Starting phenix.real_space_refine on Fri Feb 16 00:51:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/02_2024/7s0f_24789_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/02_2024/7s0f_24789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/02_2024/7s0f_24789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/02_2024/7s0f_24789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/02_2024/7s0f_24789_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0f_24789/02_2024/7s0f_24789_trim_updated.pdb" } resolution = 2.96 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= 1.053 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4461 2.51 5 N 1192 2.21 5 O 1293 1.98 5 H 6887 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ASP 87": "OD1" <-> "OD2" Residue "R ASP 138": "OD1" <-> "OD2" Residue "R ASP 184": "OD1" <-> "OD2" Residue "R PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13885 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4273 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5098 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3540 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 959 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.18, per 1000 atoms: 0.45 Number of scatterers: 13885 At special positions: 0 Unit cell: (85.88, 98.762, 132.041, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1293 8.00 N 1192 7.00 C 4461 6.00 H 6887 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 199 " distance=2.03 Simple disulfide: pdb=" SG CYS R 192 " - pdb=" SG CYS R 198 " distance=2.03 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: 10.22 Conformation dependent library (CDL) restraints added in 1.3 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 42.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'R' and resid 47 through 68 removed outlier: 3.824A pdb=" N VAL R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 104 removed outlier: 5.018A pdb=" N VAL R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 110 through 144 removed outlier: 3.584A pdb=" N CYS R 133 " --> pdb=" O ILE R 129 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 152 Processing helix chain 'R' and resid 155 through 178 removed outlier: 4.144A pdb=" N LEU R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 190 through 194 Processing helix chain 'R' and resid 205 through 215 Processing helix chain 'R' and resid 217 through 238 Processing helix chain 'R' and resid 284 through 315 removed outlier: 3.523A pdb=" N LEU R 289 " --> pdb=" O GLU R 285 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 305 - end of helix removed outlier: 3.617A pdb=" N VAL R 309 " --> pdb=" O PRO R 305 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE R 311 " --> pdb=" O PHE R 307 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL R 314 " --> pdb=" O ASN R 310 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE R 315 " --> pdb=" O ILE R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 343 removed outlier: 3.661A pdb=" N ASN R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER R 336 " --> pdb=" O GLY R 332 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA R 337 " --> pdb=" O TYR R 333 " (cutoff:3.500A) Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 347 through 355 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.921A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.530A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.168A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.841A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.997A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.766A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.004A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.805A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.740A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.983A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 981 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: 5.25 Time building geometry restraints manager: 10.