Starting phenix.real_space_refine on Fri Aug 22 19:48:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cbb_45421/08_2025/9cbb_45421_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cbb_45421/08_2025/9cbb_45421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cbb_45421/08_2025/9cbb_45421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cbb_45421/08_2025/9cbb_45421.map" model { file = "/net/cci-nas-00/data/ceres_data/9cbb_45421/08_2025/9cbb_45421_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cbb_45421/08_2025/9cbb_45421_trim.cif" } resolution = 4.15 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= -0.000 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: 5 Type Number sf(0) Gaussians S 15 5.16 5 C 2392 2.51 5 N 587 2.21 5 O 629 1.98 5 H 3733 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7356 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7344 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 25, 'TRANS': 444} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.72, per 1000 atoms: 0.23 Number of scatterers: 7356 At special positions: 0 Unit cell: (85.9845, 65.512, 70.4254, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 629 8.00 N 587 7.00 C 2392 6.00 H 3733 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.57 Conformation dependent library (CDL) restraints added in 317.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 854 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 84.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.993A pdb=" N VAL A 58 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.669A pdb=" N SER A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.619A pdb=" N LYS A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 127 removed outlier: 3.633A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 136 through 157 removed outlier: 3.683A pdb=" N ASN A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.573A pdb=" N ILE A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 Proline residue: A 186 - end of helix Processing helix chain 'A' and resid 197 through 220 removed outlier: 3.964A pdb=" N LEU A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 removed outlier: 3.521A pdb=" N LEU A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 removed outlier: 3.584A pdb=" N ALA A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.522A pdb=" N LEU A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 4.135A pdb=" N LYS A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.816A pdb=" N VAL A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 4.077A pdb=" N LEU A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 309' Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 313 through 329 removed outlier: 4.228A pdb=" N VAL A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 328 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.541A pdb=" N ALA A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 removed outlier: 4.064A pdb=" N LEU A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 4.483A pdb=" N GLU A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 3.684A pdb=" N LEU A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 429 removed outlier: 3.718A pdb=" N VAL A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.884A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.787A pdb=" N PHE A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 452 " --> pdb=" O PRO A 448 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 480 through 499 removed outlier: 4.162A pdb=" N PHE A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 498 " --> pdb=" O TYR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 519 removed outlier: 3.650A pdb=" N ILE A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 3725 1.03 - 1.22: 11 1.22 - 1.42: 1525 1.42 - 1.62: 2165 1.62 - 1.81: 22 Bond restraints: 7448 Sorted by residual: bond pdb=" C4 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.352 1.476 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C4 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.352 1.471 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C2 URC A 601 " pdb=" N1 URC A 601 " ideal model delta sigma weight residual 1.375 1.487 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C4 URC A 601 " pdb=" C5 URC A 601 " ideal model delta sigma weight residual 1.358 1.467 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C2 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.376 1.484 -0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 7443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12918 1.85 - 3.70: 509 3.70 - 5.55: 68 5.55 - 7.40: 12 7.40 - 9.25: 5 Bond angle restraints: 13512 Sorted by residual: angle pdb=" N ILE A 335 " pdb=" CA ILE A 335 " pdb=" C ILE A 335 " ideal model delta sigma weight residual 110.30 105.40 4.90 9.70e-01 1.06e+00 2.55e+01 angle pdb=" C ILE A 335 " pdb=" CA ILE A 335 " pdb=" CB ILE A 335 " ideal model delta sigma weight residual 111.81 117.36 -5.55 1.25e+00 6.40e-01 1.97e+01 angle pdb=" C ILE A 353 " pdb=" CA ILE A 353 " pdb=" CB ILE A 353 " ideal model delta sigma weight residual 111.36 117.85 -6.49 1.82e+00 3.02e-01 1.27e+01 angle pdb=" CB ARG A 381 " pdb=" CG ARG A 381 " pdb=" CD ARG A 381 " ideal model delta sigma weight residual 111.30 118.88 -7.58 2.30e+00 1.89e-01 1.09e+01 angle pdb=" CA ARG A 381 " pdb=" CB ARG A 381 " pdb=" CG