Starting phenix.real_space_refine on Mon Dec 30 20:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0g_24790/12_2024/7s0g_24790_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0g_24790/12_2024/7s0g_24790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s0g_24790/12_2024/7s0g_24790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0g_24790/12_2024/7s0g_24790.map" model { file = "/net/cci-nas-00/data/ceres_data/7s0g_24790/12_2024/7s0g_24790_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0g_24790/12_2024/7s0g_24790_trim.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.968 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 51 5.16 5 C 4451 2.51 5 N 1198 2.21 5 O 1292 1.98 5 H 6854 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13846 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4248 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 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: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3526 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 7.12, per 1000 atoms: 0.51 Number of scatterers: 13846 At special positions: 0 Unit cell: (84.8065, 98.762, 130.967, 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 51 16.00 O 1292 8.00 N 1198 7.00 C 4451 6.00 H 6854 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 47.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'R' and resid 40 through 69 removed outlier: 3.915A pdb=" N LEU R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU R 47 " --> pdb=" O GLY R 43 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 105 removed outlier: 3.591A pdb=" N LEU R 78 " --> pdb=" O THR R 74 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 5.019A 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 145 Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'R' and resid 154 through 179 removed outlier: 4.186A 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 186 through 195 Processing helix chain 'R' and resid 204 through 216 removed outlier: 3.745A pdb=" N ALA R 208 " --> pdb=" O ASN R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 241 Processing helix chain 'R' and resid 286 through 316 removed outlier: 3.672A pdb=" N ILE R 295 " --> pdb=" O THR R 291 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 305 - end of helix removed outlier: 3.584A pdb=" N VAL R 314 " --> pdb=" O ASN R 310 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE R 315 " --> pdb=" O ILE R 311 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN R 316 " --> pdb=" O VAL R 312 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 320 removed outlier: 3.665A pdb=" N VAL R 320 " --> pdb=" O ARG R 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 320' Processing helix chain 'R' and resid 321 through 344 removed outlier: 3.747A pdb=" N PHE R 325 " --> pdb=" O PRO R 321 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER R 336 " --> pdb=" O GLY R 332 " (cutoff:3.500A) removed outlier: 3.895A 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 346 through 356 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.612A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.562A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.598A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.677A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.552A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.098A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.101A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.659A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 150 removed outlier: 7.013A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 190 through 192 removed outlier: 6.663A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.611A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.746A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 