Starting phenix.real_space_refine on Wed Feb 12 11:28:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wri_32727/02_2025/7wri_32727.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wri_32727/02_2025/7wri_32727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wri_32727/02_2025/7wri_32727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wri_32727/02_2025/7wri_32727.map" model { file = "/net/cci-nas-00/data/ceres_data/7wri_32727/02_2025/7wri_32727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wri_32727/02_2025/7wri_32727.cif" } resolution = 3.03 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= 0.000 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1565 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4108 2.51 5 N 1080 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6431 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4851 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.04, per 1000 atoms: 0.78 Number of scatterers: 6431 At special positions: 0 Unit cell: (90.2, 81.4, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1205 8.00 N 1080 7.00 C 4108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 902.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 49.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.640A pdb=" N GLU A 35 " --> pdb=" O ASN A 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 removed outlier: 3.893A pdb=" N SER A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.096A pdb=" N ALA A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.585A pdb=" N LYS A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.060A pdb=" N ASP A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 172 removed outlier: 3.676A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.261A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.792A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.876A pdb=" N MET A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.579A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.899A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 383 removed outlier: 4.150A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.512A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.122A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (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 484 removed outlier: 5.785A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (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 531 removed outlier: 3.532A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.703A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.684A pdb=" N LEU A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.781A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.587A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.623A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.974A 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 347 through 352 removed outlier: 6.276A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.953A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.524A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 672 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: 1.71 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 1957 1.34 - 1.47: 1856 1.47 - 1.61: 2741 1.61 - 1.74: 0 1.74 - 1.88: 58 Bond restraints: 6612 Sorted by residual: bond pdb=" C ALA A 36 " pdb=" N GLU A 37 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.48e-02 4.57e+03 8.26e+00 bond pdb=" CA ASP A 38 " pdb=" C ASP A 38 " ideal model delta sigma weight residual 1.519 1.486 0.033 1.22e-02 6.72e+03 7.14e+00 bond pdb=" C LEU A 39 " pdb=" O LEU A 39 " ideal model delta sigma weight residual 1.236 1.203 0.034 1.26e-02 6.30e+03 7.11e+00 bond pdb=" C HIS A 353 " pdb=" O HIS A 353 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.44e-02 4.82e+03 5.44e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.44e+00 ... (remaining 6607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 8935 2.95 - 5.91: 42 5.91 - 8.86: 4 8.86 - 11.82: 1 11.82 - 14.77: 1 Bond angle restraints: 8983 Sorted by residual: angle pdb=" C ASP A 38 " pdb=" CA ASP A 38 " pdb=" CB ASP A 38 " ideal model delta sigma weight residual 109.34 97.55 11.79 1.55e+00 4.16e-01 5.79e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 129.17 -14.77 2.30e+00 1.89e-01 4.12e+01 angle pdb=" N ASP A 38 " pdb=" CA ASP A 38 " pdb=" C ASP A 38 " ideal model delta sigma weight residual 113.55 106.33 7.22 1.26e+00 6.30e-01 3.28e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.60 115.51 -6.91 1.46e+00 4.69e-01 2.24e+01 angle pdb=" N LEU A 39 " pdb=" CA LEU A 39 " pdb=" C LEU A 39 " ideal model delta sigma weight residual 111.82 106.92 4.90 1.16e+00 7.43e-01 1.79e+01 ... (remaining 8978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3447 17.86 - 35.71: 372 35.71 - 53.57: 73 53.57 - 71.43: 16 71.43 - 89.28: 11 Dihedral angle restraints: 3919 sinusoidal: 1593 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 36.41 56.59 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" C ASP A 38 " pdb=" N ASP A 38 " pdb=" CA ASP A 38 " pdb=" CB ASP A 38 " ideal model delta harmonic sigma weight residual -122.60 -106.25 -16.35 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" CA LYS A 582 " pdb=" C LYS A 582 " pdb=" N PRO A 583 " pdb=" CA PRO A 583 " ideal model delta harmonic sigma weight residual 180.00 151.27 28.73 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 3916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 