Starting phenix.real_space_refine on Tue Mar 3 17:37:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ww2_21927/03_2026/6ww2_21927.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ww2_21927/03_2026/6ww2_21927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ww2_21927/03_2026/6ww2_21927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ww2_21927/03_2026/6ww2_21927.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ww2_21927/03_2026/6ww2_21927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ww2_21927/03_2026/6ww2_21927.map" } resolution = 3.7 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= 0.039 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 32 5.16 5 C 4857 2.51 5 N 1273 2.21 5 O 1432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7594 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: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3367 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.79, per 1000 atoms: 0.24 Number of scatterers: 7594 At special positions: 0 Unit cell: (112.112, 146.608, 98.098, 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 32 16.00 O 1432 8.00 N 1273 7.00 C 4857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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=2.02 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 R 222 " - pdb=" SG CYS R 298 " distance=2.03 Simple disulfide: pdb=" SG CYS R 315 " - pdb=" SG CYS R 390 " 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: 0.50 Conformation dependent library (CDL) restraints added in 271.3 milliseconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 38.8% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.667A 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: 3.945A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.659A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 206 removed outlier: 3.703A pdb=" N GLN H 206 " --> pdb=" O LEU H 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.967A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 98 removed outlier: 3.735A pdb=" N LEU L 97 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 94 through 98' Processing helix chain 'L' and resid 185 through 189 removed outlier: 4.252A 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 'R' and resid 211 through 215 removed outlier: 3.566A pdb=" N GLN R 214 " --> pdb=" O ARG R 211 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL R 215 " --> pdb=" O THR R 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 211 through 215' Processing helix chain 'R' and resid 228 through 230 No H-bonds generated for 'chain 'R' and resid 228 through 230' Processing helix chain 'R' and resid 231 through 261 removed outlier: 4.704A pdb=" N PHE R 237 " --> pdb=" O THR R 233 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE R 239 " --> pdb=" O ALA R 235 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY R 240 " --> pdb=" O THR R 236 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP R 242 " --> pdb=" O TRP R 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU R 245 " --> pdb=" O LEU R 241 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR R 250 " --> pdb=" O CYS R 246 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 254 " --> pdb=" O THR R 250 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA R 255 " --> pdb=" O SER R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 267 No H-bonds generated for 'chain 'R' and resid 265 through 267' Processing helix chain 'R' and resid 268 through 292 removed outlier: 4.188A pdb=" N ILE R 272 " --> pdb=" O GLU R 268 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE R 273 " --> pdb=" O ARG R 269 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS R 280 " --> pdb=" O ALA R 276 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE R 285 " --> pdb=" O VAL R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 297 removed outlier: 3.679A pdb=" N VAL R 296 " --> pdb=" O GLY R 292 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA R 297 " --> pdb=" O HIS R 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 292 through 297' Processing helix chain 'R' and resid 314 through 345 removed outlier: 4.028A pdb=" N VAL R 318 " --> pdb=" O LEU R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 379 removed outlier: 3.627A pdb=" N TYR R 356 " --> pdb=" O ALA R 352 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR R 359 " --> pdb=" O GLY R 355 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU R 362 " --> pdb=" O GLN R 358 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP R 365 " --> pdb=" O HIS R 361 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU R 366 " --> pdb=" O LEU R 362 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE R 367 " --> pdb=" O ALA R 363 " (cutoff:3.500A) Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 396 through 404 Processing helix chain 'R' and resid 404 through 1025 removed outlier: 3.831A pdb=" N LEU R 408 " --> pdb=" O VAL R 404 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL R 409 " --> pdb=" O LEU R 405 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU R 412 " --> pdb=" O LEU R 408 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE R 418 " --> pdb=" O VAL R 414 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN R1018 " --> pdb=" O THR R1014 " (cutoff:3.500A) Processing helix chain 'R' and resid 1029 through 1049 removed outlier: 4.204A pdb=" N LYS R1037 " --> pdb=" O ASP R1033 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA R1048 " --> pdb=" O ASP R1044 " (cutoff:3.500A) Processing helix chain 'R' and resid 1064 through 1086 removed outlier: 4.640A pdb=" N PHE R1070 " --> pdb=" O PHE R1066 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS R1082 " --> pdb=" O ASP R1078 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU R1083 " --> pdb=" O ASP R1079 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA R1084 " --> pdb=" O ALA R1080 " (cutoff:3.500A) Processing helix chain 'R' and resid 1089 through 1098 Processing helix chain 'R' and resid 1098 through 1106 removed outlier: 4.523A pdb=" N THR R1102 " --> pdb=" O GLN R1098 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR R1106 " --> pdb=" O THR R1102 " (cutoff:3.500A) Processing helix chain 'R' and resid 1106 through 479 removed outlier: 3.804A pdb=" N ARG R1113 " --> pdb=" O LYS R1109 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU R1118 " --> pdb=" O ALA R1114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU R 446 " --> pdb=" O LYS R 442 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE R 448 " --> pdb=" O GLU R 444 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG R 449 " --> pdb=" O LYS R 445 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE R 453 " --> pdb=" O ARG R 449 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR R 454 " --> pdb=" O ILE R 450 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL R 459 " --> pdb=" O LEU R 455 " (cutoff:3.500A) Proline residue: R 460 - end of helix removed outlier: 3.919A pdb=" N HIS R 473 " --> pdb=" O LEU R 469 " (cutoff:3.500A) Processing helix chain 'R' and resid 500 through 511 removed outlier: 3.805A pdb=" N LYS R 506 " --> pdb=" O VAL R 502 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR R 507 " --> pdb=" O LEU R 503 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE R 508 " --> pdb=" O MET R 504 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 511 " --> pdb=" O TYR R 507 " (cutoff:3.500A) Processing helix chain 'R' and resid 511 through 520 removed outlier: 4.257A pdb=" N ILE R 515 " --> pdb=" O LEU R 511 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR R 516 " --> pdb=" O VAL R 512 " (cutoff:3.500A) Processing helix chain 'R' and resid 523 through 536 removed outlier: 4.233A pdb=" N ARG R 536 " --> pdb=" O ARG R 532 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.705A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 53 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.623A 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: 6.068A 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: 6.068A 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: 3.597A 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 6 removed outlier: 3.738A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY K 16 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER K 85 " --> pdb=" O GLY K 16 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.466A pdb=" N VAL K 12 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR K 118 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL K 117 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.927A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.189A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 146 through 147 removed outlier: 3.877A pdb=" N ALA L 195 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'R' and resid 381 through 383 381 hydrogen bonds defined for protein. 