Starting phenix.real_space_refine on Fri Aug 22 20:20:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jh7_36258/08_2025/8jh7_36258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jh7_36258/08_2025/8jh7_36258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jh7_36258/08_2025/8jh7_36258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jh7_36258/08_2025/8jh7_36258.map" model { file = "/net/cci-nas-00/data/ceres_data/8jh7_36258/08_2025/8jh7_36258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jh7_36258/08_2025/8jh7_36258.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4911 2.51 5 N 1273 2.21 5 O 1439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7663 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1682 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1624 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3436 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 3 Time building chain proxies: 2.03, per 1000 atoms: 0.26 Number of scatterers: 7663 At special positions: 0 Unit cell: (66.56, 100.672, 157.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1439 8.00 N 1273 7.00 C 4911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 260 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 357 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 493.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1834 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 35.1% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.626A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.605A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 200 through 205 removed outlier: 3.646A pdb=" N GLY H 204 " --> pdb=" O SER H 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 129 removed outlier: 3.821A pdb=" N LEU L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 129' Processing helix chain 'L' and resid 185 through 189 removed outlier: 3.552A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 185 through 189' Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.526A pdb=" N GLY D 177 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 211 removed outlier: 4.390A pdb=" N GLU D 196 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.625A pdb=" N LEU D 221 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 232 through 255 removed outlier: 3.908A pdb=" N TYR D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 312 removed outlier: 3.669A pdb=" N LEU D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 291 " --> pdb=" O MET D 287 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.815A pdb=" N ARG D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 395 Processing helix chain 'D' and resid 1002 through 1024 Processing helix chain 'D' and resid 1029 through 1049 removed outlier: 3.758A pdb=" N ASP D1033 " --> pdb=" O ALA D1029 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D1049 " --> pdb=" O ALA D1045 " (cutoff:3.500A) Processing helix chain 'D' and resid 1064 through 1085 Processing helix chain 'D' and resid 1089 through 1098 Processing helix chain 'D' and resid 1098 through 1105 removed outlier: 4.256A pdb=" N THR D1102 " --> pdb=" O GLN D1098 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D1105 " --> pdb=" O THR D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1107 through 1118 Processing helix chain 'D' and resid 410 through 440 removed outlier: 3.740A pdb=" N VAL D 426 " --> pdb=" O GLY D 422 " (cutoff:3.500A) Proline residue: D 427 - end of helix Processing helix chain 'D' and resid 441 through 453 Processing helix chain 'D' and resid 472 through 486 removed outlier: 4.152A pdb=" N PHE D 476 " --> pdb=" O GLU D 472 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 484 " --> pdb=" O TYR D 480 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 486 " --> pdb=" O MET D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 489 No H-bonds generated for 'chain 'D' and resid 487 through 489' Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.632A pdb=" N THR H 72 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.508A pdb=" N THR H 121 