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6859 1.03 - 1.23: 30 1.23 - 1.42: 3002 1.42 - 1.62: 4062 1.62 - 1.81: 72 Bond restraints: 14025 Sorted by residual: bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.437 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.417 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 1.457 1.491 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" CAE 5FW R 401 " pdb=" CAH 5FW R 401 " ideal model delta sigma weight residual 1.515 1.546 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" CAG 5FW R 401 " pdb=" CAJ 5FW R 401 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 14020 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.21: 256 107.21 - 113.90: 16586 113.90 - 120.58: 4737 120.58 - 127.27: 3614 127.27 - 133.96: 75 Bond angle restraints: 25268 Sorted by residual: angle pdb=" CAJ 5FW R 401 " pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 114.52 109.05 5.47 3.00e+00 1.11e-01 3.33e+00 angle pdb=" C LEU R 175 " pdb=" CA LEU R 175 " pdb=" CB LEU R 175 " ideal model delta sigma weight residual 113.49 110.32 3.17 1.82e+00 3.02e-01 3.04e+00 angle pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 113.60 116.66 -3.06 1.90e+00 2.77e-01 2.60e+00 angle pdb=" C GLN B 9 " pdb=" N GLU B 10 " pdb=" CA GLU B 10 " ideal model delta sigma weight residual 120.28 118.02 2.26 1.44e+00 4.82e-01 2.47e+00 angle pdb=" C HIS A 188 " pdb=" N PHE A 189 " pdb=" CA PHE A 189 " ideal model delta sigma weight residual 121.85 119.23 2.62 1.77e+00 3.19e-01 2.19e+00 ... (remaining 25263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 5990 16.39 - 32.78: 438 32.78 - 49.17: 123 49.17 - 65.56: 36 65.56 - 81.95: 11 Dihedral angle restraints: 6598 sinusoidal: 3503 harmonic: 3095 Sorted by residual: dihedral pdb=" CA LYS B 127 " pdb=" C LYS B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA THR B 128 " pdb=" C THR B 128 " pdb=" N ARG B 129 " pdb=" CA ARG B 129 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP A 193 " pdb=" CB ASP A 193 " pdb=" CG ASP A 193 " pdb=" OD1 ASP A 193 " ideal model delta sinusoidal sigma weight residual -30.00 -84.11 54.11 1 2.00e+01 2.50e-03 9.93e+00 ... (remaining 6595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 975 0.058 - 0.115: 120 0.115 - 0.173: 13 0.173 - 0.231: 0 0.231 - 0.289: 1 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.58 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1106 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 218 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO R 219 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 219 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 219 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 95 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO R 96 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 96 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 96 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO A 282 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.014 5.00e-02 4.00e+02 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 930 2.22 - 2.81: 29515 2.81 - 3.41: 36251 3.41 - 4.00: 48732 4.00 - 4.60: 75501 Nonbonded interactions: 190929 Sorted by model distance: nonbonded pdb=" HG1 THR B 274 " pdb=" O VAL B 315 " model vdw 1.623 1.850 nonbonded pdb=" HE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 1.653 1.850 nonbonded pdb=" O LEU R 72 " pdb="HD22 ASN R 77 " model vdw 1.689 1.850 nonbonded pdb=" OE1 GLU A 298 " pdb=" H GLU A 298 " model vdw 1.713 1.850 nonbonded pdb=" O LYS A 277 " pdb=" H SER A 281 " model vdw 1.720 1.850 ... (remaining 190924 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: 0.990 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: 0.210 Extract box with map and model: 4.130 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 46.790 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.003 0.084 7138 Z= 0.181 Angle : 0.449 5.474 9675 Z= 0.261 Chirality : 0.039 0.289 1109 Planarity : 0.002 0.030 1223 Dihedral : 13.976 