1065 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: 0.98 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2228 1.34 - 1.46: 2136 1.46 - 1.59: 3373 1.59 - 1.71: 0 1.71 - 1.83: 44 Bond restraints: 7781 Sorted by residual: bond pdb=" CB TRP H 102 " pdb=" CG TRP H 102 " ideal model delta sigma weight residual 1.498 1.420 0.078 3.10e-02 1.04e+03 6.30e+00 bond pdb=" C VAL R 459 " pdb=" N PRO R 460 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.12e+00 bond pdb=" CB TRP R 242 " pdb=" CG TRP R 242 " ideal model delta sigma weight residual 1.498 1.427 0.071 3.10e-02 1.04e+03 5.30e+00 bond pdb=" CB PHE H 180 " pdb=" CG PHE H 180 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.36e+00 bond pdb=" CB VAL R 215 " pdb=" CG2 VAL R 215 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.31e+00 ... (remaining 7776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 9956 2.06 - 4.12: 536 4.12 - 6.19: 70 6.19 - 8.25: 25 8.25 - 10.31: 3 Bond angle restraints: 10590 Sorted by residual: angle pdb=" C GLU R 202 " pdb=" N SER R 203 " pdb=" CA SER R 203 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.33e+01 angle pdb=" C PHE R 196 " pdb=" N VAL R 197 " pdb=" CA VAL R 197 " ideal model delta sigma weight residual 122.13 129.76 -7.63 1.85e+00 2.92e-01 1.70e+01 angle pdb=" C MET R 261 " pdb=" N GLU R 262 " pdb=" CA GLU R 262 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C ALA R1048 " pdb=" N THR R1049 " pdb=" CA THR R1049 " ideal model delta sigma weight residual 121.70 128.66 -6.96 1.80e+00 3.09e-01 1.50e+01 angle pdb=" C SER H 217 " pdb=" N ASN H 218 " pdb=" CA ASN H 218 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 ... (remaining 10585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4139 17.84 - 35.67: 352 35.67 - 53.51: 65 53.51 - 71.35: 9 71.35 - 89.18: 7 Dihedral angle restraints: 4572 sinusoidal: 1720 harmonic: 2852 Sorted by residual: dihedral pdb=" CA PRO H 199 " pdb=" C PRO H 199 " pdb=" N SER H 200 " pdb=" CA SER H 200 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA THR R 252 " pdb=" C THR R 252 " pdb=" N THR R 253 " pdb=" CA THR R 253 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ASN R 217 " pdb=" C ASN R 217 " pdb=" N CYS R 218 " pdb=" CA CYS R 218 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 4569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 722 0.046 - 0.092: 305 0.092 - 0.137: 115 0.137 - 0.183: 35 0.183 - 0.229: 13 Chirality restraints: 1190 Sorted by residual: chirality pdb=" CB VAL R 197 " pdb=" CA VAL R 197 " pdb=" CG1 VAL R 197 " pdb=" CG2 VAL R 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CG LEU H 89 " pdb=" CB LEU H 89 " pdb=" CD1 LEU H 89 " pdb=" CD2 LEU H 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE K 98 " pdb=" CA ILE K 98 " pdb=" CG1 ILE K 98 " pdb=" CG2 ILE K 98 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1187 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 215 " -0.046 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO H 216 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO H 216 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 216 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU R 194 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.48e+00 pdb=" N PRO R 195 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 195 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 195 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 238 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C TRP R 238 " 0.043 2.00e-02 2.50e+03 pdb=" O TRP R 238 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE R 239 " -0.014 2.00e-02 2.50e+03 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1672 2.77 - 3.30: 7298 3.30 - 3.84: 12541 3.84 - 4.37: 13931 4.37 - 4.90: 23896 Nonbonded interactions: 59338 Sorted by model distance: nonbonded pdb=" O GLN K 3 " pdb=" OG SER K 25 " model vdw 2.240 3.040 nonbonded pdb=" O VAL R 513 " pdb=" OG1 THR R 516 " model vdw 2.258 3.040 nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.261 3.040 nonbonded pdb=" O SER H 142 " pdb=" OG SER H 146 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLU R 308 " pdb=" OG SER R 379 " model vdw 2.281 3.040 ... (remaining 59333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.010 0.088 7788 Z= 0.425 Angle : 1.080 10.309 10604 Z= 0.591 Chirality : 0.062 0.229 1190 Planarity : 0.008 0.068 1334 Dihedral : 14.271 89.182 2723 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.31 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -2.34 (0.26), residues: 970 helix: -1.13 (0.26), residues: 312 sheet: -0.83 (0.34), residues: 238 loop : -2.25 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 110 TYR 0.036 0.003 TYR H 53 PHE 0.026 0.004 PHE R 325 TRP 0.035 0.003 TRP H 102 HIS 0.006 0.002 HIS R 306 Details of bonding type rmsd covalent geometry : bond 0.00967 ( 7781) covalent geometry : angle 1.07681 (10590) SS BOND : bond 0.00397 ( 7) SS BOND : angle 2.37986 ( 14) hydrogen bonds : bond 0.12880 ( 366) hydrogen bonds : angle 6.99717 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: R 411 TYR cc_start: 0.8736 (m-10) cc_final: 0.8286 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0811 time to fit residues: 8.0007 Evaluate side-chains 49 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.073771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058817 restraints weight = 34032.