Starting phenix.real_space_refine on Tue Feb 11 17:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrl_34977/02_2025/8hrl_34977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrl_34977/02_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_34977/02_2025/8hrl_34977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrl_34977/02_2025/8hrl_34977.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrl_34977/02_2025/8hrl_34977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrl_34977/02_2025/8hrl_34977.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.178 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.05, per 1000 atoms: 0.63 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: 1.52 Conformation dependent library (CDL) restraints added in 947.3 milliseconds 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: 0.69 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: 1.81 Time building geometry restraints manager: 1.79 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: 1.470 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.230 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.930 ------------------------------------------------------------------------------- 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 6592 Z= 0.259 Angle : 0.733 12.552 8958 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (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 TRP 0.028 0.002 TRP A 473 HIS 0.007 0.001 HIS A 241 PHE 0.022 0.002 PHE A 592 TYR 0.018 0.002 TYR A 279 ARG 0.004 0.001 ARG A 161 *********************** 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 : 0.696 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: 1.0466 time to fit residues: 93.3308 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 : 0.742 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 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 34 HIS A 61 ASN A 417 HIS E 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.220085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.183014 restraints weight = 7138.876| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.02 r_work: 0.4001 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6592 Z= 0.166 Angle : 0.533 8.677 8958 Z= 0.283 Chirality : 0.042 0.141 934 Planarity : 0.005 0.083 1165 Dihedral : 5.290 43.005 876 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.46 % Allowed : 25.22 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.29), residues: 787 helix: 0.36 (0.28), residues: 351 sheet: -1.11 (0.73), residues: 50 loop : -1.20 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 473 HIS 0.005 0.001 HIS A 417 PHE 0.017 0.001 PHE E 486 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG A 192 *********************** 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 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.714 Fit side-chains REVERT: A 89 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6553 (mp10) REVERT: A 297 MET cc_start: 0.1208 (ttt) cc_final: 0.0344 (mtm) REVERT: A 316 VAL cc_start: 0.6861 (t) cc_final: 0.6647 (t) REVERT: A 406 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: A 552 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: A 562 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7512 (mttt) outliers start: 24 outliers final: 6 residues processed: 89 average time/residue: 1.0980 time to fit residues: 103.3859 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 : 0.646 ------------------------------------------------------------------------------- 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 25 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.0370 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 61 ASN A 531 GLN E 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.219674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.182724 restraints weight = 7250.163| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.08 r_work: 0.4012 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6592 Z= 0.154 Angle : 0.511 8.004 8958 Z= 0.271 Chirality : 0.041 0.177 934 Planarity : 0.004 0.061 1165 Dihedral : 4.210 28.686 862 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.76 % Allowed : 24.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 787 helix: 0.67 (0.28), residues: 344 sheet: -0.83 (0.77), residues: 50 loop : -1.22 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.004 0.001 HIS A 241 PHE 0.013 0.001 PHE E 486 TYR 0.013 0.001 TYR A 385 ARG 0.002 0.000 ARG A 192 *********************** 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 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.652 Fit side-chains REVERT: A 89 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6515 (mp10) REVERT: A 171 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: A 297 MET cc_start: 0.1158 (ttt) cc_final: 0.0500 (mtp) REVERT: A 305 GLN cc_start: 0.4990 (OUTLIER) cc_final: 0.3700 (tm-30) REVERT: A 406 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6759 (mm-30) REVERT: A 552 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: A 562 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7441 (mttt) REVERT: E 474 GLN cc_start: 0.5174 (tt0) cc_final: 0.4682 (tm-30) REVERT: E 513 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6683 (tm) outliers start: 33 outliers final: 13 residues processed: 94 average time/residue: 1.1364 time to fit residues: 112.9123 Evaluate side-chains 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 291 ILE 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 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 73 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 ASN A 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.211408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174622 restraints weight = 7216.035| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.07 r_work: 0.3938 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6592 Z= 0.221 Angle : 0.587 8.150 8958 Z= 0.314 Chirality : 0.044 0.209 934 Planarity : 0.005 0.048 1165 Dihedral : 4.649 34.644 862 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.19 % Allowed : 24.