ARG A 381 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 ... (remaining 13507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 3065 16.66 - 33.33: 303 33.33 - 49.99: 85 49.99 - 66.65: 41 66.65 - 83.32: 6 Dihedral angle restraints: 3500 sinusoidal: 1880 harmonic: 1620 Sorted by residual: dihedral pdb=" CA LEU A 185 " pdb=" C LEU A 185 " pdb=" N PRO A 186 " pdb=" CA PRO A 186 " ideal model delta harmonic sigma weight residual 180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA HIS A 97 " pdb=" C HIS A 97 " pdb=" N GLY A 98 " pdb=" CA GLY A 98 " ideal model delta harmonic sigma weight residual 180.00 -157.87 -22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASN A 518 " pdb=" C ASN A 518 " pdb=" N LYS A 519 " pdb=" CA LYS A 519 " ideal model delta harmonic sigma weight residual -180.00 -159.34 -20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 3497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 360 0.033 - 0.066: 160 0.066 - 0.099: 52 0.099 - 0.132: 18 0.132 - 0.164: 5 Chirality restraints: 595 Sorted by residual: chirality pdb=" CA PRO A 256 " pdb=" N PRO A 256 " pdb=" C PRO A 256 " pdb=" CB PRO A 256 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA PRO A 186 " pdb=" N PRO A 186 " pdb=" C PRO A 186 " pdb=" CB PRO A 186 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA ASN A 504 " pdb=" N ASN A 504 " pdb=" C ASN A 504 " pdb=" CB ASN A 504 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 592 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 335 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" N TRP A 336 " -0.038 2.00e-02 2.50e+03 pdb=" CA TRP A 336 " 0.009 2.00e-02 2.50e+03 pdb=" H TRP A 336 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 184 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C VAL A 184 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL A 184 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 185 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 380 " -0.149 9.50e-02 1.11e+02 5.00e-02 3.01e+00 pdb=" NE ARG A 380 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 380 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 380 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 380 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 380 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 380 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 380 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 380 " 0.000 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 756 2.24 - 2.83: 16254 2.83 - 3.42: 19470 3.42 - 4.01: 24751 4.01 - 4.60: 38273 Nonbonded interactions: 99504 Sorted by model distance: nonbonded pdb=" O ILE A 197 " pdb=" HG SER A 200 " model vdw 1.646 2.450 nonbonded pdb=" O THR A 319 " pdb=" HG1 THR A 323 " model vdw 1.709 2.450 nonbonded pdb=" O SER A 190 " pdb="HH22 ARG A 257 " model vdw 1.714 2.450 nonbonded pdb=" O LEU A 109 " pdb=" HG1 THR A 113 " model vdw 1.714 2.450 nonbonded pdb=" O LEU A 398 " pdb=" HG1 THR A 401 " model vdw 1.722 2.450 ... (remaining 99499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.920 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: 0.050 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.770 Find NCS groups from input model: 0.020 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 : 0.007 0.124 3715 Z= 0.332 Angle : 0.921 9.252 5063 Z= 0.461 Chirality : 0.044 0.164 595 Planarity : 0.007 0.066 626 Dihedral : 14.258 83.316 1303 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.36), residues: 468 helix: -1.06 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.79 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 137 TYR 0.015 0.001 TYR A 188 PHE 0.014 0.002 PHE A 514 TRP 0.014 0.002 TRP A 315 HIS 0.001 0.000 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00713 ( 3715) covalent geometry : angle 0.92093 ( 5063) hydrogen bonds : bond 0.26390 ( 208) hydrogen bonds : angle 9.42144 ( 624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8820 (t0) cc_final: 0.8594 (t0) REVERT: A 95 ARG cc_start: 0.7787 (tpp-160) cc_final: 0.7336 (ttt180) REVERT: A 155 MET cc_start: 0.7761 (mmt) cc_final: 0.7477 (mmm) REVERT: A 166 MET cc_start: 0.8848 (pmm) cc_final: 0.8562 (pmm) REVERT: A 271 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8748 (mmtp) REVERT: A 297 ARG cc_start: 0.7946 (ptt180) cc_final: 0.6917 (tpm170) REVERT: A 359 SER cc_start: 0.8383 (m) cc_final: 0.7812 (t) REVERT: A 420 LEU cc_start: 0.8973 (mp) cc_final: 0.8652 (mp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1429 time to fit residues: 20.2155 Evaluate side-chains 102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.160911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132615 restraints weight = 21494.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138276 restraints weight = 10467.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141866 restraints weight = 6380.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143526 restraints weight = 4569.