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060345 restraints weight = 19312.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.061267 restraints weight = 13368.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.061935 restraints weight = 10604.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062391 restraints weight = 9028.772| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7788 Z= 0.147 Angle : 0.657 7.505 10604 Z= 0.351 Chirality : 0.043 0.177 1190 Planarity : 0.005 0.053 1334 Dihedral : 5.881 24.586 1067 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.73 % Allowed : 6.84 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -1.78 (0.27), residues: 970 helix: -0.34 (0.28), residues: 320 sheet: -0.80 (0.33), residues: 246 loop : -2.06 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 31 TYR 0.017 0.002 TYR K 32 PHE 0.015 0.001 PHE R 319 TRP 0.020 0.001 TRP R 333 HIS 0.009 0.001 HIS R 204 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7781) covalent geometry : angle 0.65645 (10590) SS BOND : bond 0.00238 ( 7) SS BOND : angle 1.17444 ( 14) hydrogen bonds : bond 0.04265 ( 366) hydrogen bonds : angle 5.45124 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7326 (m-10) cc_final: 0.6965 (m-10) REVERT: L 5 MET cc_start: 0.8557 (tpp) cc_final: 0.7884 (tpp) REVERT: L 163 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7243 (pp20) REVERT: R 411 TYR cc_start: 0.8798 (m-10) cc_final: 0.8389 (m-80) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.0785 time to fit residues: 7.0687 Evaluate side-chains 54 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 462 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.073219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058752 restraints weight = 34128.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.060115 restraints weight = 19700.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.060195 restraints weight = 13726.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.060536 restraints weight = 14021.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060684 restraints weight = 12094.848| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7788 Z= 0.163 Angle : 0.622 7.023 10604 Z= 0.328 Chirality : 0.042 0.149 1190 Planarity : 0.004 0.044 1334 Dihedral : 5.440 26.450 1067 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.61 % Allowed : 12.09 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -1.56 (0.27), residues: 970 helix: -0.05 (0.29), residues: 320 sheet: -0.68 (0.32), residues: 247 loop : -2.04 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 31 TYR 0.020 0.002 TYR K 32 PHE 0.015 0.001 PHE R 319 TRP 0.019 0.001 TRP R 333 HIS 0.003 0.001 HIS H 178 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7781) covalent geometry : angle 0.62114 (10590) SS BOND : bond 0.00198 ( 7) SS BOND : angle 0.98292 ( 14) hydrogen bonds : bond 0.03908 ( 366) hydrogen bonds : angle 5.11939 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7397 (m-10) cc_final: 0.7018 (m-10) REVERT: L 5 MET cc_start: 0.8486 (tpp) cc_final: 0.7835 (tpp) REVERT: R 411 TYR cc_start: 0.8755 (m-10) cc_final: 0.8294 (m-80) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.0691 time to fit residues: 6.4264 Evaluate side-chains 55 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain R residue 204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.073663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059044 restraints weight = 34274.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.060326 restraints weight = 19528.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061747 restraints weight = 13677.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061814 restraints weight = 11053.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061868 restraints weight = 9995.983| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7788 Z= 0.135 Angle : 0.596 6.836 10604 Z= 0.313 Chirality : 0.042 0.155 1190 Planarity : 0.004 0.036 1334 Dihedral : 5.094 27.008 1067 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.10 % Allowed : 14.65 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -1.36 (0.27), residues: 970 helix: 0.15 (0.29), residues: 320 sheet: -0.55 (0.33), residues: 241 loop : -1.94 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 31 TYR 0.013 0.001 TYR K 32 PHE 0.014 0.001 PHE R 319 TRP 0.018 0.001 TRP R 333 HIS 0.003 0.001 HIS H 178 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7781) covalent geometry : angle 0.59588 (10590) SS BOND : bond 0.00187 ( 7) SS BOND : angle 0.84220 ( 14) hydrogen bonds : bond 0.03577 ( 366) hydrogen bonds : angle 4.87085 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7301 (m-10) cc_final: 0.6974 (m-10) REVERT: K 83 MET cc_start: 0.7502 (ttm) cc_final: 0.7084 (ttp) REVERT: L 5 MET cc_start: 0.8409 (tpp) cc_final: 0.7726 (tpp) REVERT: R 306 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.6736 (m90) REVERT: R 411 TYR cc_start: 0.8752 (m-10) cc_final: 0.8329 (m-80) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 0.0666 time to fit residues: 6.4000 Evaluate side-chains 57 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 513 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.073615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058894 restraints weight = 34331.