Starting phenix.real_space_refine on Thu Jun 5 14:54:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrl_34977/06_2025/8hrl_34977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrl_34977/06_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_34977/06_2025/8hrl_34977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrl_34977/06_2025/8hrl_34977.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrl_34977/06_2025/8hrl_34977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrl_34977/06_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-5710/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: 4.95, per 1000 atoms: 0.77 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: 1.59 Conformation dependent library (CDL) restraints added in 962.5 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: 0.62 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: 2.12 Time building geometry restraints manager: 1.90 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: 31.160 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.190 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:14.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.650 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.16722 ( 247) hydrogen bonds : angle 5.07039 ( 705) SS BOND : bond 0.00319 ( 7) SS BOND : angle 1.16934 ( 14) covalent geometry : bond 0.00418 ( 6592) covalent geometry : angle 0.73271 ( 8958) *********************** 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 : 0.654 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: 1.0901 time to fit residues: 97.3206 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 : 0.660 ------------------------------------------------------------------------------- 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 = 0.220079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.183000 restraints weight = 7139.498| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.02 r_work: 0.4001 rms_B_bonded: 2.56 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: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6599 Z= 0.123 Angle : 0.533 8.678 8972 Z= 0.283 Chirality : 0.042 0.141 934 Planarity : 0.005 0.083 1165 Dihedral : 5.293 43.037 876 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.46 % Allowed : 25.07 % Favored : 71.47 % 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 Details of bonding type rmsd hydrogen bonds : bond 0.05343 ( 247) hydrogen bonds : angle 4.20175 ( 705) SS BOND : bond 0.00180 ( 7) SS BOND : angle 0.72943 ( 14) covalent geometry : bond 0.00256 ( 6592) covalent geometry : angle 0.53274 ( 8958) *********************** 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 : 0.698 Fit side-chains REVERT: A 89 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: A 297 MET cc_start: 0.1204 (ttt) cc_final: 0.0342 (mtm) REVERT: A 316 VAL cc_start: 0.6862 (t) cc_final: 0.6648 (t) REVERT: A 406 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: A 552 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: A 562 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7515 (mttt) outliers start: 24 outliers final: 6 residues processed: 89 average time/residue: 1.0479 time to fit residues: 98.8941 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 : 0.690 ------------------------------------------------------------------------------- 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: 0.0370 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- 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 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 = 0.4394 r_free = 0.4394 target = 0.214303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.177336 restraints weight = 7218.813| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.04 r_work: 0.3954 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3840 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6599 Z= 0.165 Angle : 0.595 8.332 8972 Z= 0.319 Chirality : 0.045 0.197 934 Planarity : 0.005 0.058 1165 Dihedral : 4.676 34.451 862 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.19 % Allowed : 23.78 % 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: -0.95 (0.28), residues: 787 helix: 0.23 (0.28), residues: 352 sheet: -0.75 (0.78), residues: 48 loop : -1.42 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 473 HIS 0.007 0.001 HIS A 241 PHE 0.013 0.002 PHE E 486 TYR 0.019 0.002 TYR A 385 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.06621 ( 247) hydrogen bonds : angle 4.29878 ( 705) SS BOND : bond 0.00404 ( 7) SS BOND : angle 1.00280 ( 14) covalent geometry : bond 0.00354 ( 6592) covalent geometry : angle 0.59396 ( 8958) *********************** 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: 36 poor density : 72 time to evaluate : 0.729 Fit side-chains REVERT: A 89 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: A 171 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: A 297 MET cc_start: 0.0999 (OUTLIER) cc_final: 0.0203 (mtp) REVERT: A 305 GLN cc_start: 0.5619 (OUTLIER) cc_final: 0.4293 (tm-30) REVERT: A 406 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: A 552 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: A 562 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7538 (mttt) REVERT: E 513 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6853 (tm) outliers start: 36 outliers final: 14 residues processed: 95 average