Starting phenix.real_space_refine on Mon Apr 28 14:09:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jh7_36258/04_2025/8jh7_36258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jh7_36258/04_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_36258/04_2025/8jh7_36258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jh7_36258/04_2025/8jh7_36258.map" model { file = "/net/cci-nas-00/data/ceres_data/8jh7_36258/04_2025/8jh7_36258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jh7_36258/04_2025/8jh7_36258.cif" } resolution = 3.2 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.20, per 1000 atoms: 0.68 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: 1.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.05 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: 2.41 Time building geometry restraints manager: 2.00 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.510 Find NCS groups from input model: 0.070 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- 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 (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: -1.48 (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 TRP 0.028 0.002 TRP D 445 HIS 0.005 0.001 HIS L 191 PHE 0.018 0.002 PHE H 114 TYR 0.027 0.002 TYR H 53 ARG 0.004 0.000 ARG K 31 Details of bonding type rmsd hydrogen bonds : bond 0.24383 ( 349) hydrogen bonds : angle 8.61234 ( 1020) SS BOND : bond 0.00214 ( 8) SS BOND : angle 0.96992 ( 16) covalent geometry : bond 0.00349 ( 7846) covalent geometry : angle 0.77012 (10657) *********************** 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 : 0.811 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: 0.1755 time to fit residues: 43.7719 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 : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 169 ASN H 213 ASN ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.158299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135736 restraints weight = 11793.021| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.65 r_work: 0.3604 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7854 Z= 0.266 Angle : 0.716 8.351 10673 Z= 0.374 Chirality : 0.047 0.173 1194 Planarity : 0.005 0.066 1340 Dihedral : 5.115 24.040 1068 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.41 % Allowed : 9.03 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.27), residues: 974 helix: -0.10 (0.29), residues: 295 sheet: 0.25 (0.33), residues: 249 loop : -1.32 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 445 HIS 0.006 0.001 HIS D 328 PHE 0.029 0.002 PHE D 358 TYR 0.027 0.003 TYR D 237 ARG 0.003 0.001 ARG D 455 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 349) hydrogen bonds : angle 5.48889 ( 1020) SS BOND : bond 0.00386 ( 8) SS BOND : angle 1.02903 ( 16) covalent geometry : bond 0.00604 ( 7846) covalent geometry : angle 0.71493 (10657) *********************** 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 184 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 21 LEU cc_start: 0.8412 (tp) cc_final: 0.8206 (tp) REVERT: H 84 LEU cc_start: 0.7820 (tt) cc_final: 0.7604 (tp) REVERT: H 131 LYS cc_start: 0.8400 (ptmm) cc_final: 0.8158 (ptmm) REVERT: H 184 LEU cc_start: 0.8248 (mt) cc_final: 0.8036 (mt) REVERT: H 191 SER cc_start: 0.8147 (p) cc_final: 0.7777 (m) REVERT: K 70 VAL cc_start: 0.8218 (t) cc_final: 0.7937 (p) REVERT: K 108 TYR cc_start: 0.7017 (m-10) cc_final: 0.6780 (m-10) REVERT: L 12 LEU cc_start: 0.7876 (mp) cc_final: 0.7641 (mt) REVERT: L 62 ARG cc_start: 0.7829 (ptt-90) cc_final: 0.7420 (ptt180) REVERT: L 83 ASP cc_start: 0.7881 (m-30) cc_final: 0.7138 (m-30) REVERT: D 250 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7976 (mt) REVERT: D 353 ILE cc_start: 0.8384 (mp) cc_final: 0.8051 (mt) REVERT: D 1032 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7850 (mtpt) REVERT: D 1088 LYS cc_start: 0.8285 (mttp) cc_final: 0.7916 (mtmm) REVERT: D 1091 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7264 (tm-30) REVERT: D 1110 TYR cc_start: 0.7820 (t80) cc_final: 0.7388 (t80) REVERT: D 423 LEU cc_start: 0.8581 (mp) cc_final: 0.8279 (mp) REVERT: D 424 TYR cc_start: 0.8765 (t80) cc_final: 0.8506 (t80) outliers start: 20 outliers final: 11 residues processed: 174 average time/residue: 0.1820 time to fit residues: 43.5711 Evaluate side-chains 165 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 419 VAL 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 69 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 1 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN K 39 GLN K 77 