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.060186 restraints weight = 19894.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.061005 restraints weight = 14510.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061155 restraints weight = 13353.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.061361 restraints weight = 11043.827| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7788 Z= 0.135 Angle : 0.590 6.833 10604 Z= 0.307 Chirality : 0.042 0.153 1190 Planarity : 0.004 0.065 1334 Dihedral : 4.924 26.939 1067 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.71 % Allowed : 15.02 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -1.23 (0.27), residues: 970 helix: 0.24 (0.28), residues: 320 sheet: -0.45 (0.33), residues: 241 loop : -1.87 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 31 TYR 0.013 0.001 TYR H 116 PHE 0.013 0.001 PHE R 319 TRP 0.014 0.001 TRP R 333 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7781) covalent geometry : angle 0.58997 (10590) SS BOND : bond 0.00189 ( 7) SS BOND : angle 0.81234 ( 14) hydrogen bonds : bond 0.03533 ( 366) hydrogen bonds : angle 4.74116 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7324 (m-10) cc_final: 0.6969 (m-10) REVERT: L 5 MET cc_start: 0.8386 (tpp) cc_final: 0.7736 (tpp) REVERT: R 306 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.6762 (m90) REVERT: R 411 TYR cc_start: 0.8756 (m-10) cc_final: 0.8299 (m-80) outliers start: 14 outliers final: 7 residues processed: 68 average time/residue: 0.0646 time to fit residues: 6.7065 Evaluate side-chains 62 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 508 PHE Chi-restraints excluded: chain R residue 513 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.0770 chunk 82 optimal weight: 0.7980 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.073537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.058250 restraints weight = 34114.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.059771 restraints weight = 19519.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060764 restraints weight = 13663.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.061394 restraints weight = 10787.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061706 restraints weight = 9245.569| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7788 Z= 0.148 Angle : 0.600 7.010 10604 Z= 0.311 Chirality : 0.042 0.158 1190 Planarity : 0.004 0.054 1334 Dihedral : 4.894 26.274 1067 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.22 % Allowed : 16.97 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -1.12 (0.27), residues: 970 helix: 0.36 (0.29), residues: 312 sheet: -0.38 (0.33), residues: 248 loop : -1.83 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 31 TYR 0.010 0.001 TYR K 32 PHE 0.014 0.001 PHE R 319 TRP 0.018 0.001 TRP R 333 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7781) covalent geometry : angle 0.59940 (10590) SS BOND : bond 0.00182 ( 7) SS BOND : angle 0.74578 ( 14) hydrogen bonds : bond 0.03529 ( 366) hydrogen bonds : angle 4.74404 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7333 (m-10) cc_final: 0.7007 (m-10) REVERT: L 5 MET cc_start: 0.8390 (tpp) cc_final: 0.7726 (tpp) REVERT: R 306 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.6825 (m90) REVERT: R 411 TYR cc_start: 0.8759 (m-10) cc_final: 0.8244 (m-80) outliers start: 10 outliers final: 6 residues processed: 67 average time/residue: 0.0607 time to fit residues: 6.3785 Evaluate side-chains 61 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 508 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 39 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 37 optimal weight: 0.0470 chunk 83 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.075021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.060575 restraints weight = 34048.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061875 restraints weight = 19169.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063176 restraints weight = 13447.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.063307 restraints weight = 11453.