Starting phenix.real_space_refine on Fri Aug 22 17:21:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrl_34977/08_2025/8hrl_34977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrl_34977/08_2025/8hrl_34977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hrl_34977/08_2025/8hrl_34977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrl_34977/08_2025/8hrl_34977.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrl_34977/08_2025/8hrl_34977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrl_34977/08_2025/8hrl_34977.cif" } resolution = 2.8 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= 0.178 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 37 5.16 5 C 4101 2.51 5 N 1066 2.21 5 O 1208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Time building chain proxies: 1.72, per 1000 atoms: 0.27 Number of scatterers: 6412 At special positions: 0 Unit cell: (77.4, 88.58, 126.42, 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 37 16.00 O 1208 8.00 N 1066 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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: 0.47 Conformation dependent library (CDL) restraints added in 311.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 52.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.635A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.590A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.817A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.568A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.526A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 220 through 249 removed outlier: 4.080A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 removed outlier: 4.234A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.936A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.291A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 4.557A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.775A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.622A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.544A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.192A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.784A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.880A pdb=" N TRP A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.635A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.845A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.111A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.047A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.580A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.837A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.844A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.294A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.737A pdb=" N TRP A 349 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.527A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP E 398 " --> pdb=" O VAL E 512 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 247 hydrogen bonds defined for protein. 705 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: 0.69 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2065 1.34 - 1.46: 1666 1.46 - 1.58: 2802 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6592 Sorted by residual: bond pdb=" CG PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 1.503 1.422 0.081 3.40e-02 8.65e+02 5.73e+00 bond pdb=" CB PRO E 499 " pdb=" CG PRO E 499 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.65e+00 bond pdb=" CA VAL A 364 " pdb=" CB VAL A 364 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.31e-02 5.83e+03 1.47e+00 bond pdb=" CA PHE E 338 " pdb=" CB PHE E 338 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.75e-02 3.27e+03 1.43e+00 bond pdb=" CB GLU A 160 " pdb=" CG GLU A 160 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 8846 2.51 - 5.02: 93 5.02 - 7.53: 11 7.53 - 10.04: 5 10.04 - 12.55: 3 Bond angle restraints: 8958 Sorted by residual: angle pdb=" CA PRO E 499 " pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 112.00 99.45 12.55 1.40e+00 5.10e-01 8.04e+01 angle pdb=" N PRO A 258 " pdb=" CD PRO A 258 " pdb=" CG PRO A 258 " ideal model delta sigma weight residual 103.20 93.53 9.67 1.50e+00 4.44e-01 4.16e+01 angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 103.88 8.12 1.40e+00 5.10e-01 3.36e+01 angle pdb=" CA GLU A 160 " pdb=" CB GLU A 160 " pdb=" CG GLU A 160 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CA PRO A 258 " pdb=" CB PRO A 258 " pdb=" CG PRO A 258 " ideal model delta sigma weight residual 104.50 97.12 7.38 1.90e+00 2.77e-01 1.51e+01 ... (remaining 8953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3268 17.52 - 35.04: 444 35.04 - 52.56: 144 52.56 - 70.08: 26 70.08 - 87.60: 11 Dihedral angle restraints: 3893 sinusoidal: 1573 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 156.69 -63.69 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual -86.00 -24.34 -61.66 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 133.78 -40.78 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 546 0.035 - 0.069: 278 0.069 - 0.103: 80 0.103 - 0.138: 27 0.138 - 0.172: 3 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA ASP A 509 " pdb=" N ASP