Starting phenix.real_space_refine on Sat Apr 6 02:17:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/04_2024/8uns_42415_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/04_2024/8uns_42415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/04_2024/8uns_42415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/04_2024/8uns_42415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/04_2024/8uns_42415_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uns_42415/04_2024/8uns_42415_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 3 5.49 5 S 42 5.16 5 C 4291 2.51 5 N 1154 2.21 5 O 1193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "R GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6683 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 242, 1776 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 171 Conformer: "B" Number of residues, atoms: 242, 1776 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 171 bond proxies already assigned to first conformer: 1797 Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2364 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 373 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2110 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.34, per 1000 atoms: 0.80 Number of scatterers: 6683 At special positions: 0 Unit cell: (83.2992, 137.097, 98.9178, 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 42 16.00 P 3 15.00 O 1193 8.00 N 1154 7.00 C 4291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.7 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 41.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.050A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.646A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.671A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.673A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.627A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 30 through 60 removed outlier: 3.546A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 3.964A pdb=" N PHE R 71 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL R 86 " --> pdb=" O GLY R 83 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL R 87 " --> pdb=" O LEU R 84 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.591A pdb=" N THR R 96 " --> pdb=" O HIS R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 119 Processing helix chain 'R' and resid 122 through 136 Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 163 removed outlier: 3.624A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 207 Processing helix chain 'R' and resid 210 through 237 removed outlier: 3.961A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 286 removed outlier: 3.909A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 298 removed outlier: 4.846A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.514A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.379A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.768A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 115 removed outlier: 3.924A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.013A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.032A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.668A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.853A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.670A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 894 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: 1.74 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1596 1.33 - 1.45: 1497 1.45 - 1.58: 3674 1.58 - 1.70: 5 1.70 - 1.82: 57 Bond restraints: 6829 Sorted by residual: bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.14e-02 7.69e+03 1.61e+01 bond pdb=" N VAL A 256 " pdb=" CA VAL A 256 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.32e-02 5.74e+03 1.03e+01 bond pdb=" CA ASP A 223 " pdb=" C ASP A 223 " ideal model delta sigma weight residual 1.521 1.485 0.037 1.19e-02 7.06e+03 9.50e+00 bond pdb=" N ARG A 61 " pdb=" CA ARG A 61 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.61e+00 bond pdb=" N ILE A 62 " pdb=" CA ILE A 62 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.46e+00 ... (remaining 6824 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 203 107.28 - 113.96: 3889 113.96 - 120.65: 2776 120.65 - 127.33: 2405 127.33 - 134.01: 76 Bond angle restraints: 9349 Sorted by residual: angle pdb=" C GLN A 262 " pdb=" CA GLN A 262 " pdb=" CB GLN A 262 " ideal model delta sigma weight residual 116.54 108.64 7.90 1.15e+00 7.56e-01 4.72e+01 angle pdb=" N GLU A 259 " pdb=" CA GLU A 259 " pdb=" C GLU A 259 " ideal model delta sigma weight residual 113.23 105.07 8.16 1.22e+00 6.72e-01 4.47e+01 angle pdb=" N GLN A 19 " pdb=" CA GLN A 19 " pdb=" C GLN A 19 " ideal model delta sigma weight residual 111.28 104.93 6.35 1.09e+00 8.42e-01 3.39e+01 angle pdb=" N ASN A 261 " pdb=" CA ASN A 261 " pdb=" C ASN A 261 " ideal model delta sigma weight residual 111.28 105.61 5.67 1.09e+00 8.42e-01 2.70e+01 angle pdb=" CA LEU A 63 " pdb=" C LEU A 63 " pdb=" O LEU A 63 " ideal model delta sigma weight residual 120.55 115.23 5.32 1.06e+00 8.90e-01 2.52e+01 ... (remaining 9344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.23: 3818 28.23 - 56.46: 112 56.46 - 84.69: 7 84.69 - 112.92: 4 112.92 - 141.15: 4 Dihedral angle restraints: 3945 sinusoidal: 1267 harmonic: 2678 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 153.31 -60.31 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -149.58 -141.15 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -28.04 132.64 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 3942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 886 0.054 - 0.107: 165 0.107 - 0.161: 53 0.161 - 0.214: 8 0.214 - 0.268: 7 Chirality restraints: 1119 Sorted by residual: chirality pdb=" CA ASP A 260 " pdb=" N ASP A 260 " pdb=" C ASP A 260 " pdb=" CB ASP A 260 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLN A 19 " pdb=" N GLN A 19 " pdb=" C GLN A 19 " pdb=" CB GLN A 19 