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.159730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136778 restraints weight = 11982.175| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.73 r_work: 0.3631 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7854 Z= 0.134 Angle : 0.606 8.563 10673 Z= 0.309 Chirality : 0.042 0.182 1194 Planarity : 0.004 0.057 1340 Dihedral : 4.624 23.755 1068 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.53 % Allowed : 13.36 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.27), residues: 974 helix: 0.53 (0.30), residues: 295 sheet: 0.46 (0.34), residues: 243 loop : -1.17 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 332 HIS 0.003 0.001 HIS L 191 PHE 0.010 0.001 PHE D 420 TYR 0.019 0.001 TYR D 237 ARG 0.002 0.000 ARG K 52 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 349) hydrogen bonds : angle 4.92327 ( 1020) SS BOND : bond 0.00335 ( 8) SS BOND : angle 0.58403 ( 16) covalent geometry : bond 0.00305 ( 7846) covalent geometry : angle 0.60603 (10657) *********************** 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 186 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 131 LYS cc_start: 0.8331 (ptmm) cc_final: 0.8038 (ptmm) REVERT: H 191 SER cc_start: 0.8123 (p) cc_final: 0.7714 (m) REVERT: L 12 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7628 (mt) REVERT: L 62 ARG cc_start: 0.7774 (ptt-90) cc_final: 0.7439 (ptt180) REVERT: L 66 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.7982 (p) REVERT: L 83 ASP cc_start: 0.7880 (m-30) cc_final: 0.7094 (m-30) REVERT: L 157 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8368 (mm-40) REVERT: D 318 GLU cc_start: 0.7357 (mp0) cc_final: 0.7156 (mp0) REVERT: D 353 ILE cc_start: 0.8323 (mp) cc_final: 0.7864 (mt) REVERT: D 1009 GLU cc_start: 0.7716 (tt0) cc_final: 0.7509 (tt0) REVERT: D 1046 GLN cc_start: 0.8271 (tt0) cc_final: 0.7987 (tt0) REVERT: D 1091 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7289 (tm-30) REVERT: D 1108 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7867 (tp-100) REVERT: D 1110 TYR cc_start: 0.7824 (t80) cc_final: 0.7452 (t80) REVERT: D 445 TRP cc_start: 0.7717 (m-10) cc_final: 0.7447 (m-10) REVERT: D 484 LEU cc_start: 0.6853 (mm) cc_final: 0.6424 (mt) outliers start: 21 outliers final: 11 residues processed: 171 average time/residue: 0.1913 time to fit residues: 44.8977 Evaluate side-chains 173 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 39 GLN 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 90 GLN 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 1106 TYR 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 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 191 HIS ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.157594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134731 restraints weight = 11885.980| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.74 r_work: 0.3606 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7854 Z= 0.149 Angle : 0.596 8.044 10673 Z= 0.306 Chirality : 0.042 0.178 1194 Planarity : 0.004 0.056 1340 Dihedral : 4.543 23.789 1068 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.05 % Allowed : 16.00 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.27), residues: 974 helix: 0.68 (0.30), residues: 297 sheet: 0.52 (0.34), residues: 238 loop : -1.17 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 332 HIS 0.004 0.001 HIS L 191 PHE 0.023 0.001 PHE H 136 TYR 0.022 0.002 TYR D 237 ARG 0.002 0.000 ARG D1039 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 349) hydrogen bonds : angle 4.73487 ( 1020) SS BOND : bond 0.00343 ( 8) SS BOND : angle 0.69527 ( 16) covalent geometry : bond 0.00344 ( 7846) covalent geometry : angle 0.59574 (10657) *********************** 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 175 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 131 LYS cc_start: 0.8396 (ptmm) cc_final: 0.8104 (ptmm) REVERT: H 191 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7666 (m) REVERT: K 108 TYR cc_start: 0.7016 (m-10) cc_final: 0.6815 (m-10) REVERT: L 66 SER cc_start: 0.8299 (m) cc_final: 0.8013 (p) REVERT: D 250 ILE cc_start: 0.8153 (mt) cc_final: 0.7850 (mt) REVERT: D 1037 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8045 (mttp) REVERT: D 1046 GLN cc_start: 0.8319 (tt0) cc_final: 0.8080 (tt0) REVERT: D 1088 LYS cc_start: 0.8296 (mtmm) cc_final: 0.8083 (mttm) REVERT: D 1091 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7301 (tm-30) REVERT: D 438 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6496 (mm-30) REVERT: D 484 LEU cc_start: 0.6937 (mm) cc_final: 0.6515 (mt) outliers