A 509 " pdb=" C ASP A 509 " pdb=" CB ASP A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA LYS A 234 " pdb=" N LYS A 234 " pdb=" C LYS A 234 " pdb=" CB LYS A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE E 410 " pdb=" N ILE E 410 " pdb=" C ILE E 410 " pdb=" CB ILE E 410 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 931 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 498 " 0.106 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO E 499 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO E 499 " 0.077 5.00e-02 4.00e+02 pdb=" CD PRO E 499 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " 0.048 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A 258 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 321 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.026 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 105 2.68 - 3.23: 5701 3.23 - 3.79: 9299 3.79 - 4.34: 12440 4.34 - 4.90: 21104 Nonbonded interactions: 48649 Sorted by model distance: nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.124 3.040 nonbonded pdb=" NH1 ARG E 346 " pdb=" O PHE E 347 " model vdw 2.185 3.120 nonbonded pdb=" OG SER E 371 " pdb=" OG SER E 373 " model vdw 2.262 3.040 nonbonded pdb=" O THR A 118 " pdb=" OG1 THR A 122 " model vdw 2.264 3.040 nonbonded pdb=" O LEU A 143 " pdb=" N LEU A 148 " model vdw 2.276 3.120 ... (remaining 48644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.940 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: 0.010 Load rotamer database and sin/cos tables:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 6599 Z= 0.184 Angle : 0.734 12.552 8972 Z= 0.410 Chirality : 0.045 0.172 934 Planarity : 0.007 0.151 1165 Dihedral : 18.125 87.601 2384 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.59 % Allowed : 27.52 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.16 (0.28), residues: 787 helix: 0.21 (0.28), residues: 348 sheet: -1.45 (0.70), residues: 50 loop : -1.58 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 161 TYR 0.018 0.002 TYR A 279 PHE 0.022 0.002 PHE A 592 TRP 0.028 0.002 TRP A 473 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6592) covalent geometry : angle 0.73271 ( 8958) SS BOND : bond 0.00319 ( 7) SS BOND : angle 1.16934 ( 14) hydrogen bonds : bond 0.16722 ( 247) hydrogen bonds : angle 5.07039 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.238 Fit side-chains REVERT: A 297 MET cc_start: 0.0877 (ttt) cc_final: -0.0262 (mtm) REVERT: A 316 VAL cc_start: 0.7139 (t) cc_final: 0.6831 (t) REVERT: A 536 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6609 (mp0) outliers start: 11 outliers final: 8 residues processed: 84 average time/residue: 0.4892 time to fit residues: 43.4496 Evaluate side-chains 77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 61 ASN A 417 HIS A 531 GLN E 437 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.219808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.182583 restraints weight = 7265.732| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.04 r_work: 0.4007 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6599 Z= 0.125 Angle : 0.536 8.599 8972 Z= 0.285 Chirality : 0.042 0.141 934 Planarity : 0.005 0.080 1165 Dihedral : 5.345 43.409 876 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.60 % Allowed : 25.22 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.78 (0.29), residues: 787 helix: 0.33 (0.28), residues: 351 sheet: -1.13 (0.73), residues: 50 loop : -1.20 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.014 0.001 TYR A 385 PHE 0.017 0.001 PHE E 486 TRP 0.019 0.001 TRP A 473 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6592) covalent geometry : angle 0.53533 ( 8958) SS BOND : bond 0.00197 ( 7) SS BOND : angle 0.71072 ( 14) hydrogen bonds : bond 0.05420 ( 247) hydrogen bonds : angle 4.22928 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.258 Fit side-chains REVERT: A 89 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: A 297 MET cc_start: 0.1143 (ttt) cc_final: 0.0268 (mtm) REVERT: A 316 VAL cc_start: 0.6836 (t) cc_final: 0.6628 (t) REVERT: A 406 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: A 552 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: A 562 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7577 (mttt) outliers start: 25 outliers final: 6 residues processed: 89 average time/residue: 0.5321 time to fit residues: 50.0816 Evaluate side-chains 76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 51 ASN E 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.217995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.180966 restraints weight = 7186.148| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.08 r_work: 0.3992 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6599 Z= 0.127 Angle : 0.537 8.049 8972 Z= 0.286 Chirality : 0.042 0.181 934 Planarity : 0.005 0.061 1165 Dihedral : 4.363 30.867 862 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.33 % Allowed : 23.78 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.64 (0.29), residues: 787 helix: 0.49 (0.28), residues: 348 sheet: -0.76 (0.79), residues: 48 loop : -1.21 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.015 