7.827A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1095 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: 5.93 Time building geometry restraints manager: 4.49 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: 6828 1.03 - 1.23: 36 1.23 - 1.43: 2999 1.43 - 1.62: 4051 1.62 - 1.82: 72 Bond restraints: 13986 Sorted by residual: bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.438 -0.085 2.00e-02 2.50e+03 1.80e+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 1.09e+01 bond pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 1.457 1.493 -0.036 2.00e-02 2.50e+03 3.26e+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 2.34e+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 2.16e+00 ... (remaining 13981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.99: 25180 21.99 - 43.98: 0 43.98 - 65.97: 0 65.97 - 87.96: 0 87.96 - 109.94: 1 Bond angle restraints: 25181 Sorted by residual: angle pdb=" HB2 GLU A 352 " pdb=" CB GLU A 352 " pdb=" HB3 GLU A 352 " ideal model delta sigma weight residual 110.00 0.06 109.94 3.00e+00 1.11e-01 1.34e+03 angle pdb=" C VAL R 95 " pdb=" CA VAL R 95 " pdb=" CB VAL R 95 " ideal model delta sigma weight residual 114.00 110.72 3.28 1.31e+00 5.83e-01 6.28e+00 angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 111.88 109.50 2.38 1.06e+00 8.90e-01 5.03e+00 angle pdb=" C VAL R 94 " pdb=" N VAL R 95 " pdb=" CA VAL R 95 " ideal model delta sigma weight residual 120.33 122.02 -1.69 8.00e-01 1.56e+00 4.44e+00 angle pdb=" CAJ 5FW R 401 " pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 114.52 109.00 5.52 3.00e+00 1.11e-01 3.39e+00 ... (remaining 25176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 5984 15.60 - 31.20: 449 31.20 - 46.81: 97 46.81 - 62.41: 50 62.41 - 78.01: 7 Dihedral angle restraints: 6587 sinusoidal: 3491 harmonic: 3096 Sorted by residual: dihedral pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " pdb=" CG ASP B 153 " pdb=" OD1 ASP B 153 " ideal model delta sinusoidal sigma weight residual -30.00 -82.44 52.44 1 2.00e+01 2.50e-03 9.37e+00 dihedral pdb=" CA ASP B 312 " pdb=" CB ASP B 312 " pdb=" CG ASP B 312 " pdb=" OD1 ASP B 312 " ideal model delta sinusoidal sigma weight residual -30.00 -82.17 52.17 1 2.00e+01 2.50e-03 9.28e+00 dihedral pdb=" CA ASN R 310 " pdb=" CB ASN R 310 " pdb=" CG ASN R 310 " pdb=" OD1 ASN R 310 " ideal model delta sinusoidal sigma weight residual 120.00 178.63 -58.63 2 2.00e+01 2.50e-03 8.75e+00 ... (remaining 6584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 984 0.057 - 0.114: 111 0.114 - 0.171: 11 0.171 - 0.229: 0 0.229 - 0.286: 1 Chirality restraints: 1107 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 2.04e+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 2.56 -0.13 2.00e-01 2.50e+01 4.28e-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 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1104 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO G 49 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 218 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO R 219 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO R 219 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 219 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 320 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.13e-01 pdb=" N PRO R 321 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 321 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 321 " -0.013 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1067 2.23 - 2.82: 30218 2.82 - 3.41: 35336 3.41 - 4.01: 47215 4.01 - 4.60: 73202 Nonbonded interactions: 187038 Sorted by model distance: nonbonded pdb=" HG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 1.635 2.450 