time/residue: 1.1078 time to fit residues: 111.1569 Evaluate side-chains 86 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 89 GLN 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 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 73 optimal weight: 0.0010 chunk 24 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.215586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179165 restraints weight = 7219.159| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.01 r_work: 0.4004 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6599 Z= 0.117 Angle : 0.521 7.953 8972 Z= 0.276 Chirality : 0.041 0.179 934 Planarity : 0.004 0.049 1165 Dihedral : 4.314 31.075 862 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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 (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: -0.58 (0.29), residues: 787 helix: 0.56 (0.28), residues: 350 sheet: -0.72 (0.77), residues: 50 loop : -1.22 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.001 PHE E 486 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 247) hydrogen bonds : angle 4.05491 ( 705) SS BOND : bond 0.00205 ( 7) SS BOND : angle 2.59048 ( 14) covalent geometry : bond 0.00241 ( 6592) covalent geometry : angle 0.51159 ( 8958) *********************** 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 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.704 Fit side-chains REVERT: A 55 THR cc_start: 0.3677 (OUTLIER) cc_final: 0.3305 (p) REVERT: A 171 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: A 297 MET cc_start: 0.1095 (OUTLIER) cc_final: 0.0349 (mtp) REVERT: A 406 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6790 (mm-30) REVERT: A 552 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: E 513 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6773 (tm) outliers start: 32 outliers final: 13 residues processed: 95 average time/residue: 1.0729 time to fit residues: 107.8628 Evaluate side-chains 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 133 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 345 HIS 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 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 58 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 42 optimal weight: 0.0030 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.214271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177859 restraints weight = 7204.013| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.08 r_work: 0.3973 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6599 Z= 0.117 Angle : 0.529 9.597 8972 Z= 0.276 Chirality : 0.041 0.184 934 Planarity : 0.004 0.043 1165 Dihedral : 4.160 28.653 862 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.04 % Allowed : 24.21 % Favored : 70.75 % 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: -0.51 (0.29), residues: 787 helix: 0.67 (0.28), residues: 352 sheet: -0.61 (0.77), residues: 50 loop : -1.26 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 PHE 0.031 0.001 PHE E 338 TYR 0.014 0.001 TYR A 279 ARG 0.002 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 247) hydrogen bonds : angle 3.97064 ( 705) SS BOND : bond 0.00210 ( 7) SS BOND : angle 1.20669 ( 14) covalent geometry : bond 0.00242 ( 6592) covalent geometry : angle 0.52713 ( 8958) *********************** 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 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 79 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7166 (tt) REVERT: A 89 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6541 (mp10) REVERT: A 171 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: A 297 MET cc_start: 0.0992 (OUTLIER) cc_final: 0.0358 (mtp) REVERT: A 369 PHE cc_start: 0.3769 (OUTLIER) cc_final: 0.3392 (m-80) REVERT: A 406 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6824 (mm-30) REVERT: A 552 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: E 513 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6649 (tm) outliers start: 35 outliers final: 16 residues processed: 96 average time/residue: 1.0359 time to fit residues: 105.3770 Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP 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 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 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 29 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** E 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170387 restraints weight = 7170.106| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.11 r_work: 0.3930 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6599 Z= 0.161 Angle : 0.605 8.198 8972 Z= 0.320 Chirality : 0.044 0.200 934 Planarity : 0.005 0.045 1165 Dihedral : 4.701 36.679 862 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.04 % Allowed : 24.64 % 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: -0.73 (0.29), residues: 787 helix: 0.45 (0.28), residues: 346 sheet: -0.34 (0.79), residues: 48 loop : -1.37 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 349 HIS 0.008 0.001 HIS A 241 PHE 0.030 0.002 PHE E 338 TYR 0.020 0.002 TYR A 279 ARG 0.003 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.06623 ( 247) hydrogen bonds : angle 4.28233 ( 705) SS BOND : bond 0.00331 ( 7) SS BOND : angle 0.87807 ( 14) covalent geometry : bond 0.00346 ( 6592) covalent geometry : angle 0.60423 ( 8958) *********************** 