0.001 TYR A 385 PHE 0.013 0.001 PHE E 486 TRP 0.014 0.001 TRP A 473 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6592) covalent geometry : angle 0.53646 ( 8958) SS BOND : bond 0.00320 ( 7) SS BOND : angle 0.65509 ( 14) hydrogen bonds : bond 0.05509 ( 247) hydrogen bonds : angle 4.11361 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 71 time to evaluate : 0.261 Fit side-chains REVERT: A 89 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6523 (mp10) REVERT: A 171 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: A 297 MET cc_start: 0.1174 (OUTLIER) cc_final: 0.0422 (mtp) REVERT: A 305 GLN cc_start: 0.5109 (OUTLIER) cc_final: 0.3807 (tm-30) REVERT: A 376 MET cc_start: 0.7443 (mmt) cc_final: 0.7199 (mmt) REVERT: A 406 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6797 (mm-30) REVERT: A 552 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: A 562 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7465 (mttt) REVERT: E 474 GLN cc_start: 0.5239 (tt0) cc_final: 0.4780 (tm-30) REVERT: E 513 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6701 (tm) outliers start: 37 outliers final: 16 residues processed: 97 average time/residue: 0.5574 time to fit residues: 57.0316 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 0.0010 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.213132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176232 restraints weight = 7170.476| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.07 r_work: 0.3960 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6599 Z= 0.146 Angle : 0.567 7.803 8972 Z= 0.301 Chirality : 0.043 0.186 934 Planarity : 0.005 0.049 1165 Dihedral : 4.518 32.770 862 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.19 % Allowed : 24.21 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.69 (0.29), residues: 787 helix: 0.48 (0.28), residues: 352 sheet: -0.53 (0.81), residues: 48 loop : -1.34 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 161 TYR 0.017 0.001 TYR A 385 PHE 0.011 0.002 PHE E 486 TRP 0.012 0.002 TRP A 473 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6592) covalent geometry : angle 0.56112 ( 8958) SS BOND : bond 0.00541 ( 7) SS BOND : angle 2.06923 ( 14) hydrogen bonds : bond 0.05958 ( 247) hydrogen bonds : angle 4.17493 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.155 Fit side-chains REVERT: A 55 THR cc_start: 0.3612 (OUTLIER) cc_final: 0.3299 (p) REVERT: A 171 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: A 297 MET cc_start: 0.0918 (OUTLIER) cc_final: 0.0263 (mtp) REVERT: A 406 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6895 (mm-30) REVERT: A 552 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: A 562 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7518 (mttt) REVERT: E 513 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6758 (tm) outliers start: 36 outliers final: 12 residues processed: 94 average time/residue: 0.5104 time to fit residues: 50.7296 Evaluate side-chains 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.213937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.177551 restraints weight = 7250.464| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.07 r_work: 0.4003 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6599 Z= 0.121 Angle : 0.519 7.493 8972 Z= 0.275 Chirality : 0.041 0.186 934 Planarity : 0.004 0.043 1165 Dihedral : 4.221 30.052 862 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.48 % Allowed : 23.49 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.46 (0.30), residues: 787 helix: 0.69 (0.28), residues: 352 sheet: -0.45 (0.80), residues: 48 loop : -1.23 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.016 0.001 TYR A 279 PHE 0.034 0.001 PHE E 338 TRP 0.010 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6592) covalent geometry : angle 0.51682 ( 8958) SS BOND : bond 0.00433 ( 7) SS BOND : angle 1.39683 ( 14) hydrogen bonds : bond 0.04910 ( 247) hydrogen bonds : angle 3.97836 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 72 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: 0.4100 (OUTLIER) cc_final: 0.3706 (p) REVERT: A 75 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6403 (mt-10) REVERT: A 79 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7200 (tt) REVERT: A 89 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6623 (mp10) REVERT: A 171 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: A 291 ILE cc_start: 0.2706 (OUTLIER) cc_final: 0.1896 (mp) REVERT: A 297 MET cc_start: 0.1073 (OUTLIER) cc_final: 0.0434 (mtp) REVERT: A 406 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6806 (mm-30) REVERT: A 552 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: E 513 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6718 (tm) outliers start: 38 outliers final: 17 residues processed: 99 average time/residue: 0.5137 time to fit residues: 53.7809 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS E 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.211507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175033 restraints weight = 7220.628| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.08 r_work: 0.3957 