nonbonded pdb=" OE1 GLU A 289 " pdb=" H GLU A 289 " model vdw 1.641 2.450 nonbonded pdb=" OD1 ASP B 205 " pdb=" HG SER B 207 " model vdw 1.668 2.450 nonbonded pdb=" OD1 ASP R 184 " pdb=" H ASP R 186 " model vdw 1.681 2.450 nonbonded pdb="HH11 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 1.686 2.450 ... (remaining 187033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.230 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 33.290 Find NCS groups from input model: 0.090 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 0.085 7132 Z= 0.188 Angle : 0.441 5.523 9669 Z= 0.261 Chirality : 0.037 0.286 1107 Planarity : 0.002 0.029 1224 Dihedral : 12.412 78.012 2543 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.27), residues: 881 helix: 0.26 (0.24), residues: 403 sheet: -2.74 (0.35), residues: 158 loop : -2.36 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 117 HIS 0.004 0.001 HIS A 347 PHE 0.009 0.001 PHE R 174 TYR 0.008 0.001 TYR G 40 ARG 0.001 0.000 ARG R 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 322 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.102 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: 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 116 LEU cc_start: 0.8061 (tt) cc_final: 0.7857 (tt) REVERT: R 236 GLU cc_start: 0.8452 (tt0) cc_final: 0.8201 (tt0) REVERT: R 240 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8394 (mttt) REVERT: R 285 GLU cc_start: 0.7637 (pm20) cc_final: 0.7348 (mt-10) REVERT: R 323 TRP cc_start: 0.7904 (p-90) cc_final: 0.7507 (p-90) REVERT: B 68 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7888 (ttt180) REVERT: B 75 GLN cc_start: 0.7283 (mt0) cc_final: 0.6931 (mt0) REVERT: B 97 SER cc_start: 0.9234 (t) cc_final: 0.8826 (p) REVERT: B 134 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6701 (mtp-110) REVERT: B 176 GLN cc_start: 0.8763 (mt0) cc_final: 0.8447 (mt0) REVERT: B 228 ASP cc_start: 0.8307 (m-30) cc_final: 0.8064 (m-30) REVERT: B 237 ASN cc_start: 0.9048 (t0) cc_final: 0.8781 (t0) REVERT: B 247 ASP cc_start: 0.7841 (t0) cc_final: 0.7453 (t0) REVERT: B 304 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.7491 (ttp80) REVERT: B 321 THR cc_start: 0.9297 (p) cc_final: 0.9062 (p) REVERT: A 16 SER cc_start: 0.8901 (p) cc_final: 0.8666 (p) REVERT: A 22 ASN cc_start: 0.8403 (m-40) cc_final: 0.8091 (m110) REVERT: A 214 CYS cc_start: 0.8533 (m) cc_final: 0.8031 (t) REVERT: A 312 LYS cc_start: 0.8307 (mttt) cc_final: 0.7964 (mmmt) REVERT: A 330 LYS cc_start: 0.8574 (mttt) cc_final: 0.8365 (mmtp) REVERT: G 27 ARG cc_start: 0.7354 (mtt-85) cc_final: 0.6339 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.4698 time to fit residues: 195.0527 Evaluate side-chains 266 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 GLN R 237 GLN R 310 ASN B 75 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7132 Z= 0.238 Angle : 0.499 5.370 9669 Z= 0.270 Chirality : 0.038 0.148 1107 Planarity : 0.003 0.035 1224 Dihedral : 3.441 13.723 970 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.35 % Allowed : 15.09 % Favored : 83.56 % 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: -0.96 (0.28), residues: 881 helix: 1.43 (0.26), residues: 407 sheet: -2.90 (0.34), residues: 155 loop : -2.16 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 117 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE A 189 TYR 0.007 0.001 TYR B 289 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 283 time to evaluate : 1.108 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8145 (mt-10) REVERT: R 150 GLN cc_start: 0.8327 (tp40) cc_final: 0.8100 (tp-100) REVERT: R 236 GLU cc_start: 0.8364 (tt0) cc_final: 0.8089 (tt0) REVERT: R 237 GLN cc_start: 0.8305 (tp-100) cc_final: 0.7435 (tp40) REVERT: R 323 TRP cc_start: 0.8191 (p-90) cc_final: 0.7451 (p-90) REVERT: B 97 SER cc_start: 0.9208 (t) cc_final: 0.8795 (p) REVERT: B 134 ARG cc_start: 0.6957 (mmm-85) cc_final: 0.6709 (mtp-110) REVERT: B 176 GLN cc_start: 0.8702 (mt0) cc_final: 0.8380 (mt0) REVERT: B 228 ASP cc_start: 0.8247 (m-30) cc_final: 0.8014 (m-30) REVERT: B 247 ASP cc_start: 0.7871 (t0) cc_final: 0.7477 (t0) REVERT: B 304 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7551 (ttp80) REVERT: B 325 MET cc_start: 0.8043 (mmt) cc_final: 0.7553 (mmt) REVERT: A 16 SER cc_start: 0.8958 (p) cc_final: 0.8624 (p) REVERT: A 22 ASN cc_start: 0.8483 (m-40) cc_final: 0.8229 (m110) REVERT: A 25 GLU cc_start: 0.7593 (tp30) cc_final: 0.7371 (tp30) REVERT: A 214 CYS cc_start: 0.8504 (m) cc_final: 0.7914 (t) REVERT: A 286 CYS cc_start: 0.8317 (p) cc_final: 0.7611 (t) REVERT: A 330 LYS cc_start: 0.8511 (mttt) cc_final: 0.8218 (mmtp) REVERT: A 333 GLN cc_start: 0.8750 (tt0) cc_final: 0.8524 (tp40) REVERT: G 27 ARG cc_start: 0.7403 (mtt-85) cc_final: 0.6914 (mtt-85) outliers start: 10 outliers final: 10 residues processed: 286 average time/residue: 0.4410 time to fit residues: 164.5329 Evaluate side-chains 285 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 275 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.0040 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7132 Z= 0.190 Angle : 0.476 6.924 9669 Z= 0.255 Chirality : 0.037 0.129 1107 Planarity : 0.003 0.041 1224 Dihedral : 3.466 17.937 970 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.02 % Allowed : 16.58 % Favored : 81.40 % 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: -0.49 (0.29), residues: 881 helix: 1.90 (0.26), residues: 407 sheet: -2.78 (0.34), residues: 156 loop : -1.99 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.001 PHE A 189 TYR 0.011 0.001 TYR B 85 ARG 0.007 0.000 ARG R 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 279 time to evaluate : 1.164 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: 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 130 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8097 (mt-10) REVERT: R 236 GLU cc_start: 0.8355 (tt0) cc_final: 0.8123 (tt0) REVERT: R 323 TRP cc_start: 0.8221 (p-90) cc_final: 0.7413 (p-90) REVERT: B 97 SER cc_start: 0.9270 (t) cc_final: 0.8943 (p) REVERT: B 134 ARG cc_start: 0.6940 (mmm-85) cc_final: 0.6694 (mtp-110) REVERT: B 176 GLN cc_start: 0.8700 (mt0) cc_final: 0.8370 (mt0) REVERT: B 228 ASP cc_start: 0.8234 (m-30) cc_final: 0.7976 (m-30) REVERT: B 247 ASP cc_start: 0.7872 (t0) cc_final: 0.7468 (t0) REVERT: B 304 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.7556 (ttp80) REVERT: B 325 MET cc_start: 0.8054 (mmt) cc_final: 0.7495 (mmt) REVERT: A 16 SER cc_start: 0.8921 (p) cc_final: 0.8695 (p) REVERT: A 22 ASN cc_start: 0.8507 (m-40) cc_final: 0.8231 (m110) REVERT: A 25 GLU cc_start: 0.7595 (tp30) cc_final: 0.7356 (tp30) REVERT: A 214 CYS cc_start: 0.8464 (m) cc_final: 0.7836 (t) REVERT: A 286 CYS cc_start: 0.8254 (p) cc_final: 0.7592 (t) REVERT: A 330 LYS cc_start: 0.8494 (mttt) cc_final: 0.8223 (mmtp) REVERT: A 333 GLN cc_start: 0.8782 (tt0) cc_final: 0.8110 (tp-100) REVERT: G 27 ARG cc_start: 0.7394 (mtt-85) cc_final: 0.7023 (mtt-85) REVERT: G 46 LYS cc_start: 0.8724 (mttp) cc_final: 0.8379 (mtpp) outliers start: 15 outliers final: 13 residues processed: 284 average time/residue: 0.4153 time to fit residues: 155.4912 Evaluate side-chains 282 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 269 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 GLN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7132 Z= 0.269 Angle : 0.503 5.644 9669 Z= 0.275 Chirality : 0.038 0.126 1107 Planarity : 0.004 0.040 1224 Dihedral : 3.636 13.878 970 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.83 % Allowed : 17.39 % Favored : 79.78 % 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: -0.44 (0.29), residues: 881 helix: 1.98 (0.25), residues: 407 sheet: -2.79 (0.34), residues: 162 loop : -1.98 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.010 0.001 HIS R 180 PHE 0.016 0.001 PHE A 189 TYR 0.009 0.001 TYR G 40 ARG 0.005 0.000 ARG R 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 1.068 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: 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: symmetry clash revert: symmetry clash REVERT: R 150 GLN cc_start: 0.8278 (tp40) cc_final: 0.8057 (tp-100) REVERT: R 236 GLU cc_start: 0.8376 (tt0) cc_final: 0.8113 (tt0) REVERT: B 97 SER cc_start: 0.9274 (t) cc_final: 0.8900 (p) REVERT: B 134 ARG cc_start: 0.6994 (mmm-85) cc_final: 0.6731 (mtp-110) REVERT: B 228 ASP cc_start: 0.8234 (m-30) cc_final: 0.7949 (m-30) REVERT: B 247 ASP cc_start: 0.7947 (t0) cc_final: 0.7488 (t0) REVERT: B 304 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7580 (ttp80) REVERT: B 325 MET cc_start: 0.7987 (mmt) cc_final: 0.7592 (mmt) REVERT: A 22 ASN cc_start: 0.8556 (m-40) cc_final: 0.8276 (m110) REVERT: A 214 CYS cc_start: 0.8490 (m) cc_final: 0.7875 (t) REVERT: A 248 LYS cc_start: 0.8869 (mttp) cc_final: 0.8466 (mtpt) REVERT: A 283 LEU cc_start: 0.8286 (tp) cc_final: 0.8022 (tt) REVERT: A 286 CYS cc_start: 0.8247 (p) cc_final: 0.7634 (t) REVERT: A 289 GLU cc_start: 0.7433 (pm20) cc_final: 0.7025 (pm20) REVERT: A 330 LYS cc_start: 0.8510 (mttt) cc_final: 0.8230 (mmtp) REVERT: A 333 GLN cc_start: 0.8807 (tt0) cc_final: 0.8083 (tp-100) REVERT: G 27 ARG cc_start: 0.7430 (mtt-85) cc_final: 0.7037 (mtt-85) REVERT: G 46 LYS cc_start: 0.8715 (mttp) cc_final: 0.8386 (mtpp) outliers start: 21 outliers final: 21 residues processed: 286 average time/residue: 0.4365 time to fit residues: 165.3029 Evaluate side-chains 291 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7132 Z= 0.210 Angle : 0.492 5.133 9669 Z= 0.266 Chirality : 0.038 0.161 1107 Planarity : 0.004 0.040 1224 Dihedral : 3.638 18.593 970 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.70 % Allowed : 18.87 % Favored : 78.44 % 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: -0.25 (0.29), residues: 881 helix: 2.16 (0.25), residues: 407 sheet: -2.77 (0.36), residues: 152 loop : -1.92 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 169 HIS 0.002 0.001 HIS B 225 PHE 0.016 0.001 PHE A 189 TYR 0.009 0.001 TYR G 40 ARG 0.008 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 275 time to evaluate : 0.980 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: 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: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7807 (mt-10) REVERT: R 188 GLN cc_start: 0.7243 (tp40) cc_final: 0.6628 (tm-30) REVERT: R 236 GLU cc_start: 0.8348 (tt0) cc_final: 0.8105 (tt0) REVERT: R 323 TRP cc_start: 0.8321 (p-90) cc_final: 0.7463 (p-90) REVERT: B 57 LYS cc_start: 0.8348 (ptpt) cc_final: 0.8022 (ptmt) REVERT: B 59 TYR cc_start: 0.8844 (m-10) cc_final: 0.8601 (m-80) REVERT: B 97 SER cc_start: 0.9368 (t) cc_final: 0.8926 (p) REVERT: B 134 ARG cc_start: 0.6981 (mmm-85) cc_final: 0.6709 (mtp-110) REVERT: B 228 ASP cc_start: 0.8250 (m-30) cc_final: 0.7952 (m-30) REVERT: B 247 ASP cc_start: 0.7902 (t0) cc_final: 0.7431 (t0) REVERT: B 304 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7522 (ttp80) REVERT: B 325 MET cc_start: 0.8043 (mmt) cc_final: 0.7567 (mmt) REVERT: A 22 ASN cc_start: 0.8457 (m-40) cc_final: 0.8171 (m110) REVERT: A 25 GLU cc_start: 0.7611 (tp30) cc_final: 0.7381 (tp30) REVERT: A 248 LYS cc_start: 0.8863 (mttp) cc_final: 0.8471 (mtpt) REVERT: A 333 GLN cc_start: 0.8798 (tt0) cc_final: 0.8091 (tp-100) REVERT: G 27 ARG cc_start: 0.7402 (mtt-85) cc_final: 0.7019 (mtt-85) outliers