Starting phenix.real_space_refine on Tue Sep 24 19:33:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/09_2024/8ejk_28185.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/09_2024/8ejk_28185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/09_2024/8ejk_28185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/09_2024/8ejk_28185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/09_2024/8ejk_28185.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/09_2024/8ejk_28185.cif" } resolution = 3.4 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= 0.004 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 51 5.16 5 C 5462 2.51 5 N 1483 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8594 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1869 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2556 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 420 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1768 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1944 Classifications: {'peptide': 267} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 248} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2YB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.30, per 1000 atoms: 0.62 Number of scatterers: 8594 At special positions: 0 Unit cell: (97.37, 116.63, 132.68, 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 51 16.00 O 1598 8.00 N 1483 7.00 C 5462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.3% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.921A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.780A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.879A pdb=" N GLN A 90 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 93 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.558A pdb=" N ASP A 154 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 175 through 195 Processing helix chain 'A' and resid 215 through 235 Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.554A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.597A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'R' and resid 5 through 35 Proline residue: R 21 - end of helix Processing helix chain 'R' and resid 39 through 69 Proline residue: R 60 - end of helix Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 78 through 110 removed outlier: 3.529A pdb=" N VAL R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Proline residue: R 89 - end of helix removed outlier: 4.090A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 118 Processing helix chain 'R' and resid 119 through 146 removed outlier: 3.624A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL R 141 " --> pdb=" O HIS R 137 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU R 145 " --> pdb=" O VAL R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 191 Proline residue: R 181 - end of helix removed outlier: 3.740A pdb=" N LEU R 186 " --> pdb=" O ALA R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 212 Processing helix chain 'R' and resid 215 through 227 Processing helix chain 'R' and resid 227 through 236 removed outlier: 3.512A pdb=" N CYS R 236 " --> pdb=" O THR R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 250 removed outlier: 3.786A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 267 removed outlier: 4.374A pdb=" N ARG R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 272 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 4.677A pdb=" N VAL A 78 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG A 35 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE A 99 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 37 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 101 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 39 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASP A 103 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 98 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 134 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 100 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN A 136 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 102 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 131 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS A 206 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 133 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.345A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.797A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.031A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.953A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.643A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.732A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.628A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.651A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.706A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 3.722A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1206 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: 2.39 Time building geometry restraints manager: 2.60 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: 2808 1.34 - 1.47: 2189 1.47 - 1.59: 3717 1.59 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 8784 Sorted by residual: bond pdb=" C27 2YB R 401 " pdb=" C28 2YB R 401 " ideal model delta sigma weight residual 1.505 1.392 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C1 2YB R 401 " pdb=" C2 2YB R 401 " ideal model delta sigma weight residual 1.503 1.392 0.111 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C14 2YB R 401 " pdb=" C15 2YB R 401 " ideal model