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 6599 Z= 0.141 Angle : 0.568 13.948 8972 Z= 0.298 Chirality : 0.043 0.194 934 Planarity : 0.005 0.043 1165 Dihedral : 4.383 30.808 862 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.61 % Allowed : 25.07 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.49 (0.29), residues: 787 helix: 0.65 (0.28), residues: 352 sheet: -0.50 (0.78), residues: 46 loop : -1.21 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 357 TYR 0.018 0.001 TYR A 279 PHE 0.031 0.001 PHE E 338 TRP 0.010 0.001 TRP A 606 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6592) covalent geometry : angle 0.56145 ( 8958) SS BOND : bond 0.00720 ( 7) SS BOND : angle 2.28343 ( 14) hydrogen bonds : bond 0.05502 ( 247) hydrogen bonds : angle 4.29254 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: 0.4532 (OUTLIER) cc_final: 0.4125 (p) REVERT: A 89 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6636 (mp10) REVERT: A 171 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: A 297 MET cc_start: 0.1011 (OUTLIER) cc_final: 0.0353 (mtp) REVERT: A 406 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6797 (mm-30) REVERT: A 552 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: A 562 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7546 (mttt) outliers start: 32 outliers final: 16 residues processed: 89 average time/residue: 0.4976 time to fit residues: 46.7796 Evaluate side-chains 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.0370 chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.4860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 394 ASN E 450 ASN E 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.213682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177513 restraints weight = 7206.332| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.06 r_work: 0.3984 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6599 Z= 0.117 Angle : 0.546 12.700 8972 Z= 0.280 Chirality : 0.041 0.179 934 Planarity : 0.004 0.038 1165 Dihedral : 4.150 27.951 862 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.75 % Allowed : 26.08 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.33 (0.30), residues: 787 helix: 0.81 (0.29), residues: 352 sheet: -0.16 (0.82), residues: 45 loop : -1.20 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 509 TYR 0.019 0.001 TYR A 279 PHE 0.031 0.001 PHE E 338 TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6592) covalent geometry : angle 0.54160 ( 8958) SS BOND : bond 0.00601 ( 7) SS BOND : angle 1.90456 ( 14) hydrogen bonds : bond 0.04649 ( 247) hydrogen bonds : angle 4.17498 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: 0.4533 (OUTLIER) cc_final: 0.4185 (p) REVERT: A 75 GLU cc_start: 0.6533 (mt-10) cc_final: 0.6307 (mt-10) REVERT: A 89 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6524 (mp10) REVERT: A 171 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: A 297 MET cc_start: 0.1091 (OUTLIER) cc_final: 0.0350 (mtp) REVERT: A 360 MET cc_start: 0.4614 (ptm) cc_final: 0.4224 (mtm) REVERT: A 369 PHE cc_start: 0.3952 (OUTLIER) cc_final: 0.3498 (m-80) REVERT: A 406 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6832 (mm-30) REVERT: A 552 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: A 577 LYS cc_start: 0.8132 (ptpt) cc_final: 0.7916 (ptmm) outliers start: 26 outliers final: 14 residues processed: 91 average time/residue: 0.5769 time to fit residues: 55.2613 Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS E 450 ASN E 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.209901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173960 restraints weight = 7199.697| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.04 r_work: 0.3945 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6599 Z= 0.138 Angle : 0.573 11.185 8972 Z= 0.298 Chirality : 0.043 0.197 934 Planarity : 0.005 0.043 1165 Dihedral : 4.251 21.599 861 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.90 % Allowed : 25.36 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.44 (0.29), residues: 787 helix: 0.78 (0.28), residues: 347 sheet: -0.38 (0.78), residues: 45 loop : -1.27 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 509 TYR 0.023 0.001 TYR A 279 PHE 0.031 0.002 PHE E 338 TRP 0.011 0.001 TRP A 606 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6592) covalent geometry : angle 0.57033 ( 8958) SS BOND : bond 0.00686 ( 7) SS BOND : angle 1.50094 ( 14) hydrogen bonds : bond 0.05625 ( 247) hydrogen bonds : angle 4.29076 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: 0.4735 (OUTLIER) cc_final: 0.4427 (p) REVERT: A 89 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6520 (mp10) REVERT: A 171 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: A 297 MET cc_start: 0.0981 (OUTLIER) cc_final: 0.0119 (mtp) REVERT: A 406 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6818 (mm-30) REVERT: A 552 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: A 562 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7531 (mttt) REVERT: A 577 LYS cc_start: 0.8165 (ptpt) cc_final: 0.7897 (ptmm) REVERT: A 582 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.5321 (mmm160) outliers