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.063322 restraints weight = 9492.989| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7788 Z= 0.105 Angle : 0.585 7.312 10604 Z= 0.299 Chirality : 0.041 0.147 1190 Planarity : 0.004 0.049 1334 Dihedral : 4.551 23.311 1067 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.34 % Allowed : 17.58 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -0.92 (0.27), residues: 970 helix: 0.53 (0.29), residues: 312 sheet: -0.14 (0.34), residues: 243 loop : -1.78 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 31 TYR 0.015 0.001 TYR H 83 PHE 0.012 0.001 PHE R 319 TRP 0.019 0.001 TRP R 333 HIS 0.003 0.001 HIS R 304 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 7781) covalent geometry : angle 0.58442 (10590) SS BOND : bond 0.00347 ( 7) SS BOND : angle 0.78142 ( 14) hydrogen bonds : bond 0.03269 ( 366) hydrogen bonds : angle 4.46995 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7247 (m-10) cc_final: 0.6934 (m-10) REVERT: K 83 MET cc_start: 0.7449 (ttm) cc_final: 0.7047 (ttp) REVERT: L 5 MET cc_start: 0.8343 (tpp) cc_final: 0.7704 (tpp) REVERT: R 306 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.6936 (m90) REVERT: R 411 TYR cc_start: 0.8699 (m-10) cc_final: 0.8251 (m-80) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.0664 time to fit residues: 6.9939 Evaluate side-chains 65 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 465 VAL Chi-restraints excluded: chain R residue 508 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.074619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.060152 restraints weight = 34153.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.061523 restraints weight = 19179.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.062797 restraints weight = 13278.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062911 restraints weight = 11101.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.062969 restraints weight = 9700.307| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7788 Z= 0.118 Angle : 0.588 7.133 10604 Z= 0.301 Chirality : 0.041 0.154 1190 Planarity : 0.004 0.046 1334 Dihedral : 4.525 22.856 1067 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.22 % Allowed : 18.56 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -0.81 (0.28), residues: 970 helix: 0.61 (0.29), residues: 312 sheet: -0.06 (0.34), residues: 243 loop : -1.72 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 31 TYR 0.011 0.001 TYR H 83 PHE 0.012 0.001 PHE R 319 TRP 0.019 0.001 TRP R 333 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7781) covalent geometry : angle 0.58796 (10590) SS BOND : bond 0.00172 ( 7) SS BOND : angle 0.78435 ( 14) hydrogen bonds : bond 0.03244 ( 366) hydrogen bonds : angle 4.46048 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7304 (m-10) cc_final: 0.6975 (m-10) REVERT: K 83 MET cc_start: 0.7451 (ttm) cc_final: 0.7045 (ttp) REVERT: L 5 MET cc_start: 0.8355 (tpp) cc_final: 0.7727 (tpp) REVERT: L 163 GLU cc_start: 0.7554 (pp20) cc_final: 0.7200 (pp20) REVERT: R 306 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.6896 (m90) REVERT: R 411 TYR cc_start: 0.8692 (m-10) cc_final: 0.8333 (m-80) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.0618 time to fit residues: 6.1847 Evaluate side-chains 64 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain R residue 204 HIS Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 305 ILE Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 465 VAL Chi-restraints excluded: chain R residue 508 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.075370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060381 restraints weight = 34009.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061957 restraints weight = 19138.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062942 restraints weight = 13151.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.063642 restraints weight = 10343.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064124 restraints weight = 8719.265| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7788 Z= 0.105 Angle : 0.592 11.898 10604 Z= 0.298 Chirality : 0.041 0.146 1190 Planarity : 0.004 0.045 1334 Dihedral : 4.383 21.298 1067 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.34 % Allowed : 18.44 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -0.70 (0.28), residues: 970 helix: 0.67 (0.29), residues: 313 sheet: 0.06 (0.34), residues: 243 loop : -1.69 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 31 TYR 0.014 0.001 TYR H 83 PHE 0.011 0.001 PHE R 319 TRP 0.019 0.001 TRP R 333 HIS 0.003 0.001 HIS R 304 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7781) covalent geometry : angle 