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1116 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO R 211 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.013 2.00e-02 2.50e+03 9.94e-03 1.98e+00 pdb=" CG TYR B 59 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 15 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C GLU A 15 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU A 15 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A 16 " 0.008 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2367 2.85 - 3.36: 6063 3.36 - 3.87: 10310 3.87 - 4.39: 11004 4.39 - 4.90: 20365 Nonbonded interactions: 50109 Sorted by model distance: nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.332 2.440 nonbonded pdb=" OD2 ASP B 258 " pdb=" NH2 ARG G 27 " model vdw 2.368 2.520 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.372 2.520 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.397 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.407 2.440 ... (remaining 50104 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=0.49 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.560 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.500 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 0.054 6829 Z= 0.296 Angle : 0.771 10.404 9349 Z= 0.494 Chirality : 0.051 0.268 1119 Planarity : 0.003 0.043 1173 Dihedral : 14.481 141.151 2201 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.29), residues: 905 helix: 2.33 (0.27), residues: 393 sheet: 0.02 (0.41), residues: 173 loop : -0.92 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 158 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE A 222 TYR 0.024 0.001 TYR B 59 ARG 0.003 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.777 Fit side-chains REVERT: G 15 LEU cc_start: 0.8931 (tp) cc_final: 0.8649 (tp) REVERT: R 171 MET cc_start: 0.7983 (mmm) cc_final: 0.7769 (mmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1626 time to fit residues: 21.4458 Evaluate side-chains 74 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.0060 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6829 Z= 0.135 Angle : 0.462 5.972 9349 Z= 0.249 Chirality : 0.040 0.158 1119 Planarity : 0.004 0.041 1173 Dihedral : 9.787 159.327 1006 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.65 % Allowed : 7.44 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.29), residues: 905 helix: 2.37 (0.27), residues: 395 sheet: 0.16 (0.40), residues: 175 loop : -0.88 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.019 0.001 TYR B 59 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.777 Fit side-chains REVERT: A 211 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8308 (mmtt) REVERT: A 267 GLN cc_start: 0.8577 (tp40) cc_final: 0.8197 (tm-30) REVERT: A 368 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7101 (m-30) REVERT: R 171 MET cc_start: 0.7981 (mmm) cc_final: 0.7718 (mmm) REVERT: R 312 ASN cc_start: 0.8071 (t0) cc_final: 0.7864 (t0) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.1680 time to fit residues: 21.0109 Evaluate side-chains 86 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 0.0060 chunk 79 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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: 0.8346 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6829 Z= 0.130 Angle : 0.437 5.977 9349 Z= 0.231 Chirality : 0.039 0.134 1119 Planarity : 0.003 0.040 1173 Dihedral : 8.076 108.420 1006 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.65 % Allowed : 9.92 % Favored : 88.43 % 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: 1.17 (0.29), residues: 905 helix: 2.44 (0.27), residues: 398 sheet: 0.01 (0.39), residues: 177 loop : -0.89 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.008 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.018 0.001 TYR B 59 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 236 GLN cc_start: 0.8912 (mt0) cc_final: 0.8672 (pt0) REVERT: A 267 GLN cc_start: 0.8688 (tp40) cc_final: 0.8276 (tm-30) REVERT: A 368 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: R 61 PHE cc_start: 0.8615 (m-80) cc_final: 0.8333 (m-10) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1739 time to fit residues: 22.1856 Evaluate side-chains 88 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8370 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6829 Z= 0.162 Angle : 0.444 6.029 9349 Z= 0.235 Chirality : 0.039 0.137 1119 Planarity : 0.003 0.040 1173 Dihedral : 7.600 101.016 1006 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.65 % Allowed : 10.58 % Favored : 87.77 % 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: 1.16 (0.29), residues: 905 helix: 2.42 (0.27), residues: 398 sheet: -0.03 (0.39), residues: 177 loop : -0.85 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.008 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.016 0.001 TYR B 59 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.8930 (mt0) cc_final: 0.8719 (pt0) REVERT: A 267 GLN cc_start: 0.8715 (tp40) cc_final: 0.8247 (tm-30) REVERT: A 368 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: R 171 MET cc_start: 0.7667 (mmm) cc_final: 0.7440 (mmm) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.1787 time to fit residues: 22.1448 Evaluate side-chains 87 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6829 Z= 0.171 Angle : 0.444 6.297 9349 Z= 0.237 Chirality : 0.039 0.140 1119 Planarity : 0.003 0.041 1173 Dihedral : 7.421 97.979 1006 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.65 % Allowed : 12.89 % Favored : 85.45 % 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: 1.15 (0.29), residues: 905 helix: 2.42 (0.27), residues: 398 sheet: -0.03 (0.40), residues: 177 loop : -0.86 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.013 0.001 TYR A 339 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8742 (tp40) cc_final: 0.8246 (tm-30) REVERT: A 368 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7194 (m-30) outliers start: 10 outliers final: 9 residues