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.29), residues: 787 helix: 0.42 (0.28), residues: 352 sheet: -0.53 (0.81), residues: 48 loop : -1.37 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 473 HIS 0.007 0.001 HIS A 241 PHE 0.012 0.002 PHE E 347 TYR 0.019 0.002 TYR A 385 ARG 0.004 0.001 ARG A 161 *********************** 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 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.686 Fit side-chains REVERT: A 55 THR cc_start: 0.3692 (OUTLIER) cc_final: 0.3377 (p) REVERT: A 89 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: A 171 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: A 297 MET cc_start: 0.1112 (OUTLIER) cc_final: 0.0410 (mtp) REVERT: A 316 VAL cc_start: 0.6831 (t) cc_final: 0.6620 (t) REVERT: A 406 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7003 (mm-30) REVERT: A 552 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: A 562 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7592 (mttt) outliers start: 36 outliers final: 12 residues processed: 98 average time/residue: 1.1233 time to fit residues: 116.3070 Evaluate side-chains 86 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 0.0000 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4182 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.215225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.178972 restraints weight = 7191.598| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.07 r_work: 0.3987 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6592 Z= 0.147 Angle : 0.516 9.272 8958 Z= 0.269 Chirality : 0.041 0.175 934 Planarity : 0.004 0.042 1165 Dihedral : 4.164 29.799 862 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.75 % Allowed : 25.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.29), residues: 787 helix: 0.83 (0.29), residues: 347 sheet: -0.49 (0.78), residues: 49 loop : -1.20 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.030 0.001 PHE E 338 TYR 0.014 0.001 TYR A 279 ARG 0.002 0.000 ARG A 245 *********************** 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 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: 0.4051 (OUTLIER) cc_final: 0.3661 (p) REVERT: A 79 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7153 (tt) REVERT: A 171 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: A 297 MET cc_start: 0.1037 (OUTLIER) cc_final: 0.0402 (mtp) REVERT: A 369 PHE cc_start: 0.3804 (OUTLIER) cc_final: 0.3379 (m-80) REVERT: A 406 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6770 (mm-30) REVERT: A 552 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7279 (mp10) outliers start: 26 outliers final: 12 residues processed: 92 average time/residue: 1.1582 time to fit residues: 112.7523 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 : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 133 CYS 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 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 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 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.211423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.175442 restraints weight = 7103.564| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.02 r_work: 0.3969 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.180 Angle : 0.545 8.214 8958 Z= 0.287 Chirality : 0.042 0.198 934 Planarity : 0.005 0.042 1165 Dihedral : 4.297 30.362 862 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.32 % Allowed : 24.35 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.29), residues: 787 helix: 0.69 (0.28), residues: 352 sheet: -0.13 (0.81), residues: 47 loop : -1.21 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.007 0.001 HIS A 241 PHE 0.032 0.002 PHE E 338 TYR 0.019 0.001 TYR A 279 ARG 0.003 0.000 ARG A 161 *********************** 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 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: 0.4476 (OUTLIER) cc_final: 0.4088 (p) REVERT: A 79 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7238 (tt) REVERT: A 89 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6564 (mp10) REVERT: A 171 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: A 297 MET cc_start: 0.1094 (OUTLIER) cc_final: 0.0401 (mtp) REVERT: A 406 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6837 (mm-30) REVERT: A 552 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: A 562 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7561 (mttt) outliers start: 30 outliers final: 15 residues processed: 89 average time/residue: 1.3976 time to fit residues: 130.7794 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 : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 297 MET Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.209560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.173702 restraints weight = 7124.392| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.06 r_work: 0.3942 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6592 Z= 0.189 Angle : 0.552 7.897 8958 Z= 0.291 Chirality : 0.043 0.192 934 Planarity : 0.004 0.041 1165 Dihedral : 4.384 33.536 862 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.61 % Allowed : 24.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.29), residues: 787 helix: 0.74 (0.28), residues: 346 sheet: -0.22 (0.80), residues: 48 loop : -1.31 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.006 0.001 HIS A 241 PHE 0.030 0.001 PHE E 338 TYR 0.025 0.001 TYR A 279 ARG 0.004 0.000 ARG E 509 *********************** 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 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: 0.4793 (OUTLIER) cc_final: 0.4438 (p) REVERT: A 89 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6608 (mp10) REVERT: A 171 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6632 (mp0) REVERT: A 297 MET cc_start: 0.1124 (OUTLIER) cc_final: 0.0108 (mtp) REVERT: A 406 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: A 552 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7372 (mp10) REVERT: A 577 LYS cc_start: 0.8196 (ptpt) cc_final: 0.7986 (ptmm) outliers start: 32 outliers final: 15 residues processed: 94 average time/residue: 1.1824 time to fit residues: 117.4186 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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 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 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.0470 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 chunk 5 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 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 = 0.4410 r_free = 0.4410 target = 0.213910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177477 restraints weight = 7164.773| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.13 r_work: 0.3995 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6592 Z= 0.146 Angle : 0.511 7.436 8958 Z= 0.265 