delta sigma weight residual 1.502 1.392 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C21 2YB R 401 " pdb=" C22 2YB R 401 " ideal model delta sigma weight residual 1.498 1.395 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C16 2YB R 401 " pdb=" C17 2YB R 401 " ideal model delta sigma weight residual 1.485 1.395 0.090 2.00e-02 2.50e+03 2.04e+01 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11718 1.92 - 3.83: 174 3.83 - 5.75: 29 5.75 - 7.66: 12 7.66 - 9.58: 2 Bond angle restraints: 11935 Sorted by residual: angle pdb=" N ASN E 194 " pdb=" CA ASN E 194 " pdb=" C ASN E 194 " ideal model delta sigma weight residual 108.60 115.15 -6.55 1.46e+00 4.69e-01 2.01e+01 angle pdb=" N SER E 193 " pdb=" CA SER E 193 " pdb=" C SER E 193 " ideal model delta sigma weight residual 111.36 115.78 -4.42 1.09e+00 8.42e-01 1.64e+01 angle pdb=" CA CYS R 79 " pdb=" C CYS R 79 " pdb=" N PRO R 80 " ideal model delta sigma weight residual 120.81 117.35 3.46 8.60e-01 1.35e+00 1.62e+01 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 113.28 107.55 5.73 1.57e+00 4.06e-01 1.33e+01 angle pdb=" N ARG E 191 " pdb=" CA ARG E 191 " pdb=" C ARG E 191 " ideal model delta sigma weight residual 113.72 108.47 5.25 1.52e+00 4.33e-01 1.19e+01 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 4835 23.80 - 47.61: 304 47.61 - 71.41: 23 71.41 - 95.21: 6 95.21 - 119.02: 1 Dihedral angle restraints: 5169 sinusoidal: 1948 harmonic: 3221 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 157.95 -64.95 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" C8 2YB R 401 " pdb=" C6 2YB R 401 " pdb=" C7 2YB R 401 " pdb=" O5 2YB R 401 " ideal model delta sinusoidal sigma weight residual 180.08 61.06 119.02 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C GLN B 17 " pdb=" N GLN B 17 " pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " ideal model delta harmonic sigma weight residual -122.60 -132.37 9.77 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 5166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1212 0.074 - 0.149: 126 0.149 - 0.223: 5 0.223 - 0.297: 0 0.297 - 0.372: 1 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CA GLN B 17 " pdb=" N GLN B 17 " pdb=" C GLN B 17 " pdb=" CB GLN B 17 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ASN R 272 " pdb=" N ASN R 272 " pdb=" C ASN R 272 " pdb=" CB ASN R 272 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CB ILE R 263 " pdb=" CA ILE R 263 " pdb=" CG1 ILE R 263 " pdb=" CG2 ILE R 263 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 1341 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.050 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO C 49 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 88 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO R 89 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 38 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C MET C 38 " -0.041 2.00e-02 2.50e+03 pdb=" O MET C 38 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 39 " 0.014 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 232 2.70 - 3.25: 8474 3.25 - 3.80: 13612 3.80 - 4.35: 17100 4.35 - 4.90: 29678 Nonbonded interactions: 69096 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASP B 27 " pdb=" NZ LYS C 29 " model vdw 2.187 3.120 nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.235 3.040 ... (remaining 69091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.000 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.004 0.113 8784 Z= 0.261 Angle : 0.613 9.576 11935 Z= 0.320 Chirality : 0.045 0.372 1344 Planarity : 0.005 0.077 1526 Dihedral : 14.172 119.016 3095 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.66 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1106 helix: 1.71 (0.27), residues: 369 sheet: 0.44 (0.32), residues: 302 loop : -0.47 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 PHE 0.016 0.001 PHE A 66 TYR 0.027 0.001 TYR B 59 ARG 0.004 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 11 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7554 (tm-30) REVERT: E 73 ASP cc_start: 0.7513 (t0) cc_final: 0.7283 (t0) REVERT: E 82 GLN cc_start: 0.8001 (tp40) cc_final: 0.7754 (mm110) REVERT: R 135 LEU cc_start: 0.9295 (mt) cc_final: 0.8892 (pp) REVERT: R 241 ASN cc_start: 0.9094 (m110) cc_final: 0.8617 (m-40) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1778 time to fit residues: 38.7286 Evaluate side-chains 132 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN E 167 HIS ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8784 Z= 0.178 Angle : 0.558 11.146 11935 Z= 0.287 Chirality : 0.044 0.241 1344 Planarity : 0.004 0.058 1526 Dihedral : 5.718 88.359 1239 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.79 % Allowed : 8.72 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1106 helix: 2.06 (0.26), residues: 376 sheet: 0.48 (0.32), residues: 294 loop : -0.37 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 PHE 0.019 0.001 PHE R 9 TYR 0.019 0.001 TYR B 59 ARG 0.003 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8196 (m-30) cc_final: 0.7990 (m-30) REVERT: A 235 TYR cc_start: 0.9159 (m-80) cc_final: 0.8859 (m-80) REVERT: B 20 ASP cc_start: 0.7944 (m-30) cc_final: 0.7623 (m-30) REVERT: B 45 MET cc_start: 0.8609 (mmm) cc_final: 0.8244 (mtp) REVERT: C 11 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7711 (tm-30) REVERT: C 42 GLU cc_start: 0.7913 (mp0) cc_final: 0.7366 (mp0) REVERT: E 82 GLN cc_start: 0.8016 (tp40) cc_final: 0.7776 (mm110) REVERT: R 241 ASN cc_start: 0.9031 (m110) cc_final: 