81.945 2550 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 1.74 % Allowed : 13.50 % Favored : 84.76 % 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: -1.72 (0.25), residues: 880 helix: -0.02 (0.24), residues: 380 sheet: -1.28 (0.32), residues: 181 loop : -2.36 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.009 0.001 PHE B 151 TYR 0.006 0.001 TYR B 105 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 205 ARG cc_start: 0.6946 (ttm110) cc_final: 0.6077 (ttt-90) REVERT: R 233 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6728 (mm-30) REVERT: R 236 GLU cc_start: 0.7471 (tt0) cc_final: 0.7086 (tt0) REVERT: R 240 LYS cc_start: 0.6338 (mmtt) cc_final: 0.5972 (mmtp) REVERT: B 18 ILE cc_start: 0.7565 (mt) cc_final: 0.7319 (mt) REVERT: B 42 ARG cc_start: 0.7522 (mmm160) cc_final: 0.7281 (tpt-90) REVERT: B 172 GLU cc_start: 0.7788 (tt0) cc_final: 0.7569 (tt0) REVERT: B 226 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 258 ASP cc_start: 0.7932 (t0) cc_final: 0.7731 (t0) REVERT: B 331 SER cc_start: 0.9120 (t) cc_final: 0.8665 (t) REVERT: B 333 ASP cc_start: 0.7904 (p0) cc_final: 0.7688 (p0) REVERT: A 17 LYS cc_start: 0.7205 (mtpp) cc_final: 0.6967 (mtmm) REVERT: A 29 LYS cc_start: 0.8309 (tttt) cc_final: 0.7988 (tmtm) REVERT: A 205 ARG cc_start: 0.7033 (mtm110) cc_final: 0.6689 (tmm-80) REVERT: A 230 TYR cc_start: 0.8963 (p90) cc_final: 0.8572 (p90) REVERT: A 247 MET cc_start: 0.8194 (mtt) cc_final: 0.7970 (mmm) REVERT: A 248 LYS cc_start: 0.7490 (mttp) cc_final: 0.7043 (mttt) REVERT: A 251 ASP cc_start: 0.7494 (t0) cc_final: 0.7233 (t0) REVERT: A 257 LYS cc_start: 0.8743 (ptpp) cc_final: 0.8537 (ptmt) REVERT: A 330 LYS cc_start: 0.7173 (mttt) cc_final: 0.6791 (mtmm) REVERT: G 47 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7348 (mt-10) REVERT: G 58 GLU cc_start: 0.7553 (mp0) cc_final: 0.7352 (mp0) REVERT: G 64 LYS cc_start: 0.6833 (mmmt) cc_final: 0.6404 (mmmm) outliers start: 13 outliers final: 7 residues processed: 254 average time/residue: 1.9431 time to fit residues: 526.8441 Evaluate side-chains 193 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 238 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 329 ASN R 339 ASN B 36 ASN B 239 ASN A 52 GLN A 304 GLN A 347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7138 Z= 0.207 Angle : 0.458 4.107 9675 Z= 0.250 Chirality : 0.039 0.142 1109 Planarity : 0.003 0.037 1223 Dihedral : 5.172 54.139 978 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 3.07 % Allowed : 22.06 % Favored : 74.87 % 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: -0.36 (0.28), residues: 880 helix: 1.34 (0.26), residues: 379 sheet: -0.80 (0.35), residues: 175 loop : -1.82 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.011 0.001 PHE B 151 TYR 0.008 0.001 TYR G 40 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: R 117 TRP cc_start: 0.8254 (t60) cc_final: 0.7936 (t60) REVERT: R 223 MET cc_start: 0.8239 (mtp) cc_final: 0.7916 (mtp) REVERT: R 233 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6617 (mm-30) REVERT: R 236 GLU cc_start: 0.7353 (tt0) cc_final: 0.6967 (tt0) REVERT: R 240 LYS cc_start: 0.6296 (mmtt) cc_final: 0.6077 (mmtp) REVERT: B 18 ILE cc_start: 0.7603 (mt) cc_final: 0.7366 (mt) REVERT: B 42 ARG cc_start: 0.7687 (mmm160) cc_final: 0.7099 (tpt-90) REVERT: B 219 ARG cc_start: 0.7721 (mmt90) cc_final: 0.7354 (mtt-85) REVERT: B 226 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7629 (mt-10) REVERT: B 258 ASP cc_start: 0.7985 (t0) cc_final: 0.7740 (t0) REVERT: B 331 SER cc_start: 0.9083 (t) cc_final: 0.8659 (t) REVERT: B 333 ASP cc_start: 0.8005 (p0) cc_final: 0.7798 (p0) REVERT: A 17 LYS cc_start: 0.7274 (mtpp) cc_final: 0.6966 (mtmm) REVERT: A 29 LYS cc_start: 0.8371 (tttt) cc_final: 0.8105 (tptm) REVERT: A 209 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8301 (ttpp) REVERT: A 230 TYR cc_start: 0.9048 (p90) cc_final: 0.8710 (p90) REVERT: A 247 MET cc_start: 0.8212 (mtt) cc_final: 0.7949 (mmm) REVERT: A 248 LYS cc_start: 0.7502 (mttp) cc_final: 0.7074 (mttt) REVERT: A 251 ASP cc_start: 0.7552 (t0) cc_final: 0.7295 (t0) REVERT: A 257 LYS cc_start: 0.8701 (ptpp) cc_final: 0.8462 (ptmt) REVERT: A 273 LEU cc_start: 0.7183 (tp) cc_final: 0.6962 (tp) REVERT: A 330 LYS cc_start: 0.7240 (mttt) cc_final: 0.6826 (mtmm) REVERT: G 28 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8001 (pp) REVERT: G 47 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7395 (mt-10) REVERT: G 58 GLU cc_start: 0.7576 (mp0) cc_final: 0.7371 (mp0) REVERT: G 64 LYS cc_start: 0.6832 (mmmt) cc_final: 0.6554 (mmmt) outliers start: 23 outliers final: 9 residues processed: 214 average time/residue: 1.9108 time to fit residues: 437.4471 Evaluate side-chains 200 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN B 35 ASN A 52 GLN A 322 HIS A 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7138 Z= 0.189 Angle : 0.442 3.930 9675 Z= 0.240 Chirality : 0.038 0.140 1109 Planarity : 0.003 0.039 1223 Dihedral : 4.094 37.653 971 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.39 % Favored : 97.50 % Rotamer: Outliers : 3.61 % Allowed : 22.86 % Favored : 73.53 % 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: 0.28 (0.28), residues: 880 helix: 1.96 (0.27), residues: 380 sheet: -0.54 (0.36), residues: 175 loop : -1.59 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.009 0.001 PHE B 151 TYR 0.009 0.001 TYR R 207 ARG 0.003 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 192 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: R 117 TRP cc_start: 0.8258 (t60) cc_final: 0.7939 (t60) REVERT: R 223 MET cc_start: 0.8249 (mtp) cc_final: 0.7891 (mtp) REVERT: R 233 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6607 (mm-30) REVERT: R 236 GLU cc_start: 0.7383 (tt0) cc_final: 0.7037 (tt0) REVERT: B 18 ILE cc_start: 0.7611 (mt) cc_final: 0.7376 (mt) REVERT: B 226 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 258 ASP cc_start: 0.7966 (t0) cc_final: 0.7704 (t0) REVERT: B 331 SER cc_start: 0.9015 (t) cc_final: 0.8623 (t) REVERT: A 17 LYS cc_start: 0.7270 (mtpp) cc_final: 0.6958 (mtmm) REVERT: A 29 LYS cc_start: 0.8385 (tttt) cc_final: 0.8174 (tptm) REVERT: A 205 ARG cc_start: 0.7153 (mtm110) cc_final: 0.6800 (tmm-80) REVERT: A 209 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8340 (ttpp) REVERT: A 230 TYR cc_start: 0.9046 (p90) cc_final: 0.8689 (p90) REVERT: A 247 MET cc_start: 0.8245 (mtt) cc_final: 0.7974 (mmm) REVERT: A 248 LYS cc_start: 0.7555 (mttp) cc_final: 0.7155 (mttt) REVERT: A 251 ASP cc_start: 0.7604 (t0) cc_final: 0.7322 (t0) REVERT: A 257 LYS cc_start: 0.8697 (ptpp) cc_final: 0.8370 (ptmt) REVERT: A 330 LYS cc_start: 0.7278 (mttt) cc_final: 0.6866 (mtmm) REVERT: G 28 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8043 (pp) REVERT: G 47 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7383 (mt-10) REVERT: G 58 GLU cc_start: 0.7580 (mp0) cc_final: 0.7368 (mp0) REVERT: G 64 LYS cc_start: 0.6751 (mmmt) cc_final: 0.6484 (mmmt) outliers start: 27 outliers final: 16 residues processed: 207 average time/residue: 1.7584 time to fit residues: 392.0886 Evaluate side-chains 205 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 339 ASN B 35 ASN A 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7138 Z= 0.234 Angle : 0.457 3.924 9675 Z= 0.251 Chirality : 0.039 0.142 1109 Planarity : 0.003 0.041 1223 Dihedral : 4.165 37.217 971 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 4.28 % Allowed : 21.79 % Favored : 73.93 % 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: 0.53 (0.29), residues: 880 helix: 2.21 (0.27), residues: 380 sheet: -0.34 (0.36), residues: 173 loop : -1.55 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR R 207 ARG 0.002 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: R 117 TRP cc_start: 0.8340 (t60) cc_final: 0.8049 (t60) REVERT: R 181 TRP cc_start: 0.6195 (OUTLIER) cc_final: 0.5606 (m-10) REVERT: R 223 MET cc_start: 0.8289 (mtp) cc_final: 0.7950 (mtp) REVERT: R 233 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6585 (mm-30) REVERT: R 236 GLU cc_start: 0.7332 (tt0) cc_final: 0.6991 (tt0) REVERT: B 18 ILE cc_start: 0.7669 (mt) cc_final: 0.7442 (mt) REVERT: B 226 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7561 (mt-10) REVERT: B 258 ASP cc_start: 0.7958 (t0) cc_final: 0.7708 (t0) REVERT: A 17 LYS cc_start: 0.7285 (mtpp) cc_final: 0.6966 (mtmm) REVERT: A 21 ARG cc_start: 0.7610 (ttm110) cc_final: 0.6968 (ttm110) REVERT: A 29 LYS cc_start: 0.8426 (tttt) cc_final: 0.8224 (tptm) REVERT: A 230 TYR cc_start: 0.9080 (p90) cc_final: 0.8713 (p90) REVERT: A 247 MET cc_start: 0.8279 (mtt) cc_final: 0.8078 (mmm) REVERT: A 248 LYS cc_start: 0.7593 (mttp) cc_final: 0.7199 (mttt) REVERT: A 251 ASP cc_start: 0.7619 (t0) cc_final: 0.7339 (t0) REVERT: A 257 LYS cc_start: 0.8679 (ptpp) cc_final: 0.8363 (ptmt) REVERT: A 330 LYS cc_start: 0.7269 (mttt) cc_final: 0.6868 (mtmm) REVERT: G 28 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8090 (pp) REVERT: G 47 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7450 (mt-10) REVERT: G 58 GLU cc_start: 0.7554 (mp0) cc_final: 0.7321 (mp0) outliers start: 32 outliers final: 22 residues processed: 208 average time/residue: 1.7598 time to fit residues: 393.6452 Evaluate side-chains 207 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 181 TRP Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 239 ASN A 52 GLN A 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7138 Z= 0.291 Angle : 0.485 4.065 9675 Z= 0.267 Chirality : 0.040 0.143 1109 Planarity : 0.003 0.041 1223 Dihedral : 4.326 39.182 971 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 5.75 % Allowed : 21.12 % Favored : 73.13 % 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: 0.50 (0.29), residues: 880 helix: 2.17 (0.27), residues: 380 sheet: -0.34 (0.37), residues: 175 loop : -1.55 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.015 0.001 PHE B 151 TYR 0.011 0.001 TYR R 207 ARG 0.002 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: R 117 TRP cc_start: 0.8370 (t60) cc_final: 0.8144 (t60) REVERT: R 181 TRP cc_start: 0.6231 (OUTLIER) cc_final: 0.5623 (m-10) REVERT: R 223 MET cc_start: 0.8276 (mtp) cc_final: 0.7951 (mtp) REVERT: R 229 ARG cc_start: 0.6544 (mmm160) cc_final: 0.6270 (ttt90) REVERT: R 233 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6558 (mm-30) REVERT: R 236 GLU cc_start: 0.7353 (tt0) cc_final: 0.7011 (tt0) REVERT: B 18 ILE cc_start: 0.7660 (mt) cc_final: 0.7437 (mt) REVERT: B 226 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7576 (mt-10) REVERT: B 258 ASP cc_start: 0.7931 (t0) cc_final: 0.7712 (t0) REVERT: A 17 LYS cc_start: 0.7299 (mtpp) cc_final: 0.6976 (mtmm) REVERT: A 21 ARG cc_start: 0.7640 (ttm110) cc_final: 0.6915 (ttm110) REVERT: A 29 LYS cc_start: 0.8476 (tttt) cc_final: 0.8265 (tptm) REVERT: A 33 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6721 (mm-30) REVERT: A 53 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7122 (mmt) REVERT: A 230 TYR cc_start: 0.9076 (p90) cc_final: 0.8737 (p90) REVERT: A 248 LYS cc_start: 0.7560 (mttp) cc_final: 0.7165 (mttt) REVERT: A 251 ASP cc_start: 0.7695 (t0) cc_final: 0.7380 (t0) REVERT: A 257 LYS cc_start: 0.8760 (ptpp) cc_final: 0.8469 (ptmt) REVERT: A 314 LYS cc_start: 0.7018 (mmtt) cc_final: 0.6732 (mmmm) REVERT: A 330 LYS cc_start: 0.7290 (mttt) cc_final: 0.6927 (mtmm) REVERT: G 28 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8043 (pp) REVERT: G 47 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7548 (mt-10) REVERT: G 58 GLU cc_start: 0.7539 (mp0) cc_final: 0.7281 (mp0) outliers start: 43 outliers final: 29 residues processed: 215 average time/residue: 1.8031 time to fit residues: 418.7418 Evaluate side-chains 221 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 181 TRP Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 64 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 259 GLN A 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7138 Z= 0.238 Angle : 0.465 3.917 9675 Z= 0.254 Chirality : 0.039 0.143 1109 Planarity : 0.003 0.041 1223 Dihedral : 4.267 38.730 971 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 4.95 % Allowed : 22.73 % Favored : 72.33 % 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: 0.70 (0.29), residues: 880 helix: 2.36 (0.27), residues: 380 sheet: -0.27 (0.37), residues: 173 loop : -1.46 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR R 207 ARG 0.002 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: R 117 TRP cc_start: 0.8365 (t60) cc_final: 0.8111 (t60) REVERT: R 181 TRP cc_start: 0.6218 (OUTLIER) cc_final: 0.5604 (m-10) REVERT: R 223 MET cc_start: 0.8294 (mtp) cc_final: 0.7994 (mtp) REVERT: R 229 ARG cc_start: 0.6542 (mmm160) cc_final: 0.6271 (ttt90) REVERT: R 233 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6592 (mm-30) REVERT: R 236 GLU cc_start: 0.7337 (tt0) cc_final: 0.6993 (tt0) REVERT: B 226 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 17 LYS cc_start: 0.7274 (mtpp) cc_final: 0.6951 (mtmm) REVERT: A 29 LYS cc_start: 0.8462 (tttt) cc_final: 0.8257 (tptm) REVERT: A 33 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6714 (mm-30) REVERT: A 53 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7074 (mmt) REVERT: A 230 TYR cc_start: 0.9051 (p90) cc_final: 0.8529 (p90) REVERT: A 248 LYS cc_start: 0.7623 (mttp) cc_final: 0.7224 (mttt) REVERT: A 251 ASP cc_start: 0.7668 (t0) cc_final: 0.7369 (t0) REVERT: A 257 LYS cc_start: 0.8755 (ptpp) cc_final: 0.8453 (ptmt) REVERT: A 314 LYS cc_start: 0.7075 (mmtt) cc_final: 0.6782 (mmmm) REVERT: A 330 LYS cc_start: 0.7295 (mttt) cc_final: 0.6894 (mtmm) REVERT: G 28 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8051 (pp) REVERT: G 47 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7521 (mt-10) REVERT: G 58 GLU cc_start: 0.7538 (mp0) cc_final: 0.7287 (mp0) outliers start: 37 outliers final: 29 residues processed: 208 average time/residue: 1.7252 time to fit residues: 386.5992 Evaluate side-chains 218 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 181 TRP Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 64 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 239 ASN A 52 GLN A 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7138 Z= 0.227 Angle : 0.466 4.934 9675 Z= 0.254 Chirality : 0.039 0.143 1109 Planarity : 0.003 0.040 1223 Dihedral : 4.234 38.594 971 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 5.21 % Allowed : 22.46 % Favored : 72.33 % 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: 0.80 (0.29), residues: 880 helix: 2.45 (0.27), residues: 380 sheet: -0.25 (0.37), residues: 173 loop : -1.41 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 151 TYR 0.009 0.001 TYR R 207 ARG 0.001 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: R 117 TRP cc_start: 0.8363 (t60) cc_final: 0.8105 (t60) REVERT: R 223 MET cc_start: 0.8287 (mtp) cc_final: 0.7955 (mtp) REVERT: R 229 ARG cc_start: 0.6573 (mmm160) cc_final: 0.6301 (ttt90) REVERT: R 233 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6586 (mm-30) REVERT: R 236 GLU cc_start: 0.7333 (tt0) cc_final: 0.6988 (tt0) REVERT: B 226 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 17 LYS cc_start: 0.7272 (mtpp) cc_final: 0.6947 (mtmm) REVERT: A 33 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6712 (mm-30) REVERT: A 53 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7117 (mmt) REVERT: A 230 TYR cc_start: 0.9028 (p90) cc_final: 0.8443 (p90) REVERT: A 248 LYS cc_start: 0.7548 (mttp) cc_final: 0.7252 (mttt) REVERT: A 251 ASP cc_start: 0.7650 (t0) cc_final: 0.7352 (t0) REVERT: A 257 LYS cc_start: 0.8757 (ptpp) cc_final: 0.8454 (ptmt) REVERT: A 314 LYS cc_start: 0.7051 (mmtt) cc_final: 0.6749 (mmmm) REVERT: A 330 LYS cc_start: 0.7293 (mttt) cc_final: 0.6901 (mtmm) REVERT: G 28 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8039 (pp) REVERT: G 29 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7334 (mttm) REVERT: G 47 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7518 (mt-10) REVERT: G 58 GLU cc_start: 0.7513 (mp0) cc_final: 0.7272 (mp0) outliers start: 39 outliers