues: 1274 helix: 0.72 (0.22), residues: 521 sheet: -0.92 (0.38), residues: 194 loop : -1.92 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 147 HIS 0.009 0.001 HIS F 113 PHE 0.027 0.001 PHE F 133 TYR 0.032 0.001 TYR F 75 ARG 0.002 0.000 ARG D 194 ********************** 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 177 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8397 (t0) cc_final: 0.7804 (t0) REVERT: A 106 ASP cc_start: 0.7567 (t70) cc_final: 0.7247 (m-30) REVERT: A 113 PHE cc_start: 0.4284 (t80) cc_final: 0.3848 (t80) REVERT: A 142 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6917 (mt) REVERT: D 110 PHE cc_start: 0.8742 (t80) cc_final: 0.8350 (t80) REVERT: D 153 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8414 (mm) REVERT: E 5 TYR cc_start: 0.5314 (t80) cc_final: 0.4950 (t80) REVERT: E 105 TYR cc_start: 0.8606 (t80) cc_final: 0.8328 (t80) REVERT: F 55 GLU cc_start: 0.8406 (pt0) cc_final: 0.7821 (tm-30) REVERT: F 73 ASP cc_start: 0.6587 (t0) cc_final: 0.4420 (t0) REVERT: F 145 CYS cc_start: 0.6439 (t) cc_final: 0.5991 (t) REVERT: F 177 MET cc_start: 0.6270 (tmm) cc_final: 0.5887 (tmm) REVERT: F 188 ASP cc_start: 0.7972 (p0) cc_final: 0.7769 (p0) REVERT: H 86 SER cc_start: 0.8789 (p) cc_final: 0.8584 (t) REVERT: H 110 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7571 (mm) outliers start: 44 outliers final: 39 residues processed: 165 average time/residue: 0.1964 time to fit residues: 47.8113 Evaluate side-chains 165 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 16 TYR Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.0070 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.066703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.057031 restraints weight = 75281.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.058478 restraints weight = 50873.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.059505 restraints weight = 37771.242| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10683 Z= 0.178 Angle : 0.697 9.440 14450 Z= 0.357 Chirality : 0.045 0.263 1631 Planarity : 0.004 0.055 1849 Dihedral : 5.810 76.709 1405 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.77 % Allowed : 22.98 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.90 (0.24), residues: 1274 helix: 0.79 (0.22), residues: 522 sheet: -0.86 (0.39), residues: 194 loop : -1.86 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 147 HIS 0.009 0.001 HIS F 113 PHE 0.031 0.002 PHE F 39 TYR 0.029 0.002 TYR F 75 ARG 0.008 0.000 ARG D 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2370.64 seconds wall clock time: 43 minutes 34.18 seconds (2614.18 seconds total)