Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 19:23:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/04_2023/7b6x_12057.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/04_2023/7b6x_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_12057/04_2023/7b6x_12057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/04_2023/7b6x_12057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/04_2023/7b6x_12057.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6x_12057/04_2023/7b6x_12057.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 5.92, 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: 4.73 Conformation dependent library (CDL) restraints added in 1.6 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: 0.46 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: 2.85 Time building geometry restraints manager: 5.10 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: 3.740 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: 14.670 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.130 Find NCS groups from input model: 0.400 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.2355 time to fit residues: 48.7524 Evaluate side-chains 102 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1386 time to fit residues: 2.0500 ------------------------------------------------------------------------------- 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: 0.6980 chunk 93 optimal weight: 4.9990 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: 0.6378 ------------------------------------------------------------------------------- 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: 0.7143 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 10683 Z= 0.224 Angle : 0.742 7.959 14450 Z= 0.390 Chirality : 0.047 0.235 1631 Planarity : 0.005 0.075 1849 Dihedral : 7.241 82.793 1405 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 28.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer Outliers : 0.94 % 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: -2.17 (0.23), residues: 1274 helix: -0.47 (0.21), residues: 532 sheet: -1.39 (0.38), residues: 193 loop : -2.42 (0.25), residues: 549 *********************** 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 145 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.269 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 141 average time/residue: 0.2206 time to fit residues: 44.7206 Evaluate side-chains 113 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1638 time to fit residues: 3.7677 ------------------------------------------------------------------------------- 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: 4.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 ** 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: 0.7131 moved from start: 0.2281 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= 0.201 Angle : 0.687 8.358 14450 Z= 0.360 Chirality : 0.045 0.216 1631 Planarity : 0.005 0.072 1849 Dihedral : 6.766 82.484 1405 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 2.32 % 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: -0.02 (0.22), residues: 523 sheet: -1.28 (0.39), residues: 190 loop : -2.21 (0.26), residues: 561 *********************** 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 157 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.316 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 148 average time/residue: 0.2049 time to fit residues: 44.5779 Evaluate side-chains 120 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1038 time to fit residues: 3.4194 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 77 ASN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** F 90 GLN ** 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: 0.7137 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 10683 Z= 0.203 Angle : 0.682 8.673 14450 Z= 0.357 Chirality : 0.044 0.197 1631 Planarity : 0.005 0.070 1849 Dihedral : 6.570 82.702 1405 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 3.34 % 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: -1.56 (0.24), residues: 1274 helix: 0.13 (0.22), residues: 527 sheet: -1.16 (0.39), residues: 199 loop : -2.14 (0.26), residues: 548 *********************** 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 169 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 156 average time/residue: 0.2156 time to fit residues: 49.1578 Evaluate side-chains 139 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1393 time to fit residues: 7.5008 ------------------------------------------------------------------------------- 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: 5.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** F 32 GLN ** 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: 0.7143 moved from start: 0.2603 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= 0.213 Angle : 0.690 11.146 14450 Z= 0.359 Chirality : 0.045 0.264 1631 Planarity : 0.005 0.070 1849 Dihedral : 6.609 83.011 1405 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer Outliers : 1.80 % 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 (0.24), residues: 1274 helix: 0.26 (0.23), residues: 523 sheet: -1.17 (0.38), residues: 199 loop : -2.10 (0.26), residues: 552 *********************** 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 145 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 136 average time/residue: 0.1931 time to fit residues: 39.5893 Evaluate side-chains 123 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1115 time to fit residues: 3.7865 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** 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: 0.7142 moved from start: 0.2765 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= 0.208 Angle : 0.673 10.023 14450 Z= 0.351 Chirality : 0.044 0.169 1631 Planarity : 0.005 0.068 1849 Dihedral : 6.423 82.740 1405 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 27.