final: 30 residues processed: 211 average time/residue: 1.8077 time to fit residues: 409.2689 Evaluate side-chains 217 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 64 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7138 Z= 0.237 Angle : 0.470 5.233 9675 Z= 0.256 Chirality : 0.039 0.143 1109 Planarity : 0.003 0.040 1223 Dihedral : 4.249 38.125 971 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 5.08 % Allowed : 23.13 % Favored : 71.79 % 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 (0.29), residues: 880 helix: 2.47 (0.27), residues: 380 sheet: -0.25 (0.37), residues: 173 loop : -1.40 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR R 207 ARG 0.001 0.000 ARG R 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: R 117 TRP cc_start: 0.8369 (t60) cc_final: 0.8112 (t60) REVERT: R 181 TRP cc_start: 0.6233 (OUTLIER) cc_final: 0.5612 (m-10) REVERT: R 205 ARG cc_start: 0.7086 (ttm110) cc_final: 0.5940 (ttt-90) REVERT: R 223 MET cc_start: 0.8289 (mtp) cc_final: 0.7954 (mtp) REVERT: R 229 ARG cc_start: 0.6517 (mmm160) cc_final: 0.6265 (ttt90) REVERT: R 233 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6586 (mm-30) REVERT: R 236 GLU cc_start: 0.7362 (tt0) cc_final: 0.7027 (tt0) REVERT: B 154 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: B 226 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7571 (mt-10) REVERT: A 17 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6947 (mtmm) REVERT: A 33 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6725 (mm-30) REVERT: A 53 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7127 (mmt) REVERT: A 230 TYR cc_start: 0.9030 (p90) cc_final: 0.8378 (p90) REVERT: A 248 LYS cc_start: 0.7577 (mttp) cc_final: 0.7269 (mttt) REVERT: A 251 ASP cc_start: 0.7649 (t0) cc_final: 0.7354 (t0) REVERT: A 257 LYS cc_start: 0.8761 (ptpp) cc_final: 0.8458 (ptmt) REVERT: A 314 LYS cc_start: 0.7124 (mmtt) cc_final: 0.6841 (mmmm) REVERT: A 330 LYS cc_start: 0.7288 (mttt) cc_final: 0.6899 (mtmm) REVERT: G 28 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8076 (pp) REVERT: G 29 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7395 (mttm) REVERT: G 47 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7527 (mt-10) REVERT: G 58 GLU cc_start: 0.7528 (mp0) cc_final: 0.7288 (mp0) outliers start: 38 outliers final: 31 residues processed: 203 average time/residue: 1.7519 time to fit residues: 382.5646 Evaluate side-chains 219 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 181 TRP Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 212 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 64 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0570 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 239 ASN A 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7138 Z= 0.162 Angle : 0.443 4.412 9675 Z= 0.240 Chirality : 0.038 0.142 1109 Planarity : 0.003 0.039 1223 Dihedral : 4.090 36.073 971 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.74 % Allowed : 24.73 % Favored : 71.52 % 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 (0.29), residues: 880 helix: 2.68 (0.27), residues: 380 sheet: -0.10 (0.38), residues: 168 loop : -1.34 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.009 0.001 PHE A 189 TYR 0.008 0.001 TYR R 207 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: R 117 TRP cc_start: 0.8353 (t60) cc_final: 0.8001 (t60) REVERT: R 205 ARG cc_start: 0.7056 (ttm110) cc_final: 0.5855 (ttt-90) REVERT: R 223 MET cc_start: 0.8242 (mtp) cc_final: 0.7908 (mtp) REVERT: R 229 ARG cc_start: 0.6527 (mmm160) cc_final: 0.6243 (ttt90) REVERT: R 233 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6552 (mm-30) REVERT: R 236 GLU cc_start: 0.7279 (tt0) cc_final: 0.6933 (tt0) REVERT: B 154 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: B 226 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7540 (mt-10) REVERT: A 17 LYS cc_start: 0.7236 (mtpp) cc_final: 0.6900 (mtmm) REVERT: A 33 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6736 (mm-30) REVERT: A 