0.8630 (m110) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 0.2356 time to fit residues: 50.0139 Evaluate side-chains 143 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 216 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8784 Z= 0.154 Angle : 0.533 10.216 11935 Z= 0.271 Chirality : 0.043 0.271 1344 Planarity : 0.004 0.056 1526 Dihedral : 5.646 89.800 1239 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.01 % Allowed : 12.08 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1106 helix: 2.19 (0.27), residues: 373 sheet: 0.61 (0.32), residues: 286 loop : -0.40 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS R 137 PHE 0.016 0.001 PHE R 9 TYR 0.009 0.001 TYR B 59 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8158 (m-30) cc_final: 0.7928 (m-30) REVERT: A 235 TYR cc_start: 0.9120 (m-80) cc_final: 0.8651 (m-80) REVERT: B 20 ASP cc_start: 0.7925 (m-30) cc_final: 0.7632 (m-30) REVERT: C 9 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7738 (tp) REVERT: C 11 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 42 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: R 54 LEU cc_start: 0.9261 (tp) cc_final: 0.9054 (tp) REVERT: R 259 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.8996 (ttpt) outliers start: 18 outliers final: 8 residues processed: 157 average time/residue: 0.1991 time to fit residues: 43.5892 Evaluate side-chains 142 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN E 186 GLN R 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8784 Z= 0.292 Angle : 0.574 8.333 11935 Z= 0.302 Chirality : 0.044 0.217 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.880 87.751 1239 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.24 % Allowed : 14.54 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1106 helix: 2.10 (0.27), residues: 376 sheet: 0.50 (0.32), residues: 275 loop : -0.33 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.016 0.002 PHE A 66 TYR 0.018 0.002 TYR A 107 ARG 0.002 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8256 (m-30) cc_final: 0.7980 (m-30) REVERT: B 20 ASP cc_start: 0.8082 (m-30) cc_final: 0.7784 (m-30) REVERT: B 291 ASP cc_start: 0.8177 (m-30) cc_final: 0.7324 (m-30) REVERT: C 9 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7748 (tp) REVERT: C 42 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: E 76 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8597 (mtmm) REVERT: R 241 ASN cc_start: 0.9058 (m110) cc_final: 0.8663 (m110) outliers start: 29 outliers final: 18 residues processed: 154 average time/residue: 0.1959 time to fit residues: 42.3013 Evaluate side-chains 147 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 0.0000 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 142 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8784 Z= 0.194 Angle : 0.555 13.585 11935 Z= 0.284 Chirality : 0.044 0.329 1344 Planarity : 0.004 0.052 1526 Dihedral : 5.805 89.223 1239 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.46 % Allowed : 16.00 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1106 helix: 2.10 (0.27), residues: 376 sheet: 0.49 (0.31), residues: 289 loop : -0.39 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 PHE 0.018 0.001 PHE R 9 TYR 0.016 0.001 TYR A 107 ARG 0.002 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8204 (m-30) cc_final: 0.7932 (m-30) REVERT: A 235 TYR cc_start: 0.9153 (m-80) cc_final: 0.8606 (m-80) REVERT: B 20 ASP cc_start: 0.7994 (m-30) cc_final: 0.7718 (m-30) REVERT: C 9 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7593 (tp) REVERT: C 15 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.7936 (mp) REVERT: C 42 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: E 73 ASP cc_start: 0.7497 (t0) cc_final: 0.7028 (t70) REVERT: R 59 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8469 (mt) REVERT: R 259 LYS cc_start: 0.9321 (ttpt) cc_final: 0.9050 (ptmt) outliers start: 22 outliers final: 12 residues processed: 153 average time/residue: 0.1992 time to fit residues: 42.7098 Evaluate side-chains 145 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8784 Z= 0.160 Angle : 0.551 14.227 11935 Z= 0.279 Chirality : 0.044 0.358 1344 Planarity : 0.004 0.049 1526 Dihedral : 5.604 86.144 1239 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.68 % Allowed : 16.67 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 1106 helix: 2.20 (0.27), residues: 373 sheet: 0.46 (0.31), residues: 294 loop : -0.36 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.020 0.001 PHE R 9 TYR 0.018 0.001 TYR A 107 ARG 0.002 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8162 (m-30) cc_final: 0.7896 (m-30) REVERT: A 229 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8494 (mt0) REVERT: A 235 TYR cc_start: 0.9150 (m-80) cc_final: 0.8646 (m-80) REVERT: B 20 ASP cc_start: 0.7968 (m-30) cc_final: 0.7683 (m-30) REVERT: B 45 MET cc_start: 0.8470 (mmm) cc_final: 0.8179 (mtp) REVERT: B 262 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7196 (mtt) REVERT: C 42 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: R 59 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8471 (mt) REVERT: R 259 LYS cc_start: 0.9279 (ttpt) cc_final: 0.8987 (ptmt) outliers start: 24 outliers final: 15 residues processed: 156 average time/residue: 0.1955 time to fit residues: 43.1232 Evaluate side-chains 150 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 142 GLN R 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8784 Z= 0.178 Angle : 0.566 15.049 11935 Z= 0.284 Chirality : 0.044 0.373 1344 Planarity : 0.004 0.056 1526 Dihedral : 5.575 85.589 1239 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.80 % Allowed : 17.34 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1106 helix: 2.24 (0.27), residues: 373 sheet: 0.47 (0.31), residues: 292 loop : -0.34 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 PHE 0.021 0.001 PHE R 9 TYR 0.018 0.001 TYR A 107 ARG 0.005 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8183 (m-30) cc_final: 0.7916 (m-30) REVERT: B 20 ASP cc_start: 0.7972 (m-30) cc_final: 0.7701 (m-30) REVERT: B 45 MET cc_start: 0.8468 (mmm) cc_final: 0.8215 (mtp) REVERT: C 42 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: E 76 LYS cc_start: 0.9072 (mtmm) cc_final: 0.8849 (mtmm) REVERT: R 59 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8471 (mt) REVERT: R 259 LYS cc_start: 0.9261 (ttpt) cc_final: 0.9013 (ptmt) outliers start: 25 outliers final: 16 residues processed: 160 average time/residue: 0.1993 time to fit residues: 44.0698 Evaluate side-chains 153 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8784 Z= 0.187 Angle : 0.577 15.597 11935 Z= 0.290 Chirality : 0.044 0.388 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.558 85.031 1239 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.57 % Allowed : 18.12 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1106 helix: 2.21 (0.27), residues: 373 sheet: 0.42 (0.31), residues: 289 loop : -0.34 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 PHE 0.022 0.001 PHE R 9 TYR 0.016 0.001 TYR A 107 ARG 0.005 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8192 (m-30) cc_final: 0.7909 (m-30) REVERT: A 235 TYR cc_start: 0.9133 (m-80) cc_final: 0.8606 (m-80) REVERT: B 20 ASP cc_start: 0.7943 (m-30) cc_final: 0.7669 (m-30) REVERT: B 45 MET cc_start: 0.8401 (mmm) cc_final: 0.8158 (mtp) REVERT: C 42 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: R 59 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8447 (mt) REVERT: R 241 ASN cc_start: 0.9118 (m110) cc_final: 0.8665 (m-40) outliers start: 23 outliers final: 16 residues processed: 154 average time/residue: 0.1866 time to fit residues: 40.4521 Evaluate side-chains 153 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.209 Angle : 0.589 16.091 11935 Z= 0.296 Chirality : 0.044 0.409 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.600 84.995 1239 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.80 % Allowed : 18.23 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1106 helix: 2.19 (0.27), residues: 373 sheet: 0.37 (0.31), residues: 289 loop : -0.37 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 PHE 0.023 0.001 PHE R 9 TYR 0.016 0.001 TYR A 107 ARG 0.006 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8215 (m-30) cc_final: 0.7925 (m-30) REVERT: A 235 TYR cc_start: 0.9152 (m-80) cc_final: 0.8638 (m-80) REVERT: B 20 ASP cc_start: 0.7961 (m-30) cc_final: 0.7690 (m-30) REVERT: C 42 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: E 82 GLN cc_start: 0.8049 (tp40) cc_final: 0.7833 (mm-40) REVERT: R 59 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8592 (mt) REVERT: R 241 ASN cc_start: 0.9140 (m110) cc_final: 0.8695 (m-40) outliers start: 25 outliers final: 18 residues processed: 155 average time/residue: 0.1889 time to fit residues: 41.3992 Evaluate side-chains 154 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 131 TRP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.0040 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8784 Z= 0.180 Angle : 0.596 16.666 11935 Z= 0.299 Chirality : 0.044 0.418 1344 Planarity : 0.004 0.055 1526 Dihedral : 5.536 83.596 1239 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.57 % Allowed : 18.57 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1106 helix: 2.18 (0.27), residues: 373 sheet: 0.39 (0.31), residues: 292 loop : -0.36 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 PHE 0.025 0.001 PHE R 9 TYR 0.021 0.001 TYR R 105 ARG 0.006 0.000 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8184 (m-30) cc_final: 0.7899 (m-30) REVERT: A 235 TYR cc_start: 0.9146 (m-80) cc_final: 0.8656 (m-80) REVERT: B 20 ASP cc_start: 0.7938 (m-30) cc_final: 0.7672 (m-30) REVERT: C 42 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: E 82 GLN cc_start: 0.8020 (tp40) cc_final: 0.7771 (mm110) REVERT: R 59 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8583 (mt) REVERT: R 241 ASN cc_start: 0.9133 (m110) cc_final: 0.8691 (m-40) outliers start: 23 outliers final: 19 residues processed: 153 average time/residue: 0.1890 time to fit residues: 40.4657 Evaluate side-chains 157 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 131 TRP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 142 GLN R 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.085605 restraints weight = 16654.150| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.66 r_work: 0.2982 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8784 Z= 0.181 Angle : 0.595 16.440 11935 Z= 0.298 Chirality : 0.044 0.392 1344 Planarity : 0.004 0.054 1526 Dihedral : 5.495 82.835 1239 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.68 % Allowed : 18.90 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1106 helix: 2.19 (0.27), residues: 373 sheet: 0.40 (0.31), residues: 292 loop : -0.37 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS E 232 PHE 0.024 0.001 PHE R 9 TYR 0.017 0.001 TYR R 105 ARG 0.006 0.000 ARG A 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2120.32 seconds wall clock time: 41 minutes 41.79 seconds (2501.79 seconds total)