Chirality : 0.041 0.176 934 Planarity : 0.004 0.037 1165 Dihedral : 4.050 26.974 862 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.17 % Allowed : 26.80 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.29), residues: 787 helix: 0.98 (0.29), residues: 346 sheet: -0.21 (0.79), residues: 48 loop : -1.26 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.031 0.001 PHE E 338 TYR 0.019 0.001 TYR A 279 ARG 0.002 0.000 ARG A 245 *********************** 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 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 141 CYS cc_start: 0.5069 (OUTLIER) cc_final: 0.4102 (t) REVERT: A 171 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: A 297 MET cc_start: 0.1056 (OUTLIER) cc_final: 0.0138 (mtp) REVERT: A 406 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: A 552 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: A 577 LYS cc_start: 0.8169 (ptpt) cc_final: 0.7911 (ptmm) REVERT: A 582 ARG cc_start: 0.5738 (OUTLIER) cc_final: 0.5309 (mmm160) outliers start: 22 outliers final: 11 residues processed: 92 average time/residue: 1.1876 time to fit residues: 115.1798 Evaluate side-chains 88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 141 CYS 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 369 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP 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 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR 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 66 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.209313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.172606 restraints weight = 7171.496| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.14 r_work: 0.3937 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6592 Z= 0.203 Angle : 0.575 7.836 8958 Z= 0.303 Chirality : 0.043 0.200 934 Planarity : 0.005 0.043 1165 Dihedral : 4.269 20.123 861 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.89 % Allowed : 25.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 787 helix: 0.65 (0.28), residues: 352 sheet: -0.08 (0.79), residues: 48 loop : -1.36 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 349 HIS 0.007 0.001 HIS A 241 PHE 0.031 0.002 PHE E 338 TYR 0.024 0.002 TYR A 279 ARG 0.003 0.000 ARG E 509 *********************** 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 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6573 (mp10) REVERT: A 141 CYS cc_start: 0.5086 (OUTLIER) cc_final: 0.4182 (t) REVERT: A 171 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: A 406 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7006 (mm-30) REVERT: A 467 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7253 (mp0) REVERT: A 552 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: A 562 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7545 (mttt) REVERT: A 577 LYS cc_start: 0.8235 (ptpt) cc_final: 0.7958 (ptmm) REVERT: A 582 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.5374 (mmm160) outliers start: 27 outliers final: 13 residues processed: 94 average time/residue: 1.2534 time to fit residues: 123.9173 Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 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 406 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP 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 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 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 450 ASN E 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.211104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.174658 restraints weight = 7218.470| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.13 r_work: 0.3961 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6592 Z= 0.171 Angle : 0.545 7.660 8958 Z= 0.285 Chirality : 0.042 0.184 934 Planarity : 0.004 0.040 1165 Dihedral : 4.110 18.412 861 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.60 % Allowed : 26.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.29), residues: 787 helix: 0.89 (0.29), residues: 345 sheet: 0.00 (0.80), residues: 48 loop : -1.28 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 PHE 0.031 0.001 PHE E 338 TYR 0.023 0.001 TYR A 279 ARG 0.003 0.000 ARG A 245 ********************** 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 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6699 (tp30) cc_final: 0.6261 (tm-30) REVERT: A 89 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6583 (mp10) REVERT: A 141 CYS cc_start: 0.5226 (OUTLIER) cc_final: 0.4244 (t) REVERT: A 171 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: A 238 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: A 406 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6918 (mm-30) REVERT: A 552 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: A 577 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7998 (ptmm) REVERT: A 582 ARG cc_start: 0.5792 (OUTLIER) cc_final: 0.5341 (mmm160) outliers start: 25 outliers final: 14 residues processed: 88 average time/residue: 1.1627 time to fit residues: 107.9803 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 : 0.720 ------------------------------------------------------------------------------- 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 238 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 406 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP 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 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 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.0050 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4532 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.213149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.176731 restraints weight = 7306.772| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.16 r_work: 0.3985 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6592 Z= 0.151 Angle : 0.525 9.439 8958 Z= 0.269 Chirality : 0.041 0.178 934 Planarity : 0.004 0.037 1165 Dihedral : 3.842 16.358 861 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.31 % Allowed : 26.66 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.30), residues: 787 helix: 1.10 (0.29), residues: 346 sheet: 0.06 (0.79), residues: 48 loop : -1.24 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 69 HIS 0.004 0.000 HIS A 241 PHE 0.026 0.001 PHE E 338 TYR 0.021 0.001 TYR A 279 ARG 0.002 0.000 ARG E 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4956.18 seconds wall clock time: 88 minutes 4.86 seconds (5284.86 seconds total)