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer Outliers : 2.06 % 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: -1.40 (0.24), residues: 1274 helix: 0.26 (0.22), residues: 528 sheet: -1.12 (0.38), residues: 199 loop : -2.04 (0.27), residues: 547 *********************** 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 145 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 139 average time/residue: 0.2107 time to fit residues: 43.3174 Evaluate side-chains 126 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1024 time to fit residues: 3.4578 ------------------------------------------------------------------------------- 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: 0.8980 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 146 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: 0.7134 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10683 Z= 0.196 Angle : 0.673 9.519 14450 Z= 0.349 Chirality : 0.044 0.174 1631 Planarity : 0.004 0.069 1849 Dihedral : 6.310 81.295 1405 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer Outliers : 1.89 % 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: -1.35 (0.24), residues: 1274 helix: 0.36 (0.22), residues: 528 sheet: -1.15 (0.38), residues: 200 loop : -2.05 (0.27), residues: 546 *********************** 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 150 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 142 average time/residue: 0.2169 time to fit residues: 45.3928 Evaluate side-chains 128 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1078 time to fit residues: 4.3137 ------------------------------------------------------------------------------- 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: 0.5980 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.0270 chunk 93 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 146 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3177 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= 0.184 Angle : 0.677 10.568 14450 Z= 0.348 Chirality : 0.044 0.186 1631 Planarity : 0.004 0.068 1849 Dihedral : 6.174 79.970 1405 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer Outliers : 1.20 % 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: -1.25 (0.24), residues: 1274 helix: 0.43 (0.23), residues: 528 sheet: -1.13 (0.38), residues: 201 loop : -1.97 (0.27), residues: 545 *********************** 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 152 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 145 average time/residue: 0.2135 time to fit residues: 45.2144 Evaluate side-chains 129 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1021 time to fit residues: 3.0951 ------------------------------------------------------------------------------- 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: 0.9980 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 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: 0.7116 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10683 Z= 0.199 Angle : 0.701 9.861 14450 Z= 0.361 Chirality : 0.045 0.230 1631 Planarity : 0.004 0.070 1849 Dihedral : 6.168 79.325 1405 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 26.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 1.29 % 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: -1.23 (0.24), residues: 1274 helix: 0.42 (0.22), residues: 528 sheet: -1.05 (0.38), residues: 200 loop : -1.96 (0.27), residues: 546 *********************** 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 141 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 132 average time/residue: 0.2037 time to fit residues: 39.7339 Evaluate side-chains 125 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.397 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1072 time to fit residues: 3.3485 ------------------------------------------------------------------------------- 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: 0.8980 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** B 77 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: 0.7104 moved from start: 0.3406 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= 0.188 Angle : 0.696 9.258 14450 Z= 0.357 Chirality : 0.045 0.224 1631 Planarity : 0.004 0.068 1849 Dihedral : 6.112 78.111 1405 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer Outliers : 0.69 % 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: -1.26 (0.24), residues: 1274 helix: 0.43 (0.22), residues: 524 sheet: -1.12 (0.38), residues: 200 loop : -1.98 (0.26), residues: 550 ********************** 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 135 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 132 average time/residue: 0.2108 time to fit residues: 42.0197 Evaluate side-chains 122 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1051 time to fit residues: 2.7676 ------------------------------------------------------------------------------- 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: 0.2980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.0270 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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** F 113 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.066571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.056697 restraints weight = 75113.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.058109 restraints weight = 50965.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.059149 restraints weight = 37986.784| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3647 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 : 0.684 9.176 14450 Z= 0.353 Chirality : 0.045 0.220 1631 Planarity : 0.004 0.069 1849 Dihedral : 5.939 77.110 1405 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.46 % Favored : 92.46 % Rotamer Outliers : 0.60 % 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: -1.21 (0.24), residues: 1274 helix: 0.48 (0.22), residues: 526 sheet: -1.17 (0.38), residues: 201 loop : -1.93 (0.27), residues: 547 =============================================================================== Job complete usr+sys time: 2210.95 seconds wall clock time: 41 minutes 19.40 seconds (2479.40 seconds total)