Starting phenix.real_space_refine on Mon Mar 11 11:36:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/03_2024/7wf7_32461_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/03_2024/7wf7_32461.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/03_2024/7wf7_32461_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/03_2024/7wf7_32461_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/03_2024/7wf7_32461_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/03_2024/7wf7_32461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/03_2024/7wf7_32461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/03_2024/7wf7_32461_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf7_32461/03_2024/7wf7_32461_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.113 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 P 1 5.49 5 S 56 5.16 5 C 5207 2.51 5 N 1380 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8136 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2189 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 5 Chain: "B" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1143 Classifications: {'peptide': 142} Link IDs: {'TRANS': 141} Chain breaks: 5 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 410 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.68, per 1000 atoms: 0.58 Number of scatterers: 8136 At special positions: 0 Unit cell: (92.4, 124.3, 132, 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 56 16.00 P 1 15.00 O 1492 8.00 N 1380 7.00 C 5207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 31.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 47 through 71 Processing helix chain 'A' and resid 79 through 103 Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 114 through 145 Processing helix chain 'A' and resid 159 through 180 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 202 through 233 Processing helix chain 'A' and resid 255 through 279 removed outlier: 5.200A pdb=" N ILE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.757A pdb=" N LEU A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.134A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.009A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 removed outlier: 4.008A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.822A pdb=" N GLU B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 350 removed outlier: 4.588A pdb=" N PHE B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS B 345 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 23 Processing helix chain 'C' and resid 30 through 36 removed outlier: 5.090A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 264 through 266 removed outlier: 6.264A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.936A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.162A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.838A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 220 through 223 removed outlier: 4.283A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 200 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.573A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 305 through 307 removed outlier: 4.009A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.090A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.316A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 7.228A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 213 through 219 removed outlier: 6.291A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 361 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: 2.64 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2565 1.34 - 1.46: 1956 1.46 - 1.58: 3686 1.58 - 1.70: 6 1.70 - 1.83: 81 Bond restraints: 8294 Sorted by residual: bond pdb=" O1 S1P A 401 " pdb=" P22 S1P A 401 " ideal model delta sigma weight residual 1.661 1.815 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C5 S1P A 401 " pdb=" C6 S1P A 401 " ideal