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.998A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER H 194 " --> pdb=" O CYS H 154 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.998A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER H 194 " --> pdb=" O CYS H 154 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.879A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.973A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.631A pdb=" N GLY K 10 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR K 118 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.712A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.445A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.553A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.781A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 146 through 151 Processing sheet with id=AB4, first strand: chain 'D' and resid 260 through 261 removed outlier: 3.741A pdb=" N ASN D 261 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR D 272 " --> pdb=" O ASN D 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 348 through 349 365 hydrogen bonds defined for protein. 1020 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: 1.28 Time building geometry restraints manager: 0.86 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: 2403 1.34 - 1.46: 1992 1.46 - 1.58: 3396 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 7846 Sorted by residual: bond pdb=" CA GLY D 255 " pdb=" C GLY D 255 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.51e+00 bond pdb=" CB PRO D 427 " pdb=" CG PRO D 427 " ideal model delta sigma weight residual 1.492 1.425 0.067 5.00e-02 4.00e+02 1.81e+00 bond pdb=" CB ASN K 77 " pdb=" CG ASN K 77 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.80e+00 bond pdb=" N GLY D 255 " pdb=" CA GLY D 255 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.77e+00 bond pdb=" N THR H 205 " pdb=" CA THR H 205 " ideal model delta sigma weight residual 1.460 1.477 -0.017 1.54e-02 4.22e+03 1.21e+00 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 10461 2.48 - 4.97: 164 4.97 - 7.45: 28 7.45 - 9.93: 3 9.93 - 12.41: 1 Bond angle restraints: 10657 Sorted by residual: angle pdb=" CA LEU D 176 " pdb=" CB LEU D 176 " pdb=" CG LEU D 176 " ideal model delta sigma weight residual 116.30 128.71 -12.41 3.50e+00 8.16e-02 1.26e+01 angle pdb=" C MET D 345 " pdb=" N ASN D 346 " pdb=" CA ASN D 346 " ideal model delta sigma weight residual 122.82 127.53 -4.71 1.42e+00 4.96e-01 1.10e+01 angle pdb=" CB MET D 294 " pdb=" CG MET D 294 " pdb=" SD MET D 294 " ideal model delta sigma weight residual 112.70 122.47 -9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C ARG D 225 " pdb=" N ARG D 226 " pdb=" CA ARG D 226 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C TYR D 463 " pdb=" N GLN D 464 " pdb=" CA GLN D 464 " ideal model delta sigma weight residual 122.61 127.58 -4.97 1.56e+00 4.11e-01 1.02e+01 ... (remaining 10652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4139 16.00 - 31.99: 373 31.99 - 47.99: 90 47.99 - 63.98: 18 63.98 - 79.98: 8 Dihedral angle restraints: 4628 sinusoidal: 1765 harmonic: 2863 Sorted by residual: dihedral pdb=" CB CYS D 282 " pdb=" SG CYS D 282 " pdb=" SG CYS D 357 " pdb=" CB CYS D 357 " ideal model delta sinusoidal sigma weight residual -86.00 -136.09 50.09 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CB CYS D 185 " pdb=" SG CYS D 185 " pdb=" SG CYS D 260 " pdb=" CB CYS D 260 " ideal model delta sinusoidal sigma weight residual 93.00 133.22 -40.22 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA PRO D 230 " pdb=" C PRO D 230 " pdb=" N GLU D 231 " pdb=" CA GLU D 231 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 4625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 833 0.043 - 0.086: 275 0.086 - 0.129: 73 0.129 - 0.172: 10 0.172 - 0.216: 3 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CB THR H 94 " pdb=" CA THR H 94 " pdb=" OG1 THR H 94 " pdb=" CG2 THR H 94 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL D 426 " pdb=" CA VAL D 426 " pdb=" CG1 VAL D 426 " pdb=" CG2 VAL D 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ASN