807 0.054 - 0.108: 116 0.108 - 0.162: 10 0.162 - 0.217: 1 0.217 - 0.271: 2 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ASP A 38 " pdb=" N ASP A 38 " pdb=" C ASP A 38 " pdb=" CB ASP A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA CYS B 432 " pdb=" N CYS B 432 " pdb=" C CYS B 432 " pdb=" CB CYS B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LEU A 39 " pdb=" N LEU A 39 " pdb=" C LEU A 39 " pdb=" CB LEU A 39 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 933 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 36 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA A 36 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA A 36 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU A 37 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 582 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO A 583 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 146 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.026 5.00e-02 4.00e+02 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 104 2.66 - 3.22: 5639 3.22 - 3.78: 9374 3.78 - 4.34: 13734 4.34 - 4.90: 22185 Nonbonded interactions: 51036 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.099 2.230 nonbonded pdb=" OG1 THR A 365 " pdb=" ND2 ASN A 368 " model vdw 2.258 3.120 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.259 3.040 nonbonded pdb=" O PHE B 490 " pdb=" NH1 ARG B 493 " model vdw 2.270 3.120 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.272 3.040 ... (remaining 51031 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: 7.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.003 0.070 6612 Z= 0.163 Angle : 0.580 14.772 8983 Z= 0.347 Chirality : 0.040 0.271 936 Planarity : 0.004 0.064 1166 Dihedral : 15.538 89.284 2416 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.03 % Allowed : 15.22 % Favored : 82.75 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: -4.19 (0.24), residues: 786 helix: -2.68 (0.22), residues: 350 sheet: -0.52 (0.72), residues: 43 loop : -3.18 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS A 353 PHE 0.005 0.001 PHE A 588 TYR 0.012 0.001 TYR A 385 ARG 0.001 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.707 Fit side-chains REVERT: A 188 ASN cc_start: 0.7948 (m-40) cc_final: 0.7735 (m110) REVERT: A 255 TYR cc_start: 0.8092 (m-80) cc_final: 0.7860 (m-80) REVERT: A 387 ARG cc_start: 0.7881 (ptm160) cc_final: 0.7670 (ptt90) REVERT: A 408 MET cc_start: 0.8615 (mmt) cc_final: 0.8182 (mmt) REVERT: B 378 LYS cc_start: 0.7771 (tptp) cc_final: 0.7543 (tptp) REVERT: B 410 ILE cc_start: 0.8446 (mm) cc_final: 0.8173 (mm) outliers start: 14 outliers final: 12 residues processed: 127 average time/residue: 0.2014 time to fit residues: 33.2010 Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.0030 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119490 restraints weight = 8197.175| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.93 r_work: 0.3291 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6612 Z= 0.165 Angle : 0.540 12.634 8983 Z= 0.279 Chirality : 0.041 0.198 936 Planarity : 0.005 0.065 1166 Dihedral : 5.228 56.081 903 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.03 % Allowed : 17.54 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.75 (0.27), residues: 786 helix: -1.21 (0.27), residues: 348 sheet: 0.11 (0.75), residues: 43 loop : -2.68 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 203 HIS 0.003 0.001 HIS A 322 PHE 0.013 0.001 PHE A 592 TYR 0.015 0.001 TYR A 510 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.704 Fit side-chains REVERT: A 188 ASN cc_start: 0.8047 (m-40) cc_final: 0.7705 (m110) REVERT: A 387 ARG cc_start: 0.8667 (ptm160) cc_final: 0.8424 (ptt90) REVERT: A 408 MET cc_start: 0.8938 (mmt) cc_final: 0.8521 (mmt) REVERT: A 510 TYR cc_start: 0.8901 (m-10) cc_final: 0.8695 (m-10) REVERT: A 579 MET cc_start: 0.7739 (mtp) cc_final: 0.7522 (mtm) REVERT: A 609 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7711 (mm-30) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.2038 time to fit residues: 25.7408 Evaluate side-chains 89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116605 restraints weight = 8226.774| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.97 r_work: 0.3233 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6612 Z= 0.208 Angle : 0.560 15.761 8983 Z= 0.288 Chirality : 0.042 0.192 936 Planarity : 0.005 0.077 1166 Dihedral : 5.208 57.196 892 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.17 % Allowed : 17.68 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.17 (0.29), residues: 786 helix: -0.60 (0.28), residues: 349 sheet: 0.21 (0.74), residues: 43 loop : -2.48 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.004 0.001 HIS A 322 PHE 0.012 0.001 PHE A 390 TYR 0.013 0.001 TYR B 365 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.734 Fit side-chains REVERT: A 188 ASN cc_start: 0.8246 (m-40) cc_final: 0.7950 (m110) REVERT: A 408 MET cc_start: 0.8985 (mmt) cc_final: 0.8576 (mmt) REVERT: A 609 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7763 (mm-30) REVERT: B 410 ILE cc_start: 0.8666 (mm) cc_final: 0.8369 (mm) outliers start: 15 outliers final: 12 residues processed: 92 average time/residue: 0.2071 time to fit residues: 24.9898 Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115435 restraints weight = 8419.289| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.91 r_work: 0.3206 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6612 