0.59231 (10590) SS BOND : bond 0.00145 ( 7) SS BOND : angle 0.69789 ( 14) hydrogen bonds : bond 0.03138 ( 366) hydrogen bonds : angle 4.38669 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: H 208 TYR cc_start: 0.7306 (m-10) cc_final: 0.6955 (m-10) REVERT: K 83 MET cc_start: 0.7485 (ttm) cc_final: 0.7059 (ttp) REVERT: L 5 MET cc_start: 0.8360 (tpp) cc_final: 0.7813 (tpp) REVERT: L 163 GLU cc_start: 0.7599 (pp20) cc_final: 0.7256 (pp20) REVERT: R 306 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.6907 (m90) REVERT: R 411 TYR cc_start: 0.8703 (m-10) cc_final: 0.8352 (m-80) outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 0.0605 time to fit residues: 6.1632 Evaluate side-chains 60 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 305 ILE Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 465 VAL Chi-restraints excluded: chain R residue 508 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 93 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 0.0010 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.075115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060556 restraints weight = 33922.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061912 restraints weight = 19145.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063018 restraints weight = 13413.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.063135 restraints weight = 11567.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.063181 restraints weight = 10203.390| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7788 Z= 0.113 Angle : 0.602 10.850 10604 Z= 0.302 Chirality : 0.042 0.228 1190 Planarity : 0.004 0.044 1334 Dihedral : 4.398 20.497 1067 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.10 % Allowed : 18.80 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -0.66 (0.28), residues: 970 helix: 0.68 (0.29), residues: 313 sheet: 0.12 (0.34), residues: 243 loop : -1.66 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 31 TYR 0.012 0.001 TYR H 83 PHE 0.011 0.001 PHE R 319 TRP 0.018 0.001 TRP R 333 HIS 0.003 0.001 HIS R 304 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7781) covalent geometry : angle 0.60210 (10590) SS BOND : bond 0.00154 ( 7) SS BOND : angle 0.71445 ( 14) hydrogen bonds : bond 0.03158 ( 366) hydrogen bonds : angle 4.39540 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: K 83 MET cc_start: 0.7551 (ttm) cc_final: 0.7063 (ttp) REVERT: L 5 MET cc_start: 0.8356 (tpp) cc_final: 0.7810 (tpp) REVERT: L 163 GLU cc_start: 0.7575 (pp20) cc_final: 0.7246 (pp20) REVERT: R 306 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.6911 (m90) REVERT: R 411 TYR cc_start: 0.8682 (m-10) cc_final: 0.8126 (m-80) outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.0649 time to fit residues: 6.2231 Evaluate side-chains 60 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain R residue 305 ILE Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 390 CYS Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 1049 THR Chi-restraints excluded: chain R residue 465 VAL Chi-restraints excluded: chain R residue 508 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 0.0370 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.075662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.060654 restraints weight = 34575.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.062225 restraints weight = 19308.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.063252 restraints weight = 13333.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.063941 restraints weight = 10446.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.064385 restraints weight = 8842.404| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7788 Z= 0.105 Angle : 0.601 11.102 10604 Z= 0.300 Chirality : 0.042 0.259 1190 Planarity : 0.004 0.044 1334 Dihedral : 4.289 19.187 1067 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.08 % Favored : 93.81 % Rotamer: Outliers : 1.10 % Allowed : 19.29 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % 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 are not related in a simple way. whole: -0.59 (0.28), residues: 970 helix: 0.77 (0.30), residues: 309 sheet: 0.18 (0.34), residues: 243 loop : -1.65 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 31 TYR 0.013 0.001 TYR H 83 PHE 0.011 0.001 PHE R 319 TRP 0.017 0.001 TRP R 333 HIS 0.004 0.001 HIS R 304 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7781) covalent geometry : angle 0.60093 (10590) SS BOND : bond 0.00135 ( 7) SS BOND : angle 0.68078 ( 14) hydrogen bonds : bond 0.03098 ( 366) hydrogen bonds : angle 4.36497 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1316.98 seconds wall clock time: 23 minutes 25.49 seconds (1405.49 seconds total)