model delta sigma weight residual 1.550 1.486 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C13 S1P A 401 " pdb=" C14 S1P A 401 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" C6 S1P A 401 " pdb=" C7 S1P A 401 " ideal model delta sigma weight residual 1.554 1.606 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" C15 S1P A 401 " pdb=" C16 S1P A 401 " ideal model delta sigma weight residual 1.561 1.510 0.051 2.00e-02 2.50e+03 6.61e+00 ... (remaining 8289 not shown) Histogram of bond angle deviations from ideal: 95.09 - 102.88: 40 102.88 - 110.67: 2514 110.67 - 118.46: 3901 118.46 - 126.25: 4634 126.25 - 134.04: 128 Bond angle restraints: 11217 Sorted by residual: angle pdb=" O1 S1P A 401 " pdb=" P22 S1P A 401 " pdb=" O25 S1P A 401 " ideal model delta sigma weight residual 109.48 95.09 14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" N PHE C 235 " pdb=" CA PHE C 235 " pdb=" C PHE C 235 " ideal model delta sigma weight residual 108.85 100.57 8.28 1.88e+00 2.83e-01 1.94e+01 angle pdb=" N TYR E 94 " pdb=" CA TYR E 94 " pdb=" C TYR E 94 " ideal model delta sigma weight residual 108.76 115.88 -7.12 1.69e+00 3.50e-01 1.78e+01 angle pdb=" C PHE C 235 " pdb=" CA PHE C 235 " pdb=" CB PHE C 235 " ideal model delta sigma weight residual 110.13 115.24 -5.11 1.34e+00 5.57e-01 1.46e+01 angle pdb=" C LEU C 70 " pdb=" CA LEU C 70 " pdb=" CB LEU C 70 " ideal model delta sigma weight residual 109.65 103.02 6.63 1.75e+00 3.27e-01 1.44e+01 ... (remaining 11212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.76: 4716 26.76 - 53.52: 170 53.52 - 80.28: 12 80.28 - 107.04: 4 107.04 - 133.80: 2 Dihedral angle restraints: 4904 sinusoidal: 1917 harmonic: 2987 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 133.38 -40.38 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" C10 S1P A 401 " pdb=" C11 S1P A 401 " pdb=" C12 S1P A 401 " pdb=" C13 S1P A 401 " ideal model delta sinusoidal sigma weight residual 222.74 88.94 133.80 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CA ASN C 293 " pdb=" C ASN C 293 " pdb=" N CYS C 294 " pdb=" CA CYS C 294 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 4901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 942 0.045 - 0.090: 263 0.090 - 0.136: 83 0.136 - 0.181: 6 0.181 - 0.226: 4 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CA ASP C 247 " pdb=" N ASP C 247 " pdb=" C ASP C 247 " pdb=" CB ASP C 247 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3 S1P A 401 " pdb=" C2 S1P A 401 " pdb=" C4 S1P A 401 " pdb=" O3 S1P A 401 " both_signs ideal model delta sigma weight residual False -2.52 -2.32 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LYS A 256 " pdb=" N LYS A 256 " pdb=" C LYS A 256 " pdb=" CB LYS A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1295 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 169 " -0.026 2.00e-02 2.50e+03 1.89e-02 8.94e+00 pdb=" CG TRP C 169 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP C 169 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 169 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 169 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 169 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.042 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO E 107 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 307 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO A 308 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.029 5.00e-02 4.00e+02 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2248 2.81 - 3.33: 7374 3.33 - 3.86: 12724 3.86 - 4.38: 14790 4.38 - 4.90: 25716 Nonbonded interactions: 62852 Sorted by model distance: nonbonded pdb=" OG1 THR C 143 " pdb=" OD1 ASP C 163 " model vdw 2.288 2.440 nonbonded pdb=" N GLY C 144 " pdb=" OD1 ASP C 163 " model vdw 2.295 2.520 nonbonded pdb=" O ARG C 314 " pdb=" OG SER C 331 " model vdw 2.297 2.440 nonbonded pdb=" OG1 THR C 34 " pdb=" O LEU