D 346 " pdb=" N ASN D 346 " pdb=" C ASN D 346 " pdb=" CB ASN D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 1191 not shown) Planarity restraints: 1340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN K 77 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C ASN K 77 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN K 77 " -0.018 2.00e-02 2.50e+03 pdb=" N THR K 78 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN K 13 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO K 14 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO K 14 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO K 14 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 182 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO D 183 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.037 5.00e-02 4.00e+02 ... (remaining 1337 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1343 2.77 - 3.30: 7131 3.30 - 3.84: 12285 3.84 - 4.37: 14088 4.37 - 4.90: 24610 Nonbonded interactions: 59457 Sorted by model distance: nonbonded pdb=" OG SER K 35 " pdb=" OH TYR K 108 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR D 167 " pdb=" OE1 GLN D 180 " model vdw 2.250 3.040 nonbonded pdb=" O TYR L 50 " pdb=" OG SER L 54 " model vdw 2.263 3.040 nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP D 351 " pdb=" OH TYR D 480 " model vdw 2.294 3.040 ... (remaining 59452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.410 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.830 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7854 Z= 0.160 Angle : 0.770 12.414 10673 Z= 0.397 Chirality : 0.047 0.216 1194 Planarity : 0.006 0.068 1340 Dihedral : 13.568 79.981 2770 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.26), residues: 974 helix: -1.26 (0.27), residues: 291 sheet: 0.11 (0.33), residues: 265 loop : -1.40 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 31 TYR 0.027 0.002 TYR H 53 PHE 0.018 0.002 PHE H 114 TRP 0.028 0.002 TRP D 445 HIS 0.005 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7846) covalent geometry : angle 0.77012 (10657) SS BOND : bond 0.00214 ( 8) SS BOND : angle 0.96992 ( 16) hydrogen bonds : bond 0.24383 ( 349) hydrogen bonds : angle 8.61234 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: H 23 LEU cc_start: 0.7979 (mp) cc_final: 0.7778 (mt) REVERT: H 76 ASP cc_start: 0.7945 (p0) cc_final: 0.7588 (p0) REVERT: H 122 LEU cc_start: 0.8677 (tp) cc_final: 0.8437 (tt) REVERT: H 131 LYS cc_start: 0.7700 (ptmm) cc_final: 0.7323 (ptmm) REVERT: H 184 LEU cc_start: 0.8301 (mt) cc_final: 0.8087 (mt) REVERT: L 47 LEU cc_start: 0.8757 (tt) cc_final: 0.8375 (tp) REVERT: L 62 ARG cc_start: 0.7809 (ptt-90) cc_final: 0.7207 (ptt180) REVERT: L 73 THR cc_start: 0.8279 (m) cc_final: 0.8020 (p) REVERT: L 83 ASP cc_start: 0.7740 (m-30) cc_final: 0.6768 (m-30) REVERT: D 238 SER cc_start: 0.7868 (p) cc_final: 0.7491 (t) REVERT: D 1032 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7824 (mtpt) REVERT: D 1033 ASP cc_start: 0.7150 (m-30) cc_final: 0.6755 (m-30) REVERT: D 1088 LYS cc_start: 0.8154 (mttp) cc_final: 0.7877 (mttm) REVERT: D 417 ILE cc_start: 0.8641 (tp) cc_final: 0.8364 (tt) REVERT: D 423 LEU cc_start: 0.8446 (mp) cc_final: 0.8239 (mt) REVERT: D 438 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6579 (mm-30) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0839 time to fit residues: 21.1754 Evaluate side-chains 170 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 169 ASN H 211 ASN H 213 ASN K 77 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.161220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138648 restraints weight = 11836.205| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.67 r_work: 0.3648 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7854 Z= 0.203 Angle : 0.673 8.565 10673 Z= 0.351 Chirality : 0.045 0.166 1194 Planarity : 0.005 0.065 1340 Dihedral : 4.865 24.581 1068 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.53 % Allowed : 8.54 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.27), residues: 974 helix: -0.07 (0.29), residues: 295 sheet: 0.17 (0.33), residues: 249 loop : -1.23 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 90 TYR 0.025 0.002 TYR D 237 PHE 0.024 0.002 PHE D 358 TRP 0.015 0.002 TRP D 445 HIS 0.004 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 7846) covalent geometry : angle 0.67313 (10657) SS BOND : bond 0.00269 ( 8) SS BOND : angle 0.79419 ( 16) hydrogen bonds : bond 0.03814 ( 349) hydrogen bonds : angle 5.32384 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: H 131 LYS cc_start: 0.8236 (ptmm) cc_final: 0.7951 (ptmm) REVERT: H 184 LEU cc_start: 0.8215 (mt) cc_final: 0.7964 (mt) REVERT: H 191 SER cc_start: 0.8127 (p) cc_final: 0.7710 (m) REVERT: H 198 VAL cc_start: 0.8196 (t) cc_final: 0.7889 (m) REVERT: L 12 LEU cc_start: 0.7816 (mp) cc_final: 0.7601 (mt) REVERT: L 62 ARG cc_start: 0.7780 (ptt-90) cc_final: 0.7252 (ptt180) REVERT: L 83 ASP cc_start: 0.7895 (m-30) cc_final: 0.7129 (m-30) REVERT: L 110 ARG cc_start: 0.8390 (ptm160) cc_final: 0.8185 (ptm160) REVERT: D 1032 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7807 (mtpt) REVERT: D 1091 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7163 (tm-30) REVERT: D 1110 TYR cc_start: 0.7772 (t80) cc_final: 0.7373 (t80) REVERT: D 438 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6728 (mm-30) outliers start: 21 outliers final: 12 residues processed: 181 average time/residue: 0.0824 time to fit residues: 20.8840 Evaluate side-chains 169 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 205 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 26 optimal weight: 0.0770 chunk 58 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN K 77 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.163012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140475 restraints weight = 11792.685| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.71 r_work: 0.3668 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7854 Z= 0.116 Angle : 0.595 8.608 10673 Z= 0.302 Chirality : 0.042 0.178 1194 Planarity : 0.004 0.057 1340 Dihedral : 4.480 23.537 1068 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.29 % Allowed : 12.27 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.27), residues: 974 helix: 0.43 (0.30), residues: 302 sheet: 0.42 (0.34), residues: 243 loop : -1.12 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 52 TYR 0.018 0.001 TYR D 237 PHE 0.011 0.001 PHE D 201 TRP 0.009 0.001 TRP D 445 HIS 0.003 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7846) covalent geometry : angle 0.59482 (10657) SS BOND : bond 0.00288 ( 8) SS BOND : angle 0.50915 ( 16) hydrogen bonds : bond 0.03410 ( 349) hydrogen bonds : angle 4.86403 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 122 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8288 (tp) REVERT: H 131 LYS cc_start: 0.8215 (ptmm) cc_final: 0.7869 (ptmm) REVERT: H 155 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7856 (tt) REVERT: H 191 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7682 (m) REVERT: L 5 MET cc_start: 0.8426 (mmt) cc_final: 0.8098 (mmt) REVERT: L 12 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7596 (mt) REVERT: L 62 ARG cc_start: 0.7752 (ptt-90) cc_final: 0.7203 (ptt180) REVERT: L 66 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7958 (p) REVERT: L 83 ASP cc_start: 0.7859 (m-30) cc_final: 0.7072 (m-30) REVERT: L 157 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8396 (mm-40) REVERT: D 1032 LYS cc_start: 0.8030 (ttmt) cc_final: 0.7826 (mtpt) REVERT: D 1091 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7155 (tm-30) REVERT: D 1108 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7795 (tp40) REVERT: D 445 TRP cc_start: 0.7669 (m-10) cc_final: 0.7435 (m-10) outliers start: 19 outliers final: 10 residues processed: 162 average time/residue: 0.0845 time to fit residues: 19.1164 Evaluate side-chains 174 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 ASN D1085 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.159492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136346 restraints weight = 