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145575 restraints weight = 3823.249| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3715 Z= 0.158 Angle : 0.652 7.122 5063 Z= 0.355 Chirality : 0.039 0.131 595 Planarity : 0.005 0.033 626 Dihedral : 5.043 23.179 504 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.37), residues: 468 helix: -0.39 (0.27), residues: 335 sheet: None (None), residues: 0 loop : -2.03 (0.51), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.008 0.001 TYR A 188 PHE 0.017 0.002 PHE A 214 TRP 0.008 0.001 TRP A 459 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3715) covalent geometry : angle 0.65213 ( 5063) hydrogen bonds : bond 0.06519 ( 208) hydrogen bonds : angle 6.33462 ( 624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8866 (t0) cc_final: 0.8662 (t0) REVERT: A 95 ARG cc_start: 0.7751 (tpp-160) cc_final: 0.7245 (ttt180) REVERT: A 155 MET cc_start: 0.7733 (mmt) cc_final: 0.7434 (mmm) REVERT: A 271 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8798 (mmtp) REVERT: A 297 ARG cc_start: 0.8005 (ptt180) cc_final: 0.7048 (tpm170) REVERT: A 359 SER cc_start: 0.8511 (m) cc_final: 0.7997 (t) REVERT: A 420 LEU cc_start: 0.9033 (mp) cc_final: 0.8788 (mp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1298 time to fit residues: 18.7467 Evaluate side-chains 101 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 0.0030 chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 overall best weight: 0.3168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.162054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134300 restraints weight = 21499.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140017 restraints weight = 10238.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143882 restraints weight = 6157.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.146202 restraints weight = 4303.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147766 restraints weight = 3378.887| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3715 Z= 0.124 Angle : 0.583 6.897 5063 Z= 0.307 Chirality : 0.038 0.135 595 Planarity : 0.005 0.035 626 Dihedral : 4.759 19.816 504 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.39), residues: 468 helix: -0.11 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -1.90 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.007 0.001 TYR A 338 PHE 0.012 0.001 PHE A 214 TRP 0.009 0.001 TRP A 459 HIS 0.006 0.001 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3715) covalent geometry : angle 0.58340 ( 5063) hydrogen bonds : bond 0.04802 ( 208) hydrogen bonds : angle 5.46275 ( 624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7687 (tpp-160) cc_final: 0.7402 (ttt180) REVERT: A 155 MET cc_start: 0.7811 (mmt) cc_final: 0.7258 (mmt) REVERT: A 271 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8762 (mmtp) REVERT: A 296 GLN cc_start: 0.7913 (mm110) cc_final: 0.7433 (mm110) REVERT: A 297 ARG cc_start: 0.8102 (ptt180) cc_final: 0.7143 (tpm170) REVERT: A 337 PHE cc_start: 0.7749 (m-10) cc_final: 0.7545 (m-10) REVERT: A 359 SER cc_start: 0.8549 (m) cc_final: 0.8108 (t) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1377 time to fit residues: 19.4485 Evaluate side-chains 102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.163609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134880 restraints weight = 22336.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140481 restraints weight = 10538.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144191 restraints weight = 6373.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145801 restraints weight = 4537.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.147443 restraints weight = 3818.033| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3715 Z= 0.135 Angle : 0.572 7.146 5063 Z= 0.305 Chirality : 0.038 0.133 595 Planarity : 0.004 0.030 626 Dihedral : 4.638 22.467 504 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.39), residues: 468 helix: 0.04 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -1.93 (0.56), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.019 0.001 TYR A 188 PHE 0.013 0.001 PHE A 235 TRP 0.022 0.002 TRP A 336 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3715) covalent geometry : angle 0.57239 ( 5063) hydrogen bonds : bond 0.04246 ( 208) hydrogen bonds : angle 5.26248 ( 624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7699 (tpp-160) cc_final: 0.7382 (ttt180) REVERT: A 271 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8786 (mmtp) REVERT: A 296 GLN cc_start: 0.7633 (mm110) cc_final: 0.7085 (mm110) REVERT: A 297 ARG cc_start: 0.8225 (ptt180) cc_final: 0.7282 (tpm170) REVERT: A 359 SER cc_start: 0.8578 (m) cc_final: 0.8142 (t) REVERT: A 420 LEU cc_start: 0.9085 (mp) cc_final: 0.8809 (mp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1321 time to fit residues: 18.4366 Evaluate side-chains 104 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.158457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129649 restraints weight = 22215.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135176 restraints weight = 10650.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138765 restraints weight = 6456.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140307 restraints weight = 4619.