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 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.945 Fit side-chains REVERT: A 55 THR cc_start: 0.4777 (OUTLIER) cc_final: 0.4324 (p) REVERT: A 89 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6574 (mp10) REVERT: A 171 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: A 297 MET cc_start: 0.1148 (OUTLIER) cc_final: 0.0395 (mtp) REVERT: A 552 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7417 (mp10) outliers start: 35 outliers final: 16 residues processed: 102 average time/residue: 1.7313 time to fit residues: 186.2782 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 34 HIS 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 0.0000 chunk 50 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS E 394 ASN 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 = 0.4398 r_free = 0.4398 target = 0.213311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177607 restraints weight = 7190.254| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.05 r_work: 0.3988 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6599 Z= 0.108 Angle : 0.515 8.005 8972 Z= 0.267 Chirality : 0.040 0.170 934 Planarity : 0.004 0.037 1165 Dihedral : 4.143 30.058 862 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.31 % Allowed : 26.37 % 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: -0.37 (0.30), residues: 787 helix: 0.76 (0.29), residues: 352 sheet: -0.23 (0.78), residues: 49 loop : -1.20 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 241 PHE 0.031 0.001 PHE E 338 TYR 0.017 0.001 TYR A 279 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 247) hydrogen bonds : angle 3.98685 ( 705) SS BOND : bond 0.00150 ( 7) SS BOND : angle 0.65504 ( 14) covalent geometry : bond 0.00221 ( 6592) covalent geometry : angle 0.51494 ( 8958) *********************** 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 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.827 Fit side-chains REVERT: A 55 THR cc_start: 0.4659 (OUTLIER) cc_final: 0.4310 (p) REVERT: A 171 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: A 238 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: A 297 MET cc_start: 0.1129 (ttt) cc_final: 0.0370 (mtp) REVERT: A 360 MET cc_start: 0.4815 (ptm) cc_final: 0.4596 (mtm) REVERT: A 369 PHE cc_start: 0.4248 (OUTLIER) cc_final: 0.3705 (m-80) REVERT: A 406 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6673 (mm-30) REVERT: A 552 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: A 577 LYS cc_start: 0.8190 (ptpt) cc_final: 0.7891 (ptmm) REVERT: A 582 ARG cc_start: 0.5729 (OUTLIER) cc_final: 0.5208 (mmm160) outliers start: 23 outliers final: 11 residues processed: 91 average time/residue: 1.8350 time to fit residues: 175.9063 Evaluate side-chains 87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 359 LEU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- 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 194 ASN A 241 HIS E 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.206042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170238 restraints weight = 7172.132| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.06 r_work: 0.3915 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6599 Z= 0.174 Angle : 0.615 8.180 8972 Z= 0.326 Chirality : 0.045 0.205 934 Planarity : 0.005 0.045 1165 Dihedral : 4.679 35.846 862 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.03 % Allowed : 25.94 % 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: -0.69 (0.29), residues: 787 helix: 0.44 (0.28), residues: 352 sheet: 0.03 (0.80), residues: 47 loop : -1.38 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 349 HIS 0.009 0.001 HIS A 241 PHE 0.030 0.002 PHE E 338 TYR 0.024 0.002 TYR A 279 ARG 0.003 0.001 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.06772 ( 247) hydrogen bonds : angle 4.32935 ( 705) SS BOND : bond 0.00343 ( 7) SS BOND : angle 0.92077 ( 14) covalent geometry : bond 0.00384 ( 6592) covalent geometry : angle 0.61403 ( 8958) *********************** 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 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 1.125 Fit side-chains REVERT: A 55 THR cc_start: 0.4944 (OUTLIER) cc_final: 0.4665 (p) REVERT: A 89 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6520 (mp10) REVERT: A 141 CYS cc_start: 0.4872 (OUTLIER) cc_final: 0.3909 (t) REVERT: A 171 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: A 238 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: A 302 TRP cc_start: 0.1876 (OUTLIER) cc_final: -0.0255 (p-90) REVERT: A 467 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7104 (mp0) REVERT: A 552 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7385 (mp10) outliers start: 28 outliers final: 12 residues processed: 99 average time/residue: 2.2837 time to fit residues: 238.5122 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 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 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 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 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** 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 = 0.4350 r_free = 0.4350 target = 0.208313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.173067 restraints weight = 7258.348| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.04 r_work: 0.3936 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6599 