start: 20 outliers final: 17 residues processed: 280 average time/residue: 0.4236 time to fit residues: 155.6210 Evaluate side-chains 285 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 268 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7132 Z= 0.217 Angle : 0.480 4.888 9669 Z= 0.262 Chirality : 0.038 0.129 1107 Planarity : 0.004 0.041 1224 Dihedral : 3.639 18.743 970 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.83 % Allowed : 18.33 % Favored : 78.84 % 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: -0.05 (0.29), residues: 881 helix: 2.43 (0.25), residues: 401 sheet: -2.70 (0.37), residues: 153 loop : -1.86 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 169 HIS 0.002 0.000 HIS A 213 PHE 0.017 0.001 PHE A 189 TYR 0.009 0.001 TYR G 40 ARG 0.005 0.000 ARG R 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 1.135 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7798 (mt-10) REVERT: R 188 GLN cc_start: 0.7244 (tp40) cc_final: 0.6548 (tm-30) REVERT: R 236 GLU cc_start: 0.8337 (tt0) cc_final: 0.8097 (tt0) REVERT: B 57 LYS cc_start: 0.8417 (ptpt) cc_final: 0.8038 (ptmt) REVERT: B 97 SER cc_start: 0.9321 (t) cc_final: 0.8916 (p) REVERT: B 134 ARG cc_start: 0.6912 (mmm-85) cc_final: 0.6634 (mtp-110) REVERT: B 176 GLN cc_start: 0.8718 (mt0) cc_final: 0.8383 (mt0) REVERT: B 228 ASP cc_start: 0.8196 (m-30) cc_final: 0.7878 (m-30) REVERT: B 247 ASP cc_start: 0.7840 (t0) cc_final: 0.7337 (t0) REVERT: B 304 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.7519 (ttp80) REVERT: B 325 MET cc_start: 0.8044 (mmt) cc_final: 0.7582 (mmt) REVERT: A 22 ASN cc_start: 0.8457 (m-40) cc_final: 0.8185 (m110) REVERT: A 248 LYS cc_start: 0.8888 (mttp) cc_final: 0.8475 (mtpt) REVERT: A 261 ASP cc_start: 0.8791 (p0) cc_final: 0.8531 (p0) REVERT: A 286 CYS cc_start: 0.8292 (p) cc_final: 0.7569 (t) REVERT: A 333 GLN cc_start: 0.8766 (tt0) cc_final: 0.8093 (tp-100) REVERT: G 27 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.7059 (mtt-85) outliers start: 21 outliers final: 19 residues processed: 271 average time/residue: 0.4154 time to fit residues: 148.9090 Evaluate side-chains 290 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 271 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7132 Z= 0.165 Angle : 0.471 8.088 9669 Z= 0.252 Chirality : 0.038 0.141 1107 Planarity : 0.003 0.040 1224 Dihedral : 3.547 20.025 970 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.29 % Allowed : 19.54 % Favored : 78.17 % 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: 0.20 (0.29), residues: 881 helix: 2.64 (0.25), residues: 401 sheet: -2.62 (0.38), residues: 147 loop : -1.75 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.005 0.001 HIS R 180 PHE 0.017 0.001 PHE A 189 TYR 0.008 0.001 TYR G 40 ARG 0.003 0.000 ARG R 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 1.166 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7709 (mt-10) REVERT: R 188 GLN cc_start: 0.7094 (tp40) cc_final: 0.6433 (tm-30) REVERT: R 236 GLU cc_start: 0.8326 (tt0) cc_final: 0.8091 (tt0) REVERT: R 323 TRP cc_start: 0.8190 (p-90) cc_final: 0.7377 (p-90) REVERT: B 57 LYS cc_start: 0.8372 (ptpt) cc_final: 0.8074 (ptmt) REVERT: B 61 MET cc_start: 0.8807 (ppp) cc_final: 0.8489 (ppp) REVERT: B 97 SER cc_start: 0.9354 (t) cc_final: 0.8942 (p) REVERT: B 134 ARG cc_start: 0.6788 (mmm-85) cc_final: 0.6503 (mtp-110) REVERT: B 176 GLN cc_start: 0.8712 (mt0) cc_final: 0.8391 (mt0) REVERT: B 228 ASP cc_start: 0.8170 (m-30) cc_final: 0.7716 (m-30) REVERT: B 247 ASP cc_start: 0.7768 (t0) cc_final: 0.7288 (t0) REVERT: B 304 ARG cc_start: 0.7742 (ttp-170) cc_final: 0.7511 (ttp80) REVERT: B 325 MET cc_start: 0.8027 (mmt) cc_final: 0.7536 (mmt) REVERT: A 22 ASN cc_start: 0.8417 (m-40) cc_final: 0.8139 (m110) REVERT: A 248 LYS cc_start: 