C 300 " model vdw 2.320 2.440 nonbonded pdb=" O SER E 120 " pdb=" OG SER E 120 " model vdw 2.328 2.440 ... (remaining 62847 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.040 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 8294 Z= 0.265 Angle : 0.835 14.386 11217 Z= 0.459 Chirality : 0.046 0.226 1298 Planarity : 0.005 0.065 1388 Dihedral : 13.778 133.800 2966 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.14 (0.26), residues: 1002 helix: 0.94 (0.30), residues: 297 sheet: -0.65 (0.30), residues: 266 loop : -2.04 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 169 HIS 0.008 0.001 HIS C 91 PHE 0.017 0.002 PHE C 151 TYR 0.023 0.002 TYR A 198 ARG 0.019 0.001 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 LYS cc_start: 0.4327 (mmtt) cc_final: 0.3759 (tttt) REVERT: C 158 VAL cc_start: 0.7379 (t) cc_final: 0.7134 (t) REVERT: C 279 SER cc_start: 0.5333 (p) cc_final: 0.4888 (t) REVERT: C 297 TRP cc_start: 0.7585 (m100) cc_final: 0.7144 (m100) REVERT: E 128 MET cc_start: 0.6835 (mmm) cc_final: 0.5816 (mmm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2187 time to fit residues: 44.4859 Evaluate side-chains 103 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8294 Z= 0.184 Angle : 0.619 7.381 11217 Z= 0.326 Chirality : 0.043 0.165 1298 Planarity : 0.004 0.045 1388 Dihedral : 7.572 117.570 1128 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.35 % Allowed : 8.44 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.55 (0.26), residues: 1002 helix: 1.72 (0.30), residues: 296 sheet: -0.40 (0.30), residues: 260 loop : -1.84 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 169 HIS 0.007 0.001 HIS E 220 PHE 0.021 0.002 PHE C 234 TYR 0.016 0.002 TYR A 198 ARG 0.006 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.902 Fit side-chains REVERT: A 141 GLU cc_start: 0.6451 (tp30) cc_final: 0.6127 (tp30) REVERT: A 150 LYS cc_start: 0.4166 (mmtt) cc_final: 0.3697 (tttt) REVERT: B 25 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6508 (tt0) REVERT: B 349 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6555 (mptt) REVERT: C 48 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7529 (mmt-90) REVERT: C 255 LEU cc_start: 0.3852 (OUTLIER) cc_final: 0.3585 (tp) REVERT: C 279 SER cc_start: 0.5014 (p) cc_final: 0.4457 (t) REVERT: C 297 TRP cc_start: 0.7708 (m100) cc_final: 0.6700 (m100) REVERT: D 38 MET cc_start: 0.4948 (tmm) cc_final: 0.4299 (tmm) REVERT: E 59 TYR cc_start: 0.7740 (m-10) cc_final: 0.7540 (m-80) REVERT: E 76 LYS cc_start: 0.6694 (mtmm) cc_final: 0.6458 (pttm) REVERT: E 171 GLN cc_start: 0.7612 (mt0) cc_final: 0.7352 (mt0) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 0.2324 time to fit residues: 33.9106 Evaluate side-chains 109 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 74 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8294 Z= 0.162 Angle : 0.567 7.243 11217 Z= 0.301 Chirality : 0.042 0.154 1298 Planarity : 0.004 0.042 1388 Dihedral : 6.943 109.573 1128 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.02 % Allowed : 10.80 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.27), residues: 1002 helix: 2.01 (0.30), residues: 296 sheet: -0.27 (0.30), residues: 250 loop : -1.67 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 169 HIS 0.005 0.001 HIS E 220 PHE 0.023 0.001 PHE A 291 TYR 0.015 0.001 TYR A 198 ARG 0.005 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.916 Fit side-chains REVERT: A 141 GLU cc_start: 0.6522 (tp30) cc_final: 0.6243 (tp30) REVERT: A 150 LYS cc_start: 0.4102 (mmtt) cc_final: 0.3589 (tttt) REVERT: A 283 LYS cc_start: 0.6367 (mmmt) cc_final: 0.5284 (mtmt) REVERT: A 312 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7306 (t) REVERT: B 189 PHE cc_start: 0.4607 (m-80) cc_final: 0.4135 (m-80) REVERT: B 349 LYS cc_start: 0.7161 (mmtt) cc_final: 0.6575 (mptt) REVERT: C 48 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7416 (mmp80) REVERT: C 179 THR cc_start: 0.7361 (m) cc_final: 0.7147 (t) REVERT: C 297 TRP cc_start: 0.7681 (m100) cc_final: 0.6643 (m100) REVERT: D 38 MET cc_start: 0.4897 (tmm) cc_final: 0.4358 (tmm) REVERT: E 59 TYR cc_start: 0.7756 (m-10) cc_final: 0.7546 (m-80) REVERT: E 171 GLN cc_start: 0.7581 (mt0) cc_final: 0.7311 (mt0) outliers start: 18 outliers final: 9 residues processed: 118 average time/residue: 0.2287 time to fit residues: 35.8456 Evaluate side-chains 115 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.0050 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8294 Z= 0.202 Angle : 0.604 8.734 11217 Z= 0.317 Chirality : 0.042 0.158 1298 Planarity : 0.004 0.040 1388 Dihedral : 6.673 97.709 1128 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.92 % Allowed : 12.49 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.29 (0.26), residues: 1002 helix: 2.02 (0.30), residues: 297 sheet: -0.32 (0.30), residues: 250 loop : -1.66 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 169 HIS 0.008 0.001 HIS E 220 PHE 0.020 0.002 PHE C 234 TYR 0.016 0.002 TYR C 105 ARG 0.005 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.894 Fit side-chains REVERT: A 141 GLU cc_start: 0.6695 (tp30) cc_final: 0.6257 (tp30) REVERT: A 150 LYS cc_start: 0.4124 (mmtt) cc_final: 0.3597 (tttt) REVERT: A 217 ILE cc_start: 0.5397 (OUTLIER) cc_final: 0.5063 (tt) REVERT: A 283 LYS cc_start: 0.6443 (mmmt) cc_final: 0.5319 (mtmt) REVERT: A 312 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7386 (t) REVERT: B 53 MET cc_start: 0.4057 (pmm) cc_final: 0.3295 (ppp) REVERT: B 349 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6637 (mttt) REVERT: C 48 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7423 (mmp80) REVERT: C 297 TRP cc_start: 0.7730 (m100) cc_final: 0.6702 (m100) REVERT: D 38 MET cc_start: 0.4728 (tmm) cc_final: 0.4335 (tmm) REVERT: E 17 SER cc_start: 0.7714 (m) cc_final: 0.7363 (p) REVERT: E 65 LYS cc_start: 0.7875 (tptm) cc_final: 0.7512 (tttt) REVERT: E 171 GLN cc_start: 0.7597 (mt0) cc_final: 0.7251 (mt0) outliers start: 26 outliers final: 17 residues processed: 121 average time/residue: 0.2701 time to fit residues: 43.7328 Evaluate side-chains 123 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 84 optimal weight: 0.0050 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8294 Z= 0.159 Angle : 0.548 8.541 11217 Z= 0.291 Chirality : 0.041 0.148 1298 Planarity : 0.004 0.039 1388 Dihedral : 6.318 87.024 1128 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.37 % Allowed : 13.95 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.08 (0.27), residues: 1002 helix: 2.23 (0.31), residues: 296 sheet: -0.21 (0.30), residues: 249 loop : -1.55 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 82 HIS 0.005 0.001 HIS E 220 PHE 0.016 0.001 PHE C 234 TYR 0.014 0.001 TYR A 198 ARG 0.004 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 0.825 Fit side-chains REVERT: A 141 GLU cc_start: 0.6487 (tp30) cc_final: 0.6079 (tp30) REVERT: A 150 LYS cc_start: 0.4045 (mmtt) cc_final: 0.3517 (tttt) REVERT: A 217 ILE cc_start: 0.5186 (OUTLIER) cc_final: 0.4963 (tt) REVERT: A 283 LYS cc_start: 0.6498 (mmmt) cc_final: 0.5332 (mtmt) REVERT: A 312 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7286 (t) REVERT: B 53 MET cc_start: 0.3951 (pmm) cc_final: 0.3054 (ppp) REVERT: C 48 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7450 (mmp80) REVERT: C 179 THR cc_start: 0.7207 (m) cc_final: 0.6981 (t) REVERT: C 267 ASP cc_start: 0.3771 (m-30) cc_final: 0.3460 (m-30) REVERT: C 297 TRP cc_start: 0.7642 (m100) cc_final: 0.6594 (m100) REVERT: E 65 LYS cc_start: 0.7839 (tptm) cc_final: 0.7492 (tttt) REVERT: E 171 GLN cc_start: 0.7537 (mt0) cc_final: 0.7240 (mt0) outliers start: 30 outliers final: 22 residues processed: 125 average time/residue: 0.2121 time to fit residues: 35.9935 Evaluate side-chains 120 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 