Starting phenix.real_space_refine on Thu Jan 18 11:11:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/01_2024/8ejk_28185_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/01_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_28185/01_2024/8ejk_28185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/01_2024/8ejk_28185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/01_2024/8ejk_28185_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejk_28185/01_2024/8ejk_28185_updated.pdb" } 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 Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8594 Number of models: 1 Model: "" Number of chains: 5 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: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1981 Unusual residues: {'2YB': 1} Classifications: {'peptide': 267, 'undetermined': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 248, None: 1} Not linked: pdbres="GLY R 280 " pdbres="2YB R 401 " 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 Time building chain proxies: 5.03, per 1000 atoms: 0.59 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 - 3.50 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 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... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 33.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.554A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'C' and resid 6 through 23 removed outlier: 4.030A pdb=" N ALA C 23 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'R' and resid 5 through 35 Proline residue: R 21 - end of helix Processing helix chain 'R' and resid 40 through 68 Proline residue: R 60 - end of helix Processing helix chain 'R' and resid 76 through 109 Proline residue: R 80 - end of helix removed outlier: 3.774A pdb=" N VAL R 84 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE R 87 " --> pdb=" O VAL R 84 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE R 88 " --> pdb=" O ALA R 85 " (cutoff:3.500A) Proline residue: R 89 - end of helix removed outlier: 3.757A pdb=" N ALA R 92 " --> pdb=" O PRO R 89 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY R 93 " --> pdb=" O LEU R 90 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU R 97 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA R 109 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 117 Processing helix chain 'R' and resid 120 through 145 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 176 through 190 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 192 through 211 Processing helix chain 'R' and resid 216 through 235 removed outlier: 3.573A pdb=" N GLY R 228 " --> pdb=" O TRP R 224 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA R 229 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 249 Processing helix chain 'R' and resid 255 through 271 removed outlier: 4.127A pdb=" N SER R 268 " --> pdb=" O THR R 264 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL R 269 " --> pdb=" O GLY R 265 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 203 through 207 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) removed outlier: 4.212A pdb=" N ALA A 97 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU A 36 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS A 74 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU A 38 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 76 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.541A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, 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= D, 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= E, first strand: chain 'B' and resid 198 through 203 removed outlier: 4.212A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) 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= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.736A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) 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= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.481A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (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= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.801A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.292A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'E' and resid 146 through 150 removed outlier: 6.193A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL E 149 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLU E 246 " --> pdb=" O VAL E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.636A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1068 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: 2.55 Time building geometry restraints manager: 3.38 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: 99.97 - 106.78: 235 106.78 - 113.58: 4753 113.58 - 120.39: 3278 120.39 - 127.20: 3568 127.20 - 134.00: 101 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: 239 2.70 - 3.25: 8489 3.25 - 3.80: 13636 3.80 - 4.35: 17194 4.35 - 4.90: 29698 Nonbonded interactions: 69256 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.166 2.440 nonbonded pdb=" OD1 ASP B 27 " pdb=" NZ LYS C 29 " model vdw 2.187 2.520 nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.212 2.440 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.235 2.440 ... (remaining 69251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.440 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 26.520 Find NCS groups from input model: 0.270 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- 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= 0.252 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 : 0.986 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: 0.1978 time to fit residues: 42.7308 Evaluate side-chains 132 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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: 1.