processed: 87 average time/residue: 0.1708 time to fit residues: 20.5638 Evaluate side-chains 89 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 0.0770 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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: 0.8362 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6829 Z= 0.138 Angle : 0.430 6.530 9349 Z= 0.227 Chirality : 0.039 0.131 1119 Planarity : 0.003 0.040 1173 Dihedral : 7.142 93.912 1006 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.15 % Allowed : 13.55 % Favored : 84.30 % 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: 1.19 (0.29), residues: 905 helix: 2.47 (0.27), residues: 397 sheet: -0.04 (0.40), residues: 177 loop : -0.85 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.013 0.001 TYR A 339 ARG 0.001 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8718 (tp40) cc_final: 0.8301 (tm-30) REVERT: A 368 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7122 (m-30) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.1664 time to fit residues: 21.7792 Evaluate side-chains 93 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.8398 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6829 Z= 0.199 Angle : 0.459 6.444 9349 Z= 0.245 Chirality : 0.040 0.141 1119 Planarity : 0.003 0.041 1173 Dihedral : 7.063 90.810 1006 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.81 % Allowed : 13.88 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.29), residues: 905 helix: 2.43 (0.27), residues: 397 sheet: -0.08 (0.40), residues: 177 loop : -0.91 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.014 0.001 TYR A 339 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8796 (tp40) cc_final: 0.8352 (tm-30) REVERT: A 368 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7214 (m-30) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.1703 time to fit residues: 22.6654 Evaluate side-chains 94 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6829 Z= 0.145 Angle : 0.438 6.307 9349 Z= 0.232 Chirality : 0.039 0.138 1119 Planarity : 0.003 0.041 1173 Dihedral : 6.914 90.244 1006 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.31 % Allowed : 14.88 % Favored : 82.81 % 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: 1.15 (0.29), residues: 905 helix: 2.47 (0.27), residues: 393 sheet: -0.07 (0.40), residues: 175 loop : -0.84 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.007 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.013 0.001 TYR A 339 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8744 (tp40) cc_final: 0.8299 (tm-30) REVERT: A 368 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: B 234 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.7740 (t80) outliers start: 14 outliers final: 11 residues processed: 94 average time/residue: 0.1709 time to fit residues: 22.4956 Evaluate side-chains 96 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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: 0.8370 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6829 Z= 0.137 Angle : 0.427 6.225 9349 Z= 0.228 Chirality : 0.039 0.136 1119 Planarity : 0.003 0.040 1173 Dihedral : 6.777 89.811 1006 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.15 % Allowed : 15.21 % Favored : 82.64 % 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: 1.19 (0.29), residues: 905 helix: 2.51 (0.27), residues: 392 sheet: -0.09 (0.40), residues: 173 loop : -0.81 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE A 222 TYR 0.012 0.001 TYR A 339 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8757 (tp40) cc_final: 0.8306 (tm-30) REVERT: A 368 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: B 234 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.7636 (t80) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.1756 time to fit residues: 23.3009 Evaluate side-chains 94 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 21 optimal weight: 0.0270 chunk 65 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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: 0.8359 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6829 Z= 0.128 Angle : 0.429 6.217 9349 Z= 0.227 Chirality : 0.039 0.136 1119 Planarity : 0.003 0.040 1173 Dihedral : 6.648 89.382 1006 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.15 % Allowed : 15.54 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 905 helix: 2.53 (0.27), residues: 392 sheet: -0.09 (0.40), residues: 175 loop : -0.80 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.007 0.001 HIS A 220 PHE 0.010 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.002 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8749 (tp40) cc_final: 0.8287 (tm-30) REVERT: A 368 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: B 234 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7626 (t80) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.1531 time to fit residues: 19.9614 Evaluate side-chains 93 residues out of total 791 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 4 optimal weight: 0.0050 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 47 optimal weight: 0.0170 overall best weight: 0.4632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101330 restraints weight = 36920.847| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.25 r_work: 0.3035 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6829 Z= 0.113 Angle : 0.417 6.235 9349 Z= 0.221 Chirality : 0.039 0.134 1119 Planarity : 0.003 0.039 1173 Dihedral : 6.485 88.573 1006 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.65 % Allowed : 16.03 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.29), residues: 905 helix: 2.56 (0.27), residues: 394 sheet: -0.10 (0.40), residues: 175 loop : -0.79 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.007 0.001 HIS A 220 PHE 0.009 0.001 PHE A 222 TYR 0.011 0.001 TYR A 339 ARG 0.001 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1754.64 seconds wall clock time: 32 minutes 40.23 seconds (1960.23 seconds total)