98 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.6420 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8294 Z= 0.211 Angle : 0.606 8.635 11217 Z= 0.318 Chirality : 0.042 0.151 1298 Planarity : 0.004 0.039 1388 Dihedral : 6.310 80.666 1128 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.49 % Allowed : 14.85 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.17 (0.26), residues: 1002 helix: 2.20 (0.30), residues: 296 sheet: -0.36 (0.30), residues: 246 loop : -1.57 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 169 HIS 0.007 0.001 HIS E 220 PHE 0.019 0.001 PHE C 234 TYR 0.015 0.002 TYR C 105 ARG 0.004 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 0.912 Fit side-chains REVERT: A 141 GLU cc_start: 0.6626 (tp30) cc_final: 0.6162 (tp30) REVERT: A 217 ILE cc_start: 0.5400 (OUTLIER) cc_final: 0.5059 (tt) REVERT: A 312 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.7325 (t) REVERT: B 53 MET cc_start: 0.3877 (pmm) cc_final: 0.2943 (ppp) REVERT: B 349 LYS cc_start: 0.7375 (mmtt) cc_final: 0.6770 (mttt) REVERT: C 48 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7486 (mmp80) REVERT: C 267 ASP cc_start: 0.3821 (m-30) cc_final: 0.3519 (m-30) REVERT: C 297 TRP cc_start: 0.7683 (m100) cc_final: 0.6653 (m100) REVERT: E 17 SER cc_start: 0.7748 (m) cc_final: 0.7407 (p) REVERT: E 65 LYS cc_start: 0.7873 (tptm) cc_final: 0.7480 (tttt) REVERT: E 171 GLN cc_start: 0.7586 (mt0) cc_final: 0.7273 (mt0) outliers start: 31 outliers final: 23 residues processed: 126 average time/residue: 0.1992 time to fit residues: 34.4268 Evaluate side-chains 122 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8294 Z= 0.152 Angle : 0.550 9.300 11217 Z= 0.288 Chirality : 0.041 0.146 1298 Planarity : 0.004 0.038 1388 Dihedral : 5.983 68.473 1128 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.26 % Allowed : 15.52 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.08 (0.27), residues: 1002 helix: 2.49 (0.31), residues: 290 sheet: -0.29 (0.30), residues: 249 loop : -1.39 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 82 HIS 0.004 0.001 HIS E 220 PHE 0.015 0.001 PHE C 234 TYR 0.013 0.001 TYR A 198 ARG 0.004 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.974 Fit side-chains REVERT: A 141 GLU cc_start: 0.6509 (tp30) cc_final: 0.6133 (tp30) REVERT: A 312 THR cc_start: 0.7548 (OUTLIER) cc_final: 0.7331 (t) REVERT: B 53 MET cc_start: 0.3896 (pmm) cc_final: 0.2814 (pmm) REVERT: C 179 THR cc_start: 0.7302 (m) cc_final: 0.7096 (t) REVERT: C 297 TRP cc_start: 0.7654 (m100) cc_final: 0.6483 (m100) REVERT: E 65 LYS cc_start: 0.7889 (tptm) cc_final: 0.7571 (tttt) REVERT: E 171 GLN cc_start: 0.7509 (mt0) cc_final: 0.7223 (mt0) outliers start: 29 outliers final: 21 residues processed: 123 average time/residue: 0.2075 time to fit residues: 35.0406 Evaluate side-chains 120 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 94 optimal weight: 0.0050 chunk 85 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 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 : 0.002 0.027 8294 Z= 0.126 Angle : 0.525 8.787 11217 Z= 0.273 Chirality : 0.040 0.160 1298 Planarity : 0.003 0.037 1388 Dihedral : 5.697 58.282 1128 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.47 % Allowed : 16.42 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.27), residues: 1002 helix: 2.62 (0.31), residues: 290 sheet: -0.31 (0.30), residues: 257 loop : -1.25 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 82 HIS 0.002 0.001 HIS C 142 PHE 0.011 0.001 PHE C 234 TYR 0.013 0.001 TYR A 198 ARG 0.004 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.975 Fit side-chains REVERT: A 141 GLU cc_start: 0.6459 (tp30) cc_final: 0.6100 (tp30) REVERT: A 312 THR cc_start: 0.7617 (OUTLIER) cc_final: 0.7400 (t) REVERT: B 53 MET cc_start: 0.3306 (pmm) cc_final: 0.2280 (pmm) REVERT: C 198 LEU cc_start: 0.5851 (pp) cc_final: 0.4969 (mt) REVERT: C 297 TRP cc_start: 0.7590 (m100) cc_final: 0.6476 (m100) REVERT: E 65 LYS cc_start: 0.7854 (tptm) cc_final: 0.7588 (tttt) outliers start: 22 outliers final: 18 residues processed: 117 average time/residue: 0.2041 time to fit residues: 32.7799 Evaluate side-chains 124 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.6350 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8294 Z= 0.161 Angle : 0.579 14.457 11217 Z= 0.296 Chirality : 0.041 0.180 1298 Planarity : 0.004 0.037 1388 Dihedral : 5.684 53.599 1128 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.70 % Allowed : 16.31 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.27), residues: 1002 helix: 2.67 (0.30), residues: 288 sheet: -0.27 (0.30), residues: 260 loop : -1.26 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 164 HIS 0.004 0.001 HIS E 220 PHE 0.024 0.001 PHE C 234 TYR 0.011 0.001 TYR A 198 ARG 0.005 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.924 Fit side-chains REVERT: A 141 GLU cc_start: 0.6592 (tp30) cc_final: 0.6169 (tp30) REVERT: A 312 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.7394 (t) REVERT: B 53 MET cc_start: 0.3323 (pmm) cc_final: 0.2461 (pmm) REVERT: C 198 LEU cc_start: 0.5801 (pp) cc_final: 0.4788 (mt) REVERT: C 297 TRP cc_start: 0.7665 (m100) cc_final: 0.6524 (m100) REVERT: E 65 LYS cc_start: 0.7890 (tptm) cc_final: 0.7608 (tttt) outliers start: 24 outliers final: 22 residues processed: 112 average time/residue: 0.2070 time to fit residues: 31.5393 Evaluate side-chains 120 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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: 0.6371 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8294 Z= 0.173 Angle : 0.576 8.854 11217 Z= 0.299 Chirality : 0.041 0.164 1298 Planarity : 0.004 0.037 1388 Dihedral : 5.672 53.976 1128 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.92 % Allowed : 15.75 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.27), residues: 1002 helix: 2.65 (0.30), residues: 288 sheet: -0.22 (0.30), residues: 258 loop : -1.32 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 164 HIS 0.005 0.001 HIS E 220 PHE 0.024 0.001 PHE C 234 TYR 0.016 0.001 TYR A 198 ARG 0.005 0.000 ARG C 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.968 Fit side-chains REVERT: A 141 GLU cc_start: 0.6598 (tp30) cc_final: 0.6176 (tp30) REVERT: A 217 ILE cc_start: 0.5172 (OUTLIER) cc_final: 0.4905 (tt) REVERT: A 312 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7408 (t) REVERT: B 53 MET cc_start: 0.3909 (pmm) cc_final: 0.3014 (pmm) REVERT: B 349 LYS cc_start: 0.7467 (mmtt) cc_final: 0.6928 (mttt) REVERT: C 297 TRP cc_start: 0.7695 (m100) cc_final: 0.6598 (m100) REVERT: E 65 LYS cc_start: 0.7863 (tptm) cc_final: 0.7569 (tttt) outliers start: 26 outliers final: 22 residues processed: 115 average time/residue: 0.2166 time to fit residues: 33.7560 Evaluate side-chains 122 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.248522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.234732 restraints weight = 9318.659| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 0.92 r_work: 0.4381 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.4342 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8294 Z= 0.263 Angle : 0.664 9.678 11217 Z= 0.343 Chirality : 0.043 0.202 1298 Planarity : 0.004 0.045 1388 Dihedral : 5.958 55.386 1128 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.04 % Allowed : 16.31 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.03 (0.27), residues: 1002 helix: 2.34 (0.30), residues: 294 sheet: -0.52 (0.30), residues: 256 loop : -1.34 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 169 HIS 0.004 0.001 HIS E 220 PHE 0.029 0.002 PHE C 234 TYR 0.019 0.002 TYR C 105 ARG 0.009 0.000 ARG C 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.40 seconds wall clock time: 36 minutes 55.94 seconds (2215.94 seconds total)