11943.560| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.75 r_work: 0.3612 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.144 Angle : 0.597 7.996 10673 Z= 0.305 Chirality : 0.042 0.181 1194 Planarity : 0.004 0.053 1340 Dihedral : 4.417 23.074 1068 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.25 % Allowed : 13.48 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.28), residues: 974 helix: 0.87 (0.31), residues: 290 sheet: 0.67 (0.34), residues: 247 loop : -1.02 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 52 TYR 0.022 0.002 TYR D 237 PHE 0.015 0.001 PHE D 358 TRP 0.011 0.001 TRP D 332 HIS 0.004 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7846) covalent geometry : angle 0.59680 (10657) SS BOND : bond 0.00308 ( 8) SS BOND : angle 0.69628 ( 16) hydrogen bonds : bond 0.03132 ( 349) hydrogen bonds : angle 4.60640 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 94 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8693 (t) REVERT: H 131 LYS cc_start: 0.8409 (ptmm) cc_final: 0.8096 (ptmm) REVERT: H 191 SER cc_start: 0.8115 (OUTLIER) cc_final: 0.7690 (m) REVERT: L 12 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7629 (mt) REVERT: L 66 SER cc_start: 0.8262 (m) cc_final: 0.7984 (p) REVERT: D 250 ILE cc_start: 0.8122 (mt) cc_final: 0.7824 (mt) REVERT: D 318 GLU cc_start: 0.7292 (mp0) cc_final: 0.7026 (mp0) REVERT: D 1009 GLU cc_start: 0.7683 (tt0) cc_final: 0.7413 (tt0) REVERT: D 1046 GLN cc_start: 0.8304 (tt0) cc_final: 0.8070 (tt0) REVERT: D 1091 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7297 (tm-30) REVERT: D 1100 LYS cc_start: 0.8043 (mmtp) cc_final: 0.7562 (mmmt) REVERT: D 1108 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7856 (tp-100) REVERT: D 1110 TYR cc_start: 0.7898 (t80) cc_final: 0.7507 (t80) REVERT: D 484 LEU cc_start: 0.6951 (mm) cc_final: 0.6511 (mt) outliers start: 27 outliers final: 19 residues processed: 179 average time/residue: 0.0863 time to fit residues: 21.5386 Evaluate side-chains 188 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.0470 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.159528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136633 restraints weight = 11873.004| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.73 r_work: 0.3618 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.130 Angle : 0.590 8.035 10673 Z= 0.300 Chirality : 0.042 0.170 1194 Planarity : 0.004 0.051 1340 Dihedral : 4.372 22.808 1068 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.77 % Allowed : 15.76 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.28), residues: 974 helix: 1.05 (0.31), residues: 290 sheet: 0.67 (0.34), residues: 241 loop : -0.98 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.020 0.001 TYR D 237 PHE 0.014 0.001 PHE D 201 TRP 0.009 0.001 TRP D 332 HIS 0.004 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7846) covalent geometry : angle 0.59026 (10657) SS BOND : bond 0.00300 ( 8) SS BOND : angle 0.60820 ( 16) hydrogen bonds : bond 0.03029 ( 349) hydrogen bonds : angle 4.49026 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: H 131 LYS cc_start: 0.8387 (ptmm) cc_final: 0.8084 (ptmm) REVERT: H 191 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7642 (m) REVERT: K 46 GLU cc_start: 0.6595 (mp0) cc_final: 0.5589 (mp0) REVERT: L 62 ARG cc_start: 0.7585 (ptt90) cc_final: 0.7086 (ptt90) REVERT: L 66 SER cc_start: 0.8274 (m) cc_final: 0.8005 (p) REVERT: L 83 ASP cc_start: 0.7786 (m-30) cc_final: 0.7109 (m-30) REVERT: D 250 ILE cc_start: 0.8130 (mt) cc_final: 0.7833 (mt) REVERT: D 390 ILE cc_start: 0.8064 (tt) cc_final: 0.7858 (tt) REVERT: D 1046 GLN cc_start: 0.8278 (tt0) cc_final: 0.8018 (tt0) REVERT: D 1091 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7242 (tm-30) REVERT: D 1100 LYS cc_start: 0.8018 (mmtp) cc_final: 0.7579 (mmmt) REVERT: D 1110 TYR cc_start: 0.7923 (t80) cc_final: 0.7549 (t80) REVERT: D 484 LEU cc_start: 0.6954 (mm) cc_final: 0.6499 (mt) outliers start: 23 outliers final: 15 residues processed: 173 average time/residue: 0.0879 time to fit residues: 21.1792 Evaluate side-chains 174 