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN R 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.0779 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 : 0.526 11.122 11935 Z= 0.267 Chirality : 0.043 0.240 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.646 86.941 1239 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.79 % Allowed : 9.17 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 1106 helix: 1.86 (0.27), residues: 375 sheet: 0.41 (0.32), residues: 304 loop : -0.42 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.019 0.001 PHE R 9 TYR 0.016 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 152 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 ASP cc_start: 0.7940 (m-30) cc_final: 0.7624 (m-30) REVERT: B 45 MET cc_start: 0.8610 (mmm) cc_final: 0.8273 (mtp) REVERT: C 11 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 42 GLU cc_start: 0.7953 (mp0) cc_final: 0.7399 (mp0) REVERT: E 82 GLN cc_start: 0.8026 (tp40) cc_final: 0.7785 (mm110) REVERT: E 140 MET cc_start: 0.8615 (mmm) cc_final: 0.7925 (mmm) REVERT: E 160 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7729 (mtm110) REVERT: R 241 ASN cc_start: 0.9029 (m110) cc_final: 0.8720 (m-40) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 0.1935 time to fit residues: 39.7411 Evaluate side-chains 140 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 262 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 175 ASP 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: 0.7980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN E 82 GLN E 167 HIS R 23 ASN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8784 Z= 0.332 Angle : 0.574 9.637 11935 Z= 0.299 Chirality : 0.044 0.226 1344 Planarity : 0.004 0.062 1526 Dihedral : 5.887 83.261 1239 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.68 % Allowed : 12.64 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1106 helix: 1.69 (0.27), residues: 375 sheet: 0.31 (0.31), residues: 302 loop : -0.38 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.017 0.001 PHE A 66 TYR 0.014 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 164 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8078 (mmt90) cc_final: 0.7835 (mmt90) REVERT: B 20 ASP cc_start: 0.8096 (m-30) cc_final: 0.7818 (m-30) REVERT: B 45 MET cc_start: 0.8616 (mmm) cc_final: 0.8268 (mtp) REVERT: B 57 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8198 (pttt) REVERT: B 258 ASP cc_start: 0.7173 (t0) cc_final: 0.6888 (t0) REVERT: C 11 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7682 (tm-30) REVERT: C 42 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: E 73 ASP cc_start: 0.7515 (t0) cc_final: 0.7213 (t0) REVERT: E 82 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7767 (mm110) REVERT: E 140 MET cc_start: 0.8846 (mmm) cc_final: 0.7958 (mmm) REVERT: R 241 ASN cc_start: 0.9063 (m110) cc_final: 0.8722 (m-40) outliers start: 24 outliers final: 11 residues processed: 151 average time/residue: 0.2109 time to fit residues: 45.0481 Evaluate side-chains 144 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 57 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 175 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8784 Z= 0.211 Angle : 0.528 9.851 11935 Z= 0.271 Chirality : 0.043 0.313 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.701 84.601 1239 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.35 % Allowed : 15.55 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1106 helix: 1.78 (0.27), residues: 375 sheet: 0.32 (0.31), residues: 302 loop : -0.37 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE R 9 TYR 0.010 0.001 TYR E 102 ARG 0.002 0.000 ARG A 24 *********************** 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 165 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7833 (mmt90) REVERT: B 20 ASP cc_start: 0.8078 (m-30) cc_final: 0.7807 (m-30) REVERT: B 45 MET cc_start: 0.8566 (mmm) cc_final: 0.8326 (mtp) REVERT: B 291 ASP cc_start: 0.8181 (m-30) cc_final: 0.7331 (m-30) REVERT: C 9 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7724 (tp) REVERT: C 11 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7863 (tm-30) REVERT: C 42 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: E 73 ASP cc_start: 0.7363 (t0) cc_final: 0.7078 (t70) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 0.2019 time to fit residues: 43.3518 Evaluate side-chains 147 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU 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 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 E residue 91 THR Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 175 ASP 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: 1.