start: 17 outliers final: 11 residues processed: 166 average time/residue: 0.1808 time to fit residues: 41.6815 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 : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 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 48 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain D residue 167 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS D1085 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.155348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132773 restraints weight = 11871.315| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.72 r_work: 0.3565 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7854 Z= 0.190 Angle : 0.636 7.911 10673 Z= 0.328 Chirality : 0.044 0.174 1194 Planarity : 0.005 0.059 1340 Dihedral : 4.723 24.050 1068 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.13 % Allowed : 17.21 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.28), residues: 974 helix: 0.94 (0.30), residues: 289 sheet: 0.60 (0.33), residues: 244 loop : -1.12 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 332 HIS 0.003 0.001 HIS H 178 PHE 0.023 0.002 PHE H 136 TYR 0.026 0.002 TYR D 237 ARG 0.004 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 349) hydrogen bonds : angle 4.75591 ( 1020) SS BOND : bond 0.00402 ( 8) SS BOND : angle 0.90886 ( 16) covalent geometry : bond 0.00440 ( 7846) covalent geometry : angle 0.63558 (10657) *********************** 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 191 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8296 (m) cc_final: 0.7983 (t) REVERT: H 131 LYS cc_start: 0.8547 (ptmm) cc_final: 0.8312 (ptmm) REVERT: H 191 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7665 (m) REVERT: H 194 SER cc_start: 0.8304 (t) cc_final: 0.7889 (p) REVERT: K 108 TYR cc_start: 0.7131 (m-10) cc_final: 0.6799 (m-10) REVERT: L 66 SER cc_start: 0.8318 (m) cc_final: 0.8039 (p) REVERT: D 250 ILE cc_start: 0.8145 (mt) cc_final: 0.7872 (mt) REVERT: D 316 SER cc_start: 0.7443 (p) cc_final: 0.7239 (p) REVERT: D 318 GLU cc_start: 0.7249 (mp0) cc_final: 0.7033 (mp0) REVERT: D 390 ILE cc_start: 0.8136 (tt) cc_final: 0.7895 (tt) REVERT: D 1046 GLN cc_start: 0.8389 (tt0) cc_final: 0.8151 (tt0) REVERT: D 1091 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7245 (tm-30) REVERT: D 1100 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7687 (mmmt) REVERT: D 484 LEU cc_start: 0.6990 (mm) cc_final: 0.6571 (mt) outliers start: 26 outliers final: 19 residues processed: 176 average time/residue: 0.1913 time to fit residues: 46.3196 Evaluate side-chains 174 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 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 97 LEU 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 359 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 0.0060 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 0.0570 chunk 23 optimal weight: 5.9990 overall best weight: 0.3114 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.157264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134738 restraints weight = 11900.558| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.70 r_work: 0.3592 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7854 Z= 0.121 Angle : 0.588 8.688 10673 Z= 0.300 Chirality : 0.042 0.170 1194 Planarity : 0.004 0.053 1340 Dihedral : 4.427 23.975 1068 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.53 % Allowed : 19.13 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 974 helix: 1.09 (0.31), residues: 290 sheet: 0.59 (0.34), residues: 237 loop : -1.00 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 117 HIS 0.002 0.000 HIS L 191 PHE 0.021 0.001 PHE H 136 TYR 0.017 0.001 TYR D 237 ARG 0.002 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 349) hydrogen bonds : angle 4.50961 ( 1020) SS BOND : bond 0.00303 ( 8) SS BOND : angle 0.54864 ( 16) covalent geometry : bond 0.00281 ( 7846) covalent geometry : angle 0.58811 (10657) *********************** 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 185 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8229 (m) cc_final: 0.7927 (t) REVERT: H 131 LYS cc_start: 0.8460 (ptmm) cc_final: 0.8157 (ptmm) REVERT: H 191 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7647 (m) REVERT: H 194 SER cc_start: 0.8151 (t) cc_final: 0.7724 (p) REVERT: L 18 ASP cc_start: 0.8198 (t0) cc_final: 0.7909 (t0) REVERT: L 66 SER cc_start: 0.8271 (m) cc_final: 0.8021 (p) REVERT: L 83 ASP cc_start: 0.7838 (m-30) cc_final: 0.7618 (m-30) REVERT: L 145 GLU cc_start: 0.7517 (mp0) cc_final: 0.7115 (mp0) REVERT: D 250 ILE cc_start: 0.8125 (mt) cc_final: 0.7857 (mt) REVERT: D 318 GLU cc_start: 0.7249 (mp0) cc_final: 0.7036 (mp0) REVERT: D 390 ILE cc_start: 0.8083 (tt) cc_final: 0.7860 (tt) REVERT: D 1046 GLN cc_start: 0.8322 (tt0) cc_final: 0.8118 (tt0) REVERT: D 1091 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 1100 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7550 (mmmt) REVERT: D 1109 LYS cc_start: 0.8170 (ttpp) cc_final: 0.7958 (ttpp) REVERT: D 484 LEU cc_start: 0.6983 (mm) cc_final: 0.6581 (mt) outliers start: 21 outliers final: 15 residues processed: 175 average time/residue: 0.1886 time to fit residues: 45.3262 Evaluate side-chains 176 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 97 LEU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 354 SER 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 38 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 1 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 ASN D1108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.155777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132621 restraints weight = 11771.001| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.77 r_work: 0.3542 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7854 Z= 0.193 Angle : 0.648 9.010 10673 Z= 0.331 Chirality : 0.044 0.181 1194 Planarity : 0.005 0.056 1340 Dihedral : 4.665 23.841 1068 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.37 % Allowed : 20.34 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 974 helix: 1.03 (0.31), residues: 290 sheet: 0.47 (0.33), residues: 245 loop : -1.06 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 332 HIS 0.002 0.001 HIS H 38 PHE 0.024 0.002 PHE H 136 TYR 0.026 0.002 TYR D 237 ARG 0.002 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 349) hydrogen bonds : angle 4.69291 ( 1020) SS BOND : bond 0.00436 ( 8) SS BOND : angle 0.89949 ( 16) covalent geometry : bond 0.00450 ( 7846) covalent geometry : angle 0.64745 (10657) *********************** 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 189 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.784 Fit side-chains REVERT: H 10 SER cc_start: 0.8259 (m) cc_final: 0.7972 (t) REVERT: H 131 LYS cc_start: 0.8548 (ptmm) cc_final: 0.8311 (ptmm) REVERT: H 160 PHE cc_start: 0.8658 (t80) cc_final: 0.8411 (t80) REVERT: H 191 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7679 (m) REVERT: H 194 SER cc_start: 0.8299 (t) cc_final: 0.7912 (p) REVERT: H 224 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.6082 (mmtt) REVERT: L 18 ASP cc_start: 0.8253 (t0) cc_final: 0.7932 (t0) REVERT: L 62 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7197 (ptt180) REVERT: L 66 SER cc_start: 0.8312 (m) cc_final: 0.8041 (p) REVERT: L 145 GLU cc_start: 0.7557 (mp0) cc_final: 0.7074 (mp0) REVERT: D 250 ILE cc_start: 0.8145 (mt) cc_final: 0.7875 (mt) REVERT: D 390 ILE cc_start: 0.8143 (tt) cc_final: 0.7905 (tt) REVERT: D 1046 GLN cc_start: 0.8403 (tt0) cc_final: 0.8165 (tt0) REVERT: D 1088 LYS cc_start: 0.8343 (mtmm) cc_final: 0.8056 (mttm) REVERT: D 1091 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7264 (tm-30) REVERT: D 1100 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7681 (mmmt) REVERT: D 482 MET cc_start: 0.7835 (mmm) cc_final: 0.7606 (mmm) REVERT: D 484 LEU cc_start: 0.7014 (mm) cc_final: 0.6636 (mt) outliers start: 28 outliers final: 23 residues processed: 176 average time/residue: 0.1960 time to fit residues: 46.4076 Evaluate side-chains 187 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 77 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 H residue 224 LYS Chi-restraints excluded: chain K residue 1 GLN Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 182 THR 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 410 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.154300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131565 restraints weight = 11953.784| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.76 r_work: 0.3547 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7854 Z= 0.182 Angle : 0.659 9.942 10673 Z= 0.336 Chirality : 0.044 0.185 1194 Planarity : 0.004 0.055 1340 Dihedral : 4.626 20.618 1068 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.01 % Allowed : 21.18 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.28), residues: 974 helix: 1.11 (0.31), residues: 290 sheet: 0.41 (0.33), residues: 245 loop : -1.04 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 445 HIS 0.008 0.001 HIS L 191 PHE 0.025 0.002 PHE H 136 TYR 0.024 0.002 TYR D 237 ARG 0.003 0.000 ARG L 213 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 349) hydrogen bonds : angle 4.68654 ( 1020) SS BOND : bond 0.00394 ( 8) SS BOND : angle 0.75935 ( 16) covalent geometry : bond 0.00424 ( 7846) covalent geometry : angle 0.65850 (10657) *********************** 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 191 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 10 SER cc_start: 0.8249 (m) cc_final: 0.7970 (t) REVERT: H 131 LYS cc_start: 0.8530 (ptmm) cc_final: 0.8274 (ptmm) REVERT: H 160 PHE cc_start: 0.8645 (t80) cc_final: 0.8405 (t80) REVERT: H 191 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7677 (m) REVERT: H 194 SER cc_start: 0.8272 (t) cc_final: 0.7877 (p) REVERT: H 224 LYS cc_start: 0.6321 (OUTLIER) cc_final: 0.6085 (mmtt) REVERT: L 18 ASP cc_start: 0.8279 (t0) cc_final: 0.7966 (t0) REVERT: L 62 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7199 (ptt180) REVERT: L 66 SER cc_start: 0.8298 (m) cc_final: 0.8043 (p) REVERT: L 137 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8362 (pp) REVERT: L 145 GLU cc_start: 0.7559 (mp0) cc_final: 0.7113 (mp0) REVERT: L 190 LYS cc_start: 0.8075 (ptmm) cc_final: 0.7873 (ptmm) REVERT: L 209 LYS cc_start: 0.8538 (mmtp) cc_final: 0.8301 (mmmm) REVERT: D 250 ILE cc_start: 0.8137 (mt) cc_final: 0.7663 (mt) REVERT: D 390 ILE cc_start: 0.8109 (tt) cc_final: 0.7903 (tt) REVERT: D 1046 GLN cc_start: 0.8398 (tt0) cc_final: 0.8167 (tt0) REVERT: D 1088 LYS cc_start: 0.8321 (mtmm) cc_final: 0.8016 (mttm) REVERT: D 1091 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7236 (tm-30) REVERT: D 1100 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7650 (mmmt) REVERT: D 484 LEU cc_start: 0.6996 (mm) cc_final: 0.6614 (mt) outliers start: 25 outliers final: 21 residues processed: 179 average time/residue: 0.1973 time to fit residues: 47.4402 Evaluate side-chains 187 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 77 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 H residue 224 LYS Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 162 GLN Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 202 ILE 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 72 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.0470 chunk 90 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.153887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131536 restraints weight = 11966.805| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.73 r_work: 0.3559 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7854 Z= 0.146 Angle : 0.654 11.046 10673 Z= 0.331 Chirality : 0.043 0.185 1194 Planarity : 0.004 0.053 1340 Dihedral : 4.548 22.267 1068 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.77 % Allowed : 22.02 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 974 helix: 1.18 (0.31), residues: 291 sheet: 0.44 (0.33), residues: 245 loop : -1.00 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 445 HIS 0.017 0.001 HIS L 191 PHE 0.025 0.001 PHE H 136 TYR 0.020 0.001 TYR D 237 ARG 0.003 0.000 ARG L 213 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 349) hydrogen bonds : angle 4.64082 ( 1020) SS BOND : bond 0.00359 ( 8) SS BOND : angle 0.63670 ( 16) covalent geometry : bond 0.00341 ( 7846) covalent geometry : angle 0.65439 (10657) *********************** 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 186 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: H 10 SER cc_start: 0.8240 (m) cc_final: 0.7955 (t) REVERT: H 131 LYS cc_start: 0.8503 (ptmm) cc_final: 0.8251 (ptmm) REVERT: H 160 PHE cc_start: 0.8643 (t80) cc_final: 0.8404 (t80) REVERT: H 191 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7663 (m) REVERT: H 194 SER cc_start: 0.8183 (t) cc_final: 0.7776 (p) REVERT: K 46 GLU cc_start: 0.6478 (mp0) cc_final: 0.5614 (mp0) REVERT: L 18 ASP cc_start: 0.8252 (t0) cc_final: 0.7948 (t0) REVERT: L 66 SER cc_start: 0.8272 (m) cc_final: 0.8031 (p) REVERT: L 137 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8345 (pp) REVERT: L 145 GLU cc_start: 0.7519 (mp0) cc_final: 0.7075 (mp0) REVERT: L 147 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8135 (pttp) REVERT: L 209 LYS cc_start: 0.8528 (mmtp) cc_final: 0.8289 (mmmm) REVERT: D 250 ILE cc_start: 0.8134 (mt) cc_final: 0.7883 (mt) REVERT: D 1046 GLN cc_start: 0.8360 (tt0) cc_final: 0.8152 (tt0) REVERT: D 1088 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7996 (mttm) REVERT: D 1091 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7226 (tm-30) REVERT: D 1100 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7620 (mmmt) REVERT: D 484 LEU cc_start: 0.6959 (mm) cc_final: 0.6572 (mt) outliers start: 23 outliers final: 17 residues processed: 174 average time/residue: 