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 0.0870 chunk 45 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 62 optimal weight: 0.1980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.158726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135732 restraints weight = 12021.692| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.77 r_work: 0.3624 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7854 Z= 0.122 Angle : 0.589 8.714 10673 Z= 0.301 Chirality : 0.042 0.177 1194 Planarity : 0.004 0.050 1340 Dihedral : 4.287 18.973 1068 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.29 % Allowed : 18.41 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.28), residues: 974 helix: 1.19 (0.31), residues: 290 sheet: 0.68 (0.33), residues: 241 loop : -0.90 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 62 TYR 0.019 0.001 TYR D 237 PHE 0.025 0.001 PHE H 136 TRP 0.010 0.001 TRP D 445 HIS 0.003 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7846) covalent geometry : angle 0.58947 (10657) SS BOND : bond 0.00290 ( 8) SS BOND : angle 0.55748 ( 16) hydrogen bonds : bond 0.02975 ( 349) hydrogen bonds : angle 4.39945 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: H 131 LYS cc_start: 0.8328 (ptmm) cc_final: 0.8033 (ptmm) REVERT: H 191 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7623 (m) REVERT: K 46 GLU cc_start: 0.6588 (mp0) cc_final: 0.5547 (mp0) REVERT: L 62 ARG cc_start: 0.7585 (ptt90) cc_final: 0.6841 (ptt180) REVERT: L 66 SER cc_start: 0.8251 (m) cc_final: 0.7991 (p) REVERT: L 83 ASP cc_start: 0.7810 (m-30) cc_final: 0.7317 (m-30) REVERT: L 135 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8006 (m) REVERT: D 250 ILE cc_start: 0.8118 (mt) cc_final: 0.7813 (mt) REVERT: D 1046 GLN cc_start: 0.8225 (tt0) cc_final: 0.8024 (tt0) REVERT: D 1091 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7218 (tm-30) REVERT: D 1100 LYS cc_start: 0.7992 (mmtp) cc_final: 0.7560 (mmmt) REVERT: D 1110 TYR cc_start: 0.7957 (t80) cc_final: 0.7605 (t80) REVERT: D 414 MET cc_start: 0.8024 (tpp) cc_final: 0.7750 (tpp) REVERT: D 484 LEU cc_start: 0.6973 (mm) cc_final: 0.6537 (mt) outliers start: 19 outliers final: 15 residues processed: 168 average time/residue: 0.0889 time to fit residues: 20.6877 Evaluate side-chains 178 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 79 optimal weight: 0.4980 chunk 46 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 1 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.157549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134314 restraints weight = 11749.424| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.78 r_work: 0.3572 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7854 Z= 0.182 Angle : 0.640 9.581 10673 Z= 0.326 Chirality : 0.044 0.184 1194 Planarity : 0.004 0.051 1340 Dihedral : 4.532 20.550 1068 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.01 % Allowed : 18.29 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.28), residues: 974 helix: 1.15 (0.31), residues: 289 sheet: 0.73 (0.33), residues: 243 loop : -0.94 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.025 0.002 TYR D 237 PHE 0.022 0.002 PHE H 136 TRP 0.014 0.002 TRP D 332 HIS 0.005 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7846) covalent geometry : angle 0.63967 (10657) SS BOND : bond 0.00386 ( 8) SS BOND : angle 0.78830 ( 16) hydrogen bonds : bond 0.03281 ( 349) hydrogen bonds : angle 4.57851 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8242 (m) cc_final: 0.7929 (t) REVERT: H 131 LYS cc_start: 0.8525 (ptmm) cc_final: 0.8281 (ptmm) REVERT: H 191 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7670 (m) REVERT: H 194 SER cc_start: 0.8314 (t) cc_final: 0.7952 (p) REVERT: L 66 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.8015 (p) REVERT: L 83 ASP cc_start: 0.7802 (m-30) cc_final: 0.7565 (m-30) REVERT: D 250 ILE cc_start: 0.8123 (mt) cc_final: 0.7825 (mt) REVERT: D 1091 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7202 (tm-30) REVERT: D 1100 LYS cc_start: 0.8182 (mmtp) cc_final: 0.7689 (mmmt) REVERT: D 414 MET cc_start: 0.8160 (tpp) cc_final: 