Z= 0.127 Angle : 0.552 7.733 8972 Z= 0.290 Chirality : 0.042 0.188 934 Planarity : 0.004 0.041 1165 Dihedral : 4.367 32.199 862 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.75 % Allowed : 26.80 % 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 (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: -0.51 (0.29), residues: 787 helix: 0.64 (0.28), residues: 352 sheet: 0.10 (0.80), residues: 47 loop : -1.32 (0.29), residues: 388 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 0.032 0.002 PHE E 338 TYR 0.022 0.001 TYR A 279 ARG 0.002 0.000 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 247) hydrogen bonds : angle 4.16336 ( 705) SS BOND : bond 0.00213 ( 7) SS BOND : angle 0.63373 ( 14) covalent geometry : bond 0.00270 ( 6592) covalent geometry : angle 0.55140 ( 8958) *********************** 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 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.872 Fit side-chains REVERT: A 75 GLU cc_start: 0.6637 (tp30) cc_final: 0.6175 (tm-30) REVERT: A 89 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6512 (mp10) REVERT: A 141 CYS cc_start: 0.5136 (OUTLIER) cc_final: 0.4227 (t) REVERT: A 171 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: A 238 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6584 (tm-30) REVERT: A 297 MET cc_start: 0.2101 (mtp) cc_final: 0.1127 (pmm) REVERT: A 302 TRP cc_start: 0.1916 (OUTLIER) cc_final: -0.0365 (p-90) REVERT: A 406 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6897 (mm-30) REVERT: A 552 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: A 577 LYS cc_start: 0.8210 (ptpt) cc_final: 0.8003 (ptmm) outliers start: 26 outliers final: 13 residues processed: 98 average time/residue: 1.5044 time to fit residues: 155.3632 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 74 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 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 = 0.4364 r_free = 0.4364 target = 0.209709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.174397 restraints weight = 7264.151| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.07 r_work: 0.3951 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6599 Z= 0.116 Angle : 0.535 8.027 8972 Z= 0.278 Chirality : 0.041 0.183 934 Planarity : 0.004 0.040 1165 Dihedral : 4.147 28.075 862 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.17 % Allowed : 26.66 % 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: -0.30 (0.29), residues: 787 helix: 0.92 (0.29), residues: 346 sheet: 0.09 (0.80), residues: 47 loop : -1.27 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.030 0.001 PHE E 338 TYR 0.020 0.001 TYR A 279 ARG 0.002 0.000 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 247) hydrogen bonds : angle 4.01845 ( 705) SS BOND : bond 0.00129 ( 7) SS BOND : angle 0.60968 ( 14) covalent geometry : bond 0.00243 ( 6592) covalent geometry : angle 0.53490 ( 8958) ********************** 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: 22 poor density : 74 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6598 (tp30) cc_final: 0.6143 (tm-30) REVERT: A 89 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6498 (mp10) REVERT: A 141 CYS cc_start: 0.5149 (OUTLIER) cc_final: 0.4227 (t) REVERT: A 171 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: A 238 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: A 259 ILE cc_start: 0.6223 (OUTLIER) cc_final: 0.6014 (mm) REVERT: A 297 MET cc_start: 0.2312 (mtp) cc_final: -0.0473 (tpp) REVERT: A 406 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: A 552 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: A 577 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7962 (ptmm) outliers start: 22 outliers final: 13 residues processed: 92 average time/residue: 1.0753 time to fit residues: 104.6334 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 259 ILE 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 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 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: 1.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 61 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 = 0.4324 r_free = 0.4324 target = 0.205671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.169868 restraints weight = 7301.057| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.09 r_work: 0.3909 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3279 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= 0.147 Angle : 0.588 7.752 8972 Z= 0.311 Chirality : 0.043 0.198 934 Planarity : 0.005 0.045 1165 Dihedral : 4.320 19.682 861 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.31 % Allowed : 27.52 % Favored : 69.16 % 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: -0.56 (0.29), residues: 787 helix: 0.62 (0.28), residues: 351 sheet: -0.09 (0.79), residues: 48 loop : -1.35 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 349 HIS 0.011 0.001 HIS A 241 PHE 0.019 0.002 PHE A 592 TYR 0.025 0.002 TYR A 279 ARG 0.005 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.06000 ( 247) hydrogen bonds : angle 4.26987 ( 705) SS BOND : bond 0.00276 ( 7) SS BOND : angle 0.77311 ( 14) covalent geometry : bond 0.00319 ( 6592) covalent geometry : angle 0.58720 ( 8958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5921.72 seconds wall clock time: 106 minutes 12.68 seconds (6372.68 seconds total)