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8784 Z= 0.260 Angle : 0.544 10.398 11935 Z= 0.283 Chirality : 0.044 0.318 1344 Planarity : 0.004 0.062 1526 Dihedral : 5.690 83.184 1239 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.80 % Allowed : 17.00 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1106 helix: 1.69 (0.27), residues: 375 sheet: 0.28 (0.31), residues: 302 loop : -0.36 (0.32), residues: 429 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 0.011 0.001 TYR A 204 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 160 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8807 (pt0) cc_final: 0.8492 (pt0) REVERT: B 20 ASP cc_start: 0.8100 (m-30) cc_final: 0.7821 (m-30) REVERT: B 45 MET cc_start: 0.8567 (mmm) cc_final: 0.8333 (mtp) REVERT: B 291 ASP cc_start: 0.8190 (m-30) cc_final: 0.7938 (m-30) REVERT: C 9 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7672 (tp) REVERT: C 11 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 42 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: E 73 ASP cc_start: 0.7396 (t0) cc_final: 0.7027 (t70) REVERT: E 140 MET cc_start: 0.9015 (mmm) cc_final: 0.8035 (mmm) REVERT: R 59 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8489 (mt) REVERT: R 135 LEU cc_start: 0.9510 (mt) cc_final: 0.9245 (mt) REVERT: R 241 ASN cc_start: 0.8962 (m110) cc_final: 0.8581 (m110) outliers start: 25 outliers final: 16 residues processed: 150 average time/residue: 0.1939 time to fit residues: 40.9742 Evaluate side-chains 148 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU 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 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 E residue 91 THR Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 175 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8784 Z= 0.219 Angle : 0.546 14.106 11935 Z= 0.278 Chirality : 0.044 0.402 1344 Planarity : 0.004 0.061 1526 Dihedral : 5.632 83.499 1239 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 17.90 % 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: 0.77 (0.26), residues: 1106 helix: 1.73 (0.27), residues: 374 sheet: 0.29 (0.31), residues: 302 loop : -0.33 (0.32), residues: 430 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 0.020 0.001 PHE R 9 TYR 0.012 0.001 TYR A 204 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 164 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8814 (pt0) cc_final: 0.8511 (pt0) REVERT: B 20 ASP cc_start: 0.8090 (m-30) cc_final: 0.7814 (m-30) REVERT: B 45 MET cc_start: 0.8510 (mmm) cc_final: 0.8291 (mtp) REVERT: C 9 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7605 (tp) REVERT: C 11 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7849 (tm-30) REVERT: C 42 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: E 73 ASP cc_start: 0.7347 (t0) cc_final: 0.6915 (t70) REVERT: E 140 MET cc_start: 0.8925 (mmm) cc_final: 0.7969 (mmm) REVERT: R 59 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8470 (mt) REVERT: R 259 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9135 (ttpt) outliers start: 25 outliers final: 16 residues processed: 153 average time/residue: 0.2026 time to fit residues: 43.2359 Evaluate side-chains 151 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU 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 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 E residue 91 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1574 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= 0.227 Angle : 0.562 14.792 11935 Z= 0.283 Chirality : 0.044 0.401 1344 Planarity : 0.004 0.059 1526 Dihedral : 5.597 82.811 1239 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.68 % Allowed : 18.46 % 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: 0.71 (0.26), residues: 1106 helix: 1.69 (0.27), residues: 374 sheet: 0.22 (0.31), residues: 307 loop : -0.34 (0.32), residues: 425 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 0.020 0.001 PHE R 9 TYR 0.012 0.001 TYR A 204 ARG 0.006 0.000 ARG A 24 *********************** 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 157 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8809 (pt0) cc_final: 0.8492 (pt0) REVERT: B 20 ASP cc_start: 0.8094 (m-30) cc_final: 0.7814 (m-30) REVERT: C 11 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7835 (tm-30) REVERT: C 42 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: E 73 ASP cc_start: 0.7335 (t0) cc_final: 0.6860 (t70) REVERT: E 82 GLN cc_start: 0.8088 (tp40) cc_final: 0.7861 (mm110) REVERT: E 140 MET cc_start: 0.8947 (mmm) cc_final: 0.8005 (mmm) REVERT: R 59 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8459 (mt) REVERT: R 259 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9058 (ttpt) outliers start: 24 outliers final: 15 residues processed: 148 average time/residue: 0.2018 time to fit residues: 41.4079 Evaluate side-chains 149 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU 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 C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8784 Z= 0.162 Angle : 0.548 15.332 11935 Z= 0.270 Chirality : 0.042 0.412 1344 Planarity : 0.004 0.053 1526 Dihedral : 5.474 84.869 1239 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.35 % Allowed : 18.90 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1106 helix: 1.79 (0.27), residues: 374 sheet: 0.31 (0.31), residues: 310 loop : -0.33 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 PHE 0.023 0.001 PHE R 9 TYR 0.015 0.001 TYR A 107 ARG 0.004 0.000 ARG A 24 *********************** 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 161 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8777 (pt0) cc_final: 0.8461 (pt0) REVERT: B 20 ASP cc_start: 0.8058 (m-30) cc_final: 0.7789 (m-30) REVERT: C 11 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7872 (tm-30) REVERT: C 42 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: E 82 GLN cc_start: 0.8069 (tp40) cc_final: 0.7845 (mm110) REVERT: E 140 MET cc_start: 0.8944 (mmm) cc_final: 0.8693 (mmm) REVERT: R 59 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8431 (mt) outliers start: 21 outliers final: 15 residues processed: 152 average time/residue: 0.1908 time to fit residues: 40.5633 Evaluate side-chains 146 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU 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 175 ASP 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: 9.