0.7867 (ttt) REVERT: D 484 LEU cc_start: 0.6993 (mm) cc_final: 0.6557 (mt) outliers start: 25 outliers final: 19 residues processed: 170 average time/residue: 0.0914 time to fit residues: 21.4432 Evaluate side-chains 175 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 1 GLN Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.156751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133885 restraints weight = 11907.367| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.77 r_work: 0.3568 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7854 Z= 0.168 Angle : 0.641 10.064 10673 Z= 0.327 Chirality : 0.044 0.186 1194 Planarity : 0.004 0.051 1340 Dihedral : 4.515 21.417 1068 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.53 % Allowed : 19.37 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.28), residues: 974 helix: 1.16 (0.31), residues: 289 sheet: 0.65 (0.33), residues: 244 loop : -0.98 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 213 TYR 0.023 0.002 TYR D 237 PHE 0.025 0.001 PHE H 136 TRP 0.010 0.001 TRP D 332 HIS 0.009 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 7846) covalent geometry : angle 0.64092 (10657) SS BOND : bond 0.00371 ( 8) SS BOND : angle 0.71775 ( 16) hydrogen bonds : bond 0.03251 ( 349) hydrogen bonds : angle 4.56464 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.300 Fit side-chains REVERT: H 10 SER cc_start: 0.8248 (m) cc_final: 0.7939 (t) REVERT: H 131 LYS cc_start: 0.8529 (ptmm) cc_final: 0.8275 (ptmm) REVERT: H 160 PHE cc_start: 0.8663 (t80) cc_final: 0.8381 (t80) REVERT: H 191 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7679 (m) REVERT: H 194 SER cc_start: 0.8280 (t) cc_final: 0.7929 (p) REVERT: L 18 ASP cc_start: 0.8234 (t0) cc_final: 0.7953 (t0) REVERT: L 66 SER cc_start: 0.8300 (m) cc_final: 0.8036 (p) REVERT: L 209 LYS cc_start: 0.8550 (mmtp) cc_final: 0.8276 (mmmt) REVERT: D 250 ILE cc_start: 0.8131 (mt) cc_final: 0.7899 (mt) REVERT: D 1091 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7238 (tm-30) REVERT: D 1100 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7664 (mmmt) REVERT: D 1118 LEU cc_start: 0.7658 (tp) cc_final: 0.7434 (tt) REVERT: D 414 MET cc_start: 0.8169 (tpp) cc_final: 0.7904 (ttm) REVERT: D 484 LEU cc_start: 0.7015 (mm) cc_final: 0.6596 (mt) outliers start: 21 outliers final: 19 residues processed: 169 average time/residue: 0.0923 time to fit residues: 21.3697 Evaluate side-chains 181 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.158418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.135430 restraints weight = 12006.604| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.76 r_work: 0.3569 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7854 Z= 0.155 Angle : 0.643 11.065 10673 Z= 0.325 Chirality : 0.043 0.189 1194 Planarity : 0.004 0.051 1340 Dihedral : 4.455 23.566 1068 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.77 % Allowed : 19.74 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.28), residues: 974 helix: 1.21 (0.31), residues: 289 sheet: 0.62 (0.32), residues: 250 loop : -0.95 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 455 TYR 0.022 0.002 TYR D 237 PHE 0.026 0.001 PHE H 136 TRP 0.010 0.001 TRP D 332 HIS 0.005 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7846) covalent geometry : angle 0.64256 (10657) SS BOND : bond 0.00351 ( 8) SS BOND : angle 0.64532 ( 16) hydrogen bonds : bond 0.03207 ( 349) hydrogen bonds : angle 4.52683 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8238 (m) cc_final: 0.7946 (t) REVERT: H 131 LYS cc_start: 0.8512 (ptmm) cc_final: 0.8250 (ptmm) REVERT: H 160 PHE cc_start: 0.8671 (t80) cc_final: 0.8408 (t80) REVERT: H 191 SER cc_start: 0.8112 (OUTLIER) cc_final: 0.7670 (m) REVERT: H 194 SER cc_start: 0.8194 (t) cc_final: 0.7850 (p) REVERT: L 18 ASP cc_start: 0.8238 (t0) cc_final: 0.7957 (t0) REVERT: L 62 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7278 (ptt180) REVERT: L 66 SER cc_start: 0.8295 (m) cc_final: 0.8055 (p) REVERT: D 250 ILE cc_start: 0.8121 (mt) cc_final: 0.7898 (mt) REVERT: D 1091 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7206 (tm-30) REVERT: D 1100 LYS cc_start: 0.8110 (mmtp) cc_final: 0.7613 (mmmt) REVERT: D 1118 LEU cc_start: 0.7690 (tp) cc_final: 0.7467 (tt) REVERT: D 414 MET cc_start: 0.8207 (tpp) cc_final: 0.7931 (ttm) REVERT: D 484 LEU cc_start: 0.7012 (mm) cc_final: 0.6619 (mt) outliers start: 23 outliers final: 20 residues processed: 168 average time/residue: 0.0960 time to fit residues: 21.9690 Evaluate side-chains 181 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 1097 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.0170 chunk 27 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.157032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134619 restraints weight = 11850.658| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.72 r_work: 0.3583 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7854 Z= 0.142 Angle : 0.645 11.808 10673 Z= 0.327 Chirality : 0.043 0.191 1194 Planarity : 0.004 0.051 1340 Dihedral : 4.412 21.584 1068 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.77 % Allowed : 20.46 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.28), residues: 974 helix: 1.24 (0.31), residues: 290 sheet: 0.65 (0.33), residues: 251 loop : -0.91 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 213 TYR 0.020 0.001 TYR D 237 PHE 0.025 0.001 PHE H 136 TRP 0.009 0.001 TRP D 332 HIS 0.007 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7846) covalent geometry : angle 0.64459 (10657) SS BOND : bond 0.00350 ( 8) SS BOND : angle 0.62425 ( 16) hydrogen bonds : bond 0.03152 ( 349) hydrogen bonds : angle 4.46560 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8221 (m) cc_final: 0.7927 (t) REVERT: H 86 MET cc_start: 0.7688 (mmt) cc_final: 0.7224 (mmt) REVERT: H 131 LYS cc_start: 0.8492 (ptmm) cc_final: 0.8216 (ptmm) REVERT: H 160 PHE cc_start: 0.8670 (t80) cc_final: 0.8418 (t80) REVERT: H 191 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7653 (m) REVERT: H 194 SER cc_start: 0.8133 (t) cc_final: 0.7781 (p) REVERT: L 18 ASP cc_start: 0.8292 (t0) cc_final: 0.7989 (t0) REVERT: L 62 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7240 (ptt180) REVERT: L 66 SER cc_start: 0.8265 (m) cc_final: 0.8030 (p) REVERT: D 171 GLN cc_start: 0.7241 (mp10) cc_final: 0.7032 (mp10) REVERT: D 250 ILE cc_start: 0.8108 (mt) cc_final: 0.7883 (mt) REVERT: D 1091 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 1100 LYS cc_start: 0.8068 (mmtp) cc_final: 0.7585 (mmmt) REVERT: D 1118 LEU cc_start: 0.7705 (tp) cc_final: 0.7467 (tt) REVERT: D 414 MET cc_start: 0.8199 (tpp) cc_final: 0.7929 (ttm) REVERT: D 484 LEU cc_start: 0.6975 (mm) cc_final: 0.6596 (mt) outliers start: 23 outliers final: 17 residues processed: 171 average time/residue: 0.0955 time to fit residues: 22.1452 Evaluate side-chains 182 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 434 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 19 optimal weight: 0.0370 chunk 85 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 57 optimal weight: 0.6980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134541 restraints weight = 11850.401| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.73 r_work: 0.3589 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7854 Z= 0.124 Angle : 0.637 11.862 10673 Z= 0.321 Chirality : 0.043 0.188 1194 Planarity : 0.004 0.051 1340 Dihedral : 4.363 23.062 1068 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.17 % Allowed : 21.42 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.28), residues: 974 helix: 1.30 (0.31), residues: 290 sheet: 0.65 (0.33), residues: 245 loop : -0.87 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 213 TYR 0.018 0.001 TYR D 237 PHE 0.024 0.001 PHE H 136 TRP 0.010 0.001 TRP D 445 HIS 0.009 0.001 HIS L 191 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7846) covalent geometry : angle 0.63667 (10657) SS BOND : bond 0.00320 ( 8) SS BOND : angle 0.51920 ( 16) hydrogen bonds : bond 0.03054 ( 349) hydrogen bonds : angle 4.38115 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1830.47 seconds wall clock time: 32 minutes 18.52 seconds (1938.52 seconds total)