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142220 restraints weight = 3912.162| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3715 Z= 0.172 Angle : 0.597 7.068 5063 Z= 0.321 Chirality : 0.038 0.135 595 Planarity : 0.005 0.032 626 Dihedral : 4.590 20.877 504 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.26 % Allowed : 2.07 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.40), residues: 468 helix: 0.11 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -1.94 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 137 TYR 0.023 0.001 TYR A 188 PHE 0.018 0.001 PHE A 235 TRP 0.005 0.001 TRP A 93 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3715) covalent geometry : angle 0.59709 ( 5063) hydrogen bonds : bond 0.03877 ( 208) hydrogen bonds : angle 5.10533 ( 624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.7361 (ttt180) REVERT: A 155 MET cc_start: 0.8011 (mmt) cc_final: 0.7657 (mmp) REVERT: A 271 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8787 (mmtp) REVERT: A 296 GLN cc_start: 0.7620 (mm110) cc_final: 0.7030 (mm110) REVERT: A 297 ARG cc_start: 0.8151 (ptt180) cc_final: 0.7196 (tpm170) REVERT: A 359 SER cc_start: 0.8416 (m) cc_final: 0.8016 (t) REVERT: A 420 LEU cc_start: 0.9133 (mp) cc_final: 0.8930 (mp) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1292 time to fit residues: 18.8213 Evaluate side-chains 99 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.159423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.130782 restraints weight = 22089.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136439 restraints weight = 10404.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140099 restraints weight = 6240.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141602 restraints weight = 4444.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143584 restraints weight = 3765.386| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3715 Z= 0.127 Angle : 0.573 7.009 5063 Z= 0.302 Chirality : 0.038 0.132 595 Planarity : 0.005 0.036 626 Dihedral : 4.539 22.019 504 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.41), residues: 468 helix: 0.37 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.53 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.017 0.001 TYR A 494 PHE 0.009 0.001 PHE A 251 TRP 0.027 0.002 TRP A 336 HIS 0.002 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3715) covalent geometry : angle 0.57340 ( 5063) hydrogen bonds : bond 0.03650 ( 208) hydrogen bonds : angle 4.90357 ( 624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7254 (ttt180) REVERT: A 271 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8779 (mmtp) REVERT: A 296 GLN cc_start: 0.7620 (mm110) cc_final: 0.7002 (mm110) REVERT: A 297 ARG cc_start: 0.8160 (ptt180) cc_final: 0.7199 (tpm170) REVERT: A 359 SER cc_start: 0.8397 (m) cc_final: 0.7976 (t) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1147 time to fit residues: 16.8063 Evaluate side-chains 104 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** 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 = 0.4071 r_free = 0.4071 target = 0.159057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130478 restraints weight = 21993.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136074 restraints weight = 10306.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139684 restraints weight = 6235.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141743 restraints weight = 4459.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142661 restraints weight = 3642.267| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3715 Z= 0.128 Angle : 0.564 7.166 5063 Z= 0.295 Chirality : 0.038 0.131 595 Planarity : 0.004 0.031 626 Dihedral : 4.488 21.870 504 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.41), residues: 468 helix: 0.46 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.49 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.008 0.001 TYR A 188 PHE 0.008 0.001 PHE A 514 TRP 0.009 0.001 TRP A 336 HIS 0.002 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3715) covalent geometry : angle 0.56430 ( 5063) hydrogen bonds : bond 0.03529 ( 208) hydrogen bonds : angle 4.82486 ( 624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.7245 (ttt180) REVERT: A 155 MET cc_start: 0.8085 (mmt) cc_final: 0.6924 (mmt) REVERT: A 271 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8792 (mmtp) REVERT: A 297 ARG cc_start: 0.8176 (ptt180) cc_final: 0.7211 (tpm170) REVERT: A 359 SER cc_start: 0.8221 (m) cc_final: 0.7777 (t) REVERT: A 420 LEU cc_start: 0.9141 (mp) cc_final: 0.8816 (mp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1233 time to fit residues: 17.9765 Evaluate side-chains 100 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.159983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131245 restraints weight = 22327.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136933 restraints weight = 10370.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140538 restraints weight = 6239.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142403 restraints weight = 4466.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.144036 restraints weight = 3692.143| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3715 Z= 0.119 Angle : 0.560 7.136 5063 Z= 0.292 Chirality : 0.038 0.132 595 Planarity : 0.004 0.033 626 Dihedral : 4.441 21.499 504 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.41), residues: 468 helix: 0.47 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.43 (0.62), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.007 0.001 TYR A 188 PHE 0.008 0.001 PHE A 514 TRP 0.030 0.002 TRP A 336 HIS 0.001 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3715) covalent geometry : angle 0.55979 ( 5063) hydrogen bonds : bond 0.03448 ( 208) hydrogen bonds : angle 4.72627 ( 624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7337 (ttt180) REVERT: A 155 MET cc_start: 0.8059 (mmt) cc_final: 0.6914 (mmt) REVERT: A 271 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8765 (mmtp) REVERT: A 297 ARG cc_start: 0.8128 (ptt180) cc_final: 0.7150 (tpm170) REVERT: A 359 SER cc_start: 0.8183 (m) cc_final: 0.7727 (t) REVERT: A 420 LEU cc_start: 0.9147 (mp) cc_final: 0.8864 (mp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1148 time to fit residues: 16.9991 Evaluate side-chains 102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** 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 = 0.4067 r_free = 0.4067 target = 0.158397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129921 restraints weight = 21748.