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 77 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 75 GLN E 82 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8784 Z= 0.150 Angle : 0.548 15.594 11935 Z= 0.271 Chirality : 0.042 0.395 1344 Planarity : 0.004 0.058 1526 Dihedral : 5.339 86.224 1239 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.80 % Allowed : 18.46 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1106 helix: 1.90 (0.27), residues: 374 sheet: 0.36 (0.31), residues: 302 loop : -0.38 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.023 0.001 PHE R 9 TYR 0.017 0.001 TYR A 107 ARG 0.004 0.000 ARG A 24 *********************** 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 166 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8774 (pt0) cc_final: 0.8446 (pt0) REVERT: B 20 ASP cc_start: 0.7935 (m-30) cc_final: 0.7629 (m-30) REVERT: B 45 MET cc_start: 0.8601 (mmm) cc_final: 0.8326 (mtp) REVERT: C 11 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7895 (tm-30) REVERT: C 42 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: E 82 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7736 (mm110) REVERT: E 140 MET cc_start: 0.8929 (mmm) cc_final: 0.8696 (mmm) REVERT: R 59 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8450 (mt) REVERT: R 259 LYS cc_start: 0.9269 (ptpt) cc_final: 0.8986 (ptpp) outliers start: 25 outliers final: 19 residues processed: 155 average time/residue: 0.1896 time to fit residues: 41.7459 Evaluate side-chains 153 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE 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 262 MET 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 E residue 91 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 123 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 175 ASP 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: 6.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 75 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8784 Z= 0.337 Angle : 0.617 15.317 11935 Z= 0.313 Chirality : 0.046 0.403 1344 Planarity : 0.004 0.063 1526 Dihedral : 5.643 82.150 1239 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.57 % Allowed : 19.35 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1106 helix: 1.66 (0.27), residues: 374 sheet: 0.15 (0.31), residues: 307 loop : -0.43 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS E 232 PHE 0.021 0.002 PHE R 9 TYR 0.021 0.002 TYR A 107 ARG 0.004 0.000 ARG A 24 ********************** 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 147 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.8108 (m-30) cc_final: 0.7797 (m-30) REVERT: B 45 MET cc_start: 0.8658 (mmm) cc_final: 0.8300 (mtp) REVERT: C 11 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7826 (tm-30) REVERT: C 42 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: E 82 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7678 (mm110) REVERT: E 140 MET cc_start: 0.8993 (mmm) cc_final: 0.7925 (mmm) REVERT: R 59 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8574 (mt) REVERT: R 241 ASN cc_start: 0.8899 (m-40) cc_final: 0.8538 (m110) REVERT: R 259 LYS cc_start: 0.9293 (ptpt) cc_final: 0.9003 (ptpp) outliers start: 23 outliers final: 19 residues processed: 139 average time/residue: 0.2248 time to fit residues: 43.2255 Evaluate side-chains 141 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE 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 186 ASP Chi-restraints excluded: chain B residue 228 ASP 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 E residue 91 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 123 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 175 ASP 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: 8.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.0370 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 0.0030 overall best weight: 0.5668 ------------------------------------------------------------------------------- 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** R 23 ASN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.085807 restraints weight = 16610.060| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.60 r_work: 0.2995 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8784 Z= 0.148 Angle : 0.556 16.140 11935 Z= 0.274 Chirality : 0.043 0.402 1344 Planarity : 0.004 0.061 1526 Dihedral : 5.403 87.512 1239 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.24 % Allowed : 19.91 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1106 helix: 1.83 (0.27), residues: 374 sheet: 0.37 (0.31), residues: 303 loop : -0.49 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 PHE 0.018 0.001 PHE R 142 TYR 0.017 0.001 TYR A 107 ARG 0.004 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.86 seconds wall clock time: 38 minutes 40.11 seconds (2320.11 seconds total)