230 TYR cc_start: 0.8991 (p90) cc_final: 0.8354 (p90) REVERT: A 248 LYS cc_start: 0.7632 (mttp) cc_final: 0.7343 (mttt) REVERT: A 251 ASP cc_start: 0.7567 (t0) cc_final: 0.7283 (t0) REVERT: A 257 LYS cc_start: 0.8757 (ptpp) cc_final: 0.8454 (ptmt) REVERT: A 314 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6821 (mmmm) REVERT: A 330 LYS cc_start: 0.7279 (mttt) cc_final: 0.6899 (mtmm) REVERT: G 21 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7648 (ttp) REVERT: G 28 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8061 (pp) REVERT: G 47 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7487 (mt-10) REVERT: G 58 GLU cc_start: 0.7517 (mp0) cc_final: 0.7293 (mp0) outliers start: 28 outliers final: 19 residues processed: 194 average time/residue: 1.7754 time to fit residues: 369.9366 Evaluate side-chains 203 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7138 Z= 0.200 Angle : 0.459 5.548 9675 Z= 0.248 Chirality : 0.038 0.143 1109 Planarity : 0.003 0.039 1223 Dihedral : 4.108 35.580 971 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.48 % Allowed : 25.00 % Favored : 71.52 % 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: 1.06 (0.29), residues: 880 helix: 2.69 (0.27), residues: 380 sheet: -0.17 (0.38), residues: 173 loop : -1.26 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 151 TYR 0.009 0.001 TYR R 207 ARG 0.004 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 115 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7404 (mt-10) REVERT: R 117 TRP cc_start: 0.8366 (t60) cc_final: 0.8120 (t60) REVERT: R 223 MET cc_start: 0.8263 (mtp) cc_final: 0.7931 (mtp) REVERT: R 229 ARG cc_start: 0.6506 (mmm160) cc_final: 0.6248 (ttt90) REVERT: R 233 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6574 (mm-30) REVERT: R 236 GLU cc_start: 0.7276 (tt0) cc_final: 0.6931 (tt0) REVERT: B 154 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: B 226 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7563 (mt-10) REVERT: A 17 LYS cc_start: 0.7241 (mtpp) cc_final: 0.6913 (mtmm) REVERT: A 33 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6729 (mm-30) REVERT: A 53 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7066 (mmt) REVERT: A 230 TYR cc_start: 0.8999 (p90) cc_final: 0.8296 (p90) REVERT: A 248 LYS cc_start: 0.7624 (mttp) cc_final: 0.7321 (mttt) REVERT: A 251 ASP cc_start: 0.7573 (t0) cc_final: 0.7280 (t0) REVERT: A 257 LYS cc_start: 0.8760 (ptpp) cc_final: 0.8437 (ptmt) REVERT: A 314 LYS cc_start: 0.7121 (mmtt) cc_final: 0.6826 (mmmm) REVERT: A 330 LYS cc_start: 0.7251 (mttt) cc_final: 0.6883 (mtmm) REVERT: G 21 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7656 (ttp) REVERT: G 29 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7585 (mttm) REVERT: G 47 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7511 (mt-10) REVERT: G 58 GLU cc_start: 0.7519 (mp0) cc_final: 0.7295 (mp0) outliers start: 26 outliers final: 19 residues processed: 193 average time/residue: 1.7768 time to fit residues: 368.3212 Evaluate side-chains 203 residues out of total 767 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 115 GLU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 239 ASN A 52 GLN A 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.103497 restraints weight = 23359.430| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.24 r_work: 0.2952 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7138 Z= 0.209 Angle : 0.465 5.524 9675 Z= 0.251 Chirality : 0.038 0.143 1109 Planarity : 0.004 0.076 1223 Dihedral : 4.126 34.994 971 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.88 % Allowed : 24.33 % Favored : 71.79 % 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 (0.29), residues: 880 helix: 2.67 (0.27), residues: 381 sheet: -0.15 (0.38), residues: 173 loop : -1.23 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 151 TYR 0.009 0.001 TYR R 207 ARG 0.012 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7095.27 seconds wall clock time: 124 minutes 21.14 seconds (7461.14 seconds total)