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.135535 restraints weight = 10211.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.139158 restraints weight = 6156.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141006 restraints weight = 4401.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142421 restraints weight = 3632.538| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3715 Z= 0.128 Angle : 0.570 6.796 5063 Z= 0.295 Chirality : 0.038 0.130 595 Planarity : 0.004 0.031 626 Dihedral : 4.421 21.976 504 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.41), residues: 468 helix: 0.54 (0.29), residues: 340 sheet: None (None), residues: 0 loop : -1.44 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.006 0.001 TYR A 188 PHE 0.008 0.001 PHE A 441 TRP 0.007 0.001 TRP A 93 HIS 0.002 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3715) covalent geometry : angle 0.57027 ( 5063) hydrogen bonds : bond 0.03329 ( 208) hydrogen bonds : angle 4.71352 ( 624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7261 (ttt180) REVERT: A 271 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8782 (mmtp) REVERT: A 296 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7718 (mm110) REVERT: A 297 ARG cc_start: 0.8167 (ptt180) cc_final: 0.7140 (tpm170) REVERT: A 324 MET cc_start: 0.7601 (ttm) cc_final: 0.7358 (ttp) REVERT: A 359 SER cc_start: 0.8162 (m) cc_final: 0.7704 (t) REVERT: A 391 MET cc_start: 0.8241 (ppp) cc_final: 0.7977 (ptt) REVERT: A 420 LEU cc_start: 0.9135 (mp) cc_final: 0.8857 (mp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1114 time to fit residues: 15.9575 Evaluate side-chains 102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** 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 = 0.4047 r_free = 0.4047 target = 0.156551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128270 restraints weight = 22145.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133756 restraints weight = 10276.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.137211 restraints weight = 6183.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139506 restraints weight = 4454.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140220 restraints weight = 3567.661| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3715 Z= 0.147 Angle : 0.583 7.027 5063 Z= 0.308 Chirality : 0.038 0.129 595 Planarity : 0.005 0.041 626 Dihedral : 4.402 21.869 504 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.40), residues: 468 helix: 0.59 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.59 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.006 0.001 TYR A 413 PHE 0.012 0.001 PHE A 514 TRP 0.044 0.002 TRP A 336 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3715) covalent geometry : angle 0.58346 ( 5063) hydrogen bonds : bond 0.03326 ( 208) hydrogen bonds : angle 4.71804 ( 624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7708 (tpp-160) cc_final: 0.7174 (ttt180) REVERT: A 271 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8774 (mmtp) REVERT: A 297 ARG cc_start: 0.8148 (ptt180) cc_final: 0.7110 (tpm170) REVERT: A 359 SER cc_start: 0.8221 (m) cc_final: 0.7758 (t) REVERT: A 391 MET cc_start: 0.8212 (ppp) cc_final: 0.7968 (ptt) REVERT: A 420 LEU cc_start: 0.9151 (mp) cc_final: 0.8846 (mp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1224 time to fit residues: 17.5609 Evaluate side-chains 103 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.158537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130149 restraints weight = 22254.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135819 restraints weight = 10365.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139500 restraints weight = 6193.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141410 restraints weight = 4381.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143010 restraints weight = 3588.941| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3715 Z= 0.119 Angle : 0.563 7.013 5063 Z= 0.291 Chirality : 0.038 0.131 595 Planarity : 0.004 0.040 626 Dihedral : 4.413 21.299 504 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.41), residues: 468 helix: 0.57 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.35 (0.62), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.007 0.001 TYR A 188 PHE 0.007 0.001 PHE A 441 TRP 0.008 0.001 TRP A 93 HIS 0.002 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3715) covalent geometry : angle 0.56344 ( 5063) hydrogen bonds : bond 0.03220 ( 208) hydrogen bonds : angle 4.58900 ( 624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.40 seconds wall clock time: 33 minutes 18.34 seconds (1998.34 seconds total)