start: 34 outliers final: 17 residues processed: 95 average time/residue: 0.5923 time to fit residues: 59.2536 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS A 540 HIS E 450 ASN E 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.213296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.176460 restraints weight = 7337.476| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.14 r_work: 0.3980 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6599 Z= 0.122 Angle : 0.541 10.759 8972 Z= 0.281 Chirality : 0.042 0.182 934 Planarity : 0.004 0.040 1165 Dihedral : 4.084 20.489 861 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.75 % Allowed : 26.37 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.32 (0.29), residues: 787 helix: 0.90 (0.29), residues: 347 sheet: -0.39 (0.76), residues: 45 loop : -1.23 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.023 0.001 TYR A 279 PHE 0.031 0.001 PHE E 338 TRP 0.011 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6592) covalent geometry : angle 0.53813 ( 8958) SS BOND : bond 0.00574 ( 7) SS BOND : angle 1.52380 ( 14) hydrogen bonds : bond 0.04828 ( 247) hydrogen bonds : angle 4.21431 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6595 (mp10) REVERT: A 141 CYS cc_start: 0.5085 (OUTLIER) cc_final: 0.4149 (t) REVERT: A 171 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: A 297 MET cc_start: 0.1137 (OUTLIER) cc_final: 0.0144 (mtp) REVERT: A 360 MET cc_start: 0.5217 (ptm) cc_final: 0.4881 (mtm) REVERT: A 369 PHE cc_start: 0.4698 (OUTLIER) cc_final: 0.4087 (m-80) REVERT: A 406 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6926 (mm-30) REVERT: A 552 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: A 577 LYS cc_start: 0.8175 (ptpt) cc_final: 0.7914 (ptmm) outliers start: 26 outliers final: 15 residues processed: 92 average time/residue: 0.5696 time to fit residues: 55.3663 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS E 450 ASN E 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.209923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.174480 restraints weight = 7106.426| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.02 r_work: 0.3942 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6599 Z= 0.130 Angle : 0.573 10.300 8972 Z= 0.295 Chirality : 0.042 0.189 934 Planarity : 0.004 0.041 1165 Dihedral : 4.134 19.994 861 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.60 % Allowed : 26.80 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.31 (0.29), residues: 787 helix: 0.91 (0.29), residues: 346 sheet: -0.25 (0.77), residues: 45 loop : -1.23 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.023 0.001 TYR A 279 PHE 0.029 0.001 PHE E 338 TRP 0.012 0.001 TRP A 69 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6592) covalent geometry : angle 0.57103 ( 8958) SS BOND : bond 0.00610 ( 7) SS BOND : angle 1.43655 ( 14) hydrogen bonds : bond 0.05193 ( 247) hydrogen bonds : angle 4.20728 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6518 (tp30) cc_final: 0.6259 (mt-10) REVERT: A 89 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6531 (mp10) REVERT: A 141 CYS cc_start: 0.5007 (OUTLIER) cc_final: 0.4109 (t) REVERT: A 171 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: A 302 TRP cc_start: 0.1837 (OUTLIER) cc_final: -0.0621 (p-90) REVERT: A 360 MET cc_start: 0.5337 (ptm) cc_final: 0.4987 (mtm) REVERT: A 369 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.4354 (m-80) REVERT: A 406 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6785 (mm-30) REVERT: A 552 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: A 562 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7494 (mttt) REVERT: A 577 LYS cc_start: 0.8213 (ptpt) cc_final: 0.7922 (ptmm) REVERT: A 582 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.5249 (mmm160) outliers start: 25 outliers final: 14 residues processed: 91 average time/residue: 0.5668 time to fit residues: 54.4797 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.0470 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN E 450 ASN E 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.211585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.176316 restraints weight = 7242.245| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.01 r_work: 0.3972 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 6599 Z= 0.115 Angle : 0.544 9.775 8972 Z= 0.278 Chirality : 0.041 0.177 934 Planarity : 0.004 0.038 1165 Dihedral : 3.966 19.281 861 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.17 % Allowed : 27.38 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.29), residues: 787 helix: 1.02 (0.29), residues: 346 sheet: -0.34 (0.77), residues: 45 loop : -1.19 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.022 0.001 TYR A 279 PHE 0.031 0.001 PHE E 338 TRP 0.010 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6592) covalent geometry : angle 0.54216 ( 8958) SS BOND : bond 0.00576 ( 7) SS BOND : angle 1.37620 ( 14) hydrogen bonds : bond 0.04490 ( 247) hydrogen bonds : angle 4.15820 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2583.57 seconds wall clock time: 44 minutes 38.42 seconds (2678.42 seconds total)