0.8884 (mttp) cc_final: 0.8474 (mtpt) REVERT: A 261 ASP cc_start: 0.8791 (p0) cc_final: 0.8514 (p0) REVERT: A 286 CYS cc_start: 0.8288 (p) cc_final: 0.7605 (t) REVERT: G 27 ARG cc_start: 0.7363 (mtt-85) cc_final: 0.7024 (mtt-85) outliers start: 17 outliers final: 16 residues processed: 275 average time/residue: 0.4188 time to fit residues: 153.1704 Evaluate side-chains 279 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7132 Z= 0.207 Angle : 0.479 5.384 9669 Z= 0.261 Chirality : 0.038 0.130 1107 Planarity : 0.003 0.041 1224 Dihedral : 3.586 19.093 970 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.43 % Allowed : 19.00 % Favored : 78.57 % 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: 0.22 (0.29), residues: 881 helix: 2.61 (0.25), residues: 402 sheet: -2.52 (0.38), residues: 152 loop : -1.73 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 99 HIS 0.003 0.001 HIS R 180 PHE 0.018 0.001 PHE A 189 TYR 0.009 0.001 TYR B 105 ARG 0.003 0.000 ARG R 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 267 time to evaluate : 1.181 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: 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: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7718 (mt-10) REVERT: R 188 GLN cc_start: 0.7117 (tp40) cc_final: 0.6450 (tm-30) REVERT: R 236 GLU cc_start: 0.8330 (tt0) cc_final: 0.8090 (tt0) REVERT: B 57 LYS cc_start: 0.8407 (ptpt) cc_final: 0.8137 (ptmt) REVERT: B 97 SER cc_start: 0.9342 (t) cc_final: 0.8931 (p) REVERT: B 134 ARG cc_start: 0.6817 (mmm-85) cc_final: 0.6554 (mtp-110) REVERT: B 163 ASP cc_start: 0.7449 (t0) cc_final: 0.7181 (t0) REVERT: B 176 GLN cc_start: 0.8747 (mt0) cc_final: 0.8437 (mt0) REVERT: B 188 MET cc_start: 0.7647 (mmm) cc_final: 0.7401 (mmm) REVERT: B 228 ASP cc_start: 0.8119 (m-30) cc_final: 0.7842 (m-30) REVERT: B 247 ASP cc_start: 0.7809 (t0) cc_final: 0.7341 (t0) REVERT: B 304 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7520 (ttp80) REVERT: A 22 ASN cc_start: 0.8438 (m-40) cc_final: 0.8158 (m110) REVERT: A 216 GLU cc_start: 0.8309 (tp30) cc_final: 0.7652 (tp30) REVERT: A 248 LYS cc_start: 0.8898 (mttp) cc_final: 0.8477 (mtpt) REVERT: A 286 CYS cc_start: 0.8246 (p) cc_final: 0.7788 (t) REVERT: A 289 GLU cc_start: 0.7298 (pm20) cc_final: 0.6949 (pm20) REVERT: A 298 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7371 (tt0) REVERT: G 27 ARG cc_start: 0.7357 (mtt-85) cc_final: 0.7060 (mtt-85) outliers start: 18 outliers final: 18 residues processed: 273 average time/residue: 0.4249 time to fit residues: 154.5116 Evaluate side-chains 285 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 267 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7132 Z= 0.217 Angle : 0.490 5.938 9669 Z= 0.267 Chirality : 0.038 0.129 1107 Planarity : 0.004 0.052 1224 Dihedral : 3.640 19.679 970 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.43 % Allowed : 19.41 % Favored : 78.17 % 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: 0.27 (0.29), residues: 881 helix: 2.60 (0.25), residues: 403 sheet: -2.42 (0.39), residues: 150 loop : -1.68 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.002 0.001 HIS A 213 PHE 0.018 0.001 PHE A 189 TYR 0.009 0.001 TYR B 105 ARG 0.007 0.000 ARG R 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 257 time to evaluate : 1.209 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7751 (mt-10) REVERT: R 188 GLN cc_start: 0.7153 (tp40) cc_final: 0.6492 (tm-30) REVERT: R 236 GLU cc_start: 0.8327 (tt0) cc_final: 0.8093 (tt0) REVERT: B 57 LYS cc_start: 0.8451 (ptpt) cc_final: 0.8142 (ptmt) REVERT: B 97 SER cc_start: 0.9332 (t) cc_final: 0.8911 (p) REVERT: B 134 ARG cc_start: 0.6859 (mmm-85) cc_final: 0.6538 (mtp-110) REVERT: B 163 ASP cc_start: 0.7468 (t0) cc_final: 0.7199 (t0) REVERT: B 176 