0.1989 time to fit residues: 46.7580 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 : 0.807 ------------------------------------------------------------------------------- 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 77 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 75 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 188 MET 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 56 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** D1016 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.153583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131839 restraints weight = 11828.052| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.66 r_work: 0.3546 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7854 Z= 0.178 Angle : 0.680 11.702 10673 Z= 0.344 Chirality : 0.044 0.189 1194 Planarity : 0.004 0.054 1340 Dihedral : 4.668 23.143 1068 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.01 % Allowed : 23.10 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.28), residues: 974 helix: 1.15 (0.31), residues: 291 sheet: 0.40 (0.34), residues: 245 loop : -1.01 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 332 HIS 0.002 0.001 HIS L 191 PHE 0.027 0.002 PHE H 136 TYR 0.023 0.002 TYR D 237 ARG 0.002 0.000 ARG L 213 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 349) hydrogen bonds : angle 4.74009 ( 1020) SS BOND : bond 0.00406 ( 8) SS BOND : angle 0.80810 ( 16) covalent geometry : bond 0.00418 ( 7846) covalent geometry : angle 0.67962 (10657) ********************** 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 179 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.757 Fit side-chains REVERT: H 10 SER cc_start: 0.8233 (m) cc_final: 0.7965 (t) REVERT: H 131 LYS cc_start: 0.8504 (ptmm) cc_final: 0.8265 (ptmm) REVERT: H 160 PHE cc_start: 0.8630 (t80) cc_final: 0.8414 (t80) REVERT: H 191 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7684 (m) REVERT: H 194 SER cc_start: 0.8211 (t) cc_final: 0.7845 (p) REVERT: H 224 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.6234 (mmtt) REVERT: K 46 GLU cc_start: 0.6500 (mp0) cc_final: 0.5668 (mp0) REVERT: L 18 ASP cc_start: 0.8249 (t0) cc_final: 0.7981 (t0) REVERT: L 62 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7207 (ptt180) REVERT: L 66 SER cc_start: 0.8280 (m) cc_final: 0.8022 (p) REVERT: L 147 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8130 (pttp) REVERT: L 209 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8325 (mmmm) REVERT: D 167 THR cc_start: 0.5440 (OUTLIER) cc_final: 0.4287 (m) REVERT: D 250 ILE cc_start: 0.8142 (mt) cc_final: 0.7895 (mt) REVERT: D 1046 GLN cc_start: 0.8396 (tt0) cc_final: 0.8167 (tt0) REVERT: D 1088 LYS cc_start: 0.8260 (mtmm) cc_final: 0.8012 (mttp) REVERT: D 1091 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7155 (tm-30) REVERT: D 1100 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7653 (mmmt) REVERT: D 484 LEU cc_start: 0.6940 (mm) cc_final: 0.6539 (mt) outliers start: 25 outliers final: 17 residues processed: 168 average time/residue: 0.2062 time to fit residues: 46.2201 Evaluate side-chains 178 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 77 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 H residue 224 LYS Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 202 ILE 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 69 optimal weight: 0.4980 chunk 96 optimal weight: 0.0980 chunk 97 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 92 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132512 restraints weight = 11833.812| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.70 r_work: 0.3564 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7854 Z= 0.141 Angle : 0.656 12.641 10673 Z= 0.330 Chirality : 0.043 0.186 1194 Planarity : 0.004 0.053 1340 Dihedral : 4.552 22.174 1068 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Rotamer: Outliers : 2.65 % Allowed : 23.59 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.28), residues: 974 helix: 1.26 (0.31), residues: 291 sheet: 0.61 (0.34), residues: 235 loop : -1.00 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 445 HIS 0.003 0.001 HIS L 191 PHE 0.026 0.002 PHE H 136 TYR 0.020 0.001 TYR D 237 ARG 0.002 0.000 ARG L 213 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 349) hydrogen bonds : angle 4.56836 ( 1020) SS BOND : bond 0.00345 ( 8) SS BOND : angle 0.60409 ( 16) covalent geometry : bond 0.00331 ( 7846) covalent geometry : angle 0.65584 (10657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3634.58 seconds wall clock time: 63 minutes 40.45 seconds (3820.45 seconds total)