GLN cc_start: 0.8803 (mt0) cc_final: 0.8496 (mt0) REVERT: B 188 MET cc_start: 0.7653 (mmm) cc_final: 0.7350 (mmm) REVERT: B 228 ASP cc_start: 0.8121 (m-30) cc_final: 0.7609 (m-30) REVERT: B 247 ASP cc_start: 0.7854 (t0) cc_final: 0.7440 (t0) REVERT: B 304 ARG cc_start: 0.7795 (ttp-170) cc_final: 0.7525 (ttp80) REVERT: A 22 ASN cc_start: 0.8458 (m-40) cc_final: 0.8202 (m110) REVERT: A 216 GLU cc_start: 0.8306 (tp30) cc_final: 0.7587 (tp30) REVERT: A 248 LYS cc_start: 0.8875 (mttp) cc_final: 0.8469 (mtpt) REVERT: G 27 ARG cc_start: 0.7361 (mtt-85) cc_final: 0.7094 (mtt-85) outliers start: 18 outliers final: 18 residues processed: 264 average time/residue: 0.4490 time to fit residues: 158.5741 Evaluate side-chains 274 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7132 Z= 0.212 Angle : 0.492 5.283 9669 Z= 0.269 Chirality : 0.038 0.193 1107 Planarity : 0.004 0.043 1224 Dihedral : 3.655 19.802 970 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.29 % Allowed : 19.95 % Favored : 77.76 % 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: 0.27 (0.29), residues: 881 helix: 2.60 (0.25), residues: 403 sheet: -2.38 (0.40), residues: 148 loop : -1.71 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.002 0.001 HIS R 180 PHE 0.017 0.001 PHE A 189 TYR 0.009 0.001 TYR B 105 ARG 0.006 0.000 ARG R 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 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 LEU 113 is missing expected H atoms. Skipping. Residue LEU 190 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. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 0.906 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 130 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7759 (mt-10) REVERT: R 188 GLN cc_start: 0.7154 (tp40) cc_final: 0.6494 (tm-30) REVERT: R 236 GLU cc_start: 0.8311 (tt0) cc_final: 0.8084 (tt0) REVERT: B 57 LYS cc_start: 0.8436 (ptpt) cc_final: 0.8152 (ptmt) REVERT: B 97 SER cc_start: 0.9289 (t) cc_final: 0.8835 (p) REVERT: B 134 ARG cc_start: 0.6861 (mmm-85) cc_final: 0.6539 (mtp-110) REVERT: B 176 GLN cc_start: 0.8819 (mt0) cc_final: 0.8545 (mt0) REVERT: B 188 MET cc_start: 0.7625 (mmm) cc_final: 0.7383 (mmm) REVERT: B 247 ASP cc_start: 0.7887 (t0) cc_final: 0.7501 (t0) REVERT: B 304 ARG cc_start: 0.7803 (ttp-170) cc_final: 0.7526 (ttp80) REVERT: A 22 ASN cc_start: 0.8460 (m-40) cc_final: 0.8213 (m110) REVERT: A 216 GLU cc_start: 0.8343 (tp30) cc_final: 0.7651 (tp30) REVERT: A 248 LYS cc_start: 0.8886 (mttp) cc_final: 0.8471 (mtpt) REVERT: G 27 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.7117 (mtt-85) outliers start: 17 outliers final: 17 residues processed: 266 average time/residue: 0.4122 time to fit residues: 144.7343 Evaluate side-chains 270 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 253 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113963 restraints weight = 24487.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120181 restraints weight = 11400.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.124212 restraints weight = 6958.241| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7132 Z= 0.212 Angle : 0.490 5.294 9669 Z= 0.268 Chirality : 0.038 0.129 1107 Planarity : 0.004 0.051 1224 Dihedral : 3.639 19.690 970 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.43 % Allowed : 19.68 % Favored : 77.90 % 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: 0.31 (0.30), residues: 881 helix: 2.66 (0.25), residues: 403 sheet: -2.40 (0.40), residues: 146 loop : -1.72 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.001 0.000 HIS B 225 PHE 0.017 0.001 PHE A 189 TYR 0.015 0.001 TYR A 287 ARG 0.006 0.000 ARG R 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4277.47 seconds wall clock time: 77 minutes 8.38 seconds (4628.38 seconds total)