Z= 0.254 Angle : 0.583 15.003 8983 Z= 0.301 Chirality : 0.043 0.198 936 Planarity : 0.005 0.084 1166 Dihedral : 5.454 57.471 892 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.61 % Allowed : 16.96 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.29), residues: 786 helix: -0.38 (0.28), residues: 347 sheet: 0.14 (0.74), residues: 43 loop : -2.28 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 610 HIS 0.005 0.001 HIS A 322 PHE 0.015 0.002 PHE A 390 TYR 0.014 0.001 TYR B 365 ARG 0.002 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.778 Fit side-chains REVERT: A 188 ASN cc_start: 0.8033 (m-40) cc_final: 0.7762 (m110) REVERT: A 408 MET cc_start: 0.8970 (mmt) cc_final: 0.8357 (mmt) REVERT: A 609 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8007 (mm-30) REVERT: B 410 ILE cc_start: 0.8565 (mm) cc_final: 0.8250 (mm) outliers start: 18 outliers final: 15 residues processed: 98 average time/residue: 0.1856 time to fit residues: 24.7290 Evaluate side-chains 96 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.0870 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 0.0170 chunk 65 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117234 restraints weight = 8322.803| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.96 r_work: 0.3270 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 6612 Z= 0.156 Angle : 0.524 13.893 8983 Z= 0.271 Chirality : 0.041 0.183 936 Planarity : 0.005 0.080 1166 Dihedral : 5.096 54.196 891 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.59 % Allowed : 18.70 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.55 (0.30), residues: 786 helix: -0.07 (0.29), residues: 348 sheet: 0.15 (0.76), residues: 43 loop : -2.11 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A 322 PHE 0.009 0.001 PHE A 315 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.744 Fit side-chains REVERT: A 188 ASN cc_start: 0.8161 (m-40) cc_final: 0.7823 (m110) REVERT: A 249 MET cc_start: 0.7667 (ttm) cc_final: 0.7356 (ttp) REVERT: A 408 MET cc_start: 0.8949 (mmt) cc_final: 0.8326 (mmt) REVERT: A 609 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 410 ILE cc_start: 0.8625 (mm) cc_final: 0.8342 (mm) outliers start: 11 outliers final: 10 residues processed: 96 average time/residue: 0.1948 time to fit residues: 25.3731 Evaluate side-chains 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.0870 chunk 71 optimal weight: 0.7980 chunk 8 optimal weight: 0.0070 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 73 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120768 restraints weight = 8296.590| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.96 r_work: 0.3316 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 6612 Z= 0.127 Angle : 0.497 12.673 8983 Z= 0.255 Chirality : 0.040 0.194 936 Planarity : 0.005 0.075 1166 Dihedral : 4.806 53.950 891 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.74 % Allowed : 18.70 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.30), residues: 786 helix: 0.26 (0.29), residues: 351 sheet: 0.33 (0.76), residues: 43 loop : -1.89 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS A 322 PHE 0.008 0.001 PHE B 374 TYR 0.012 0.001 TYR A 385 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.754 Fit side-chains REVERT: A 188 ASN cc_start: 0.8098 (m-40) cc_final: 0.7763 (m110) REVERT: A 249 MET cc_start: 0.7554 (ttm) cc_final: 0.7262 (ttp) REVERT: A 408 MET cc_start: 0.8947 (mmt) cc_final: 0.8434 (mmt) REVERT: A 609 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8062 (mm-30) REVERT: B 410 ILE cc_start: 0.8598 (mm) cc_final: 0.8324 (mm) outliers start: 12 outliers final: 11 residues processed: 94 average time/residue: 0.1778 time to fit residues: 22.7514 Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1166 > 50: distance: 28 - 32: 3.361 distance: 32 - 33: 15.362 distance: 33 - 34: 21.429 distance: 33 - 36: 12.642 distance: 34 - 35: 18.974 distance: 34 - 39: 14.050 distance: 36 - 37: 31.317 distance: 36 - 38: 26.874 distance: 39 - 40: 31.630 distance: 40 - 41: 32.594 distance: 41 - 42: 5.160 distance: 41 - 43: 29.037 distance: 43 - 44: 29.974 distance: 44 - 45: 10.510 distance: 44 - 47: 36.351 distance: 45 - 46: 23.997 distance: 45 - 51: 27.177 distance: 47 - 48: 13.316 distance: 48 - 49: 25.863 distance: 48 - 50: 37.204 distance: 51 - 52: 17.868 distance: 51 - 57: 19.474 distance: 52 - 53: 22.339 distance: 52 - 55: 23.047 distance: 53 - 54: 16.652 distance: 53 - 58: 35.073 distance: 56 - 57: 27.583 distance: 58 - 59: 22.508 distance: 59 - 60: 9.667 distance: 59 - 62: 6.379 distance: 60 - 61: 10.713 distance: 60 - 68: 7.352 distance: 62 - 63: 18.000 distance: 63 - 64: 8.718 distance: 63 - 65: 3.317 distance: 64 - 66: 12.749 distance: 65 - 67: 10.759 distance: 66 - 67: 3.926 distance: 68 - 69: 6.535 distance: 69 - 70: 11.480 distance: 69 - 72: 24.720 distance: 70 - 71: 13.920 distance: 70 - 76: 29.293 distance: 72 - 73: 14.207 distance: 73 - 74: 9.925 distance: 74 - 75: 17.574 distance: 76 - 77: 15.924 distance: 77 - 78: 15.181 distance: 77 - 80: 6.128 distance: 78 - 79: 7.184 distance: 78 - 83: 44.099 distance: 80 - 81: 6.683 distance: 80 - 82: 24.227 distance: 83 - 84: 22.640 distance: 84 - 85: 25.899 distance: 84 - 87: 10.469 distance: 85 - 86: 8.523 distance: 85 - 92: 24.874 distance: 87 - 88: 21.822 distance: 88 - 89: 13.025 distance: 89 - 90: 21.874 distance: 89 - 91: 15.943 distance: 92 - 93: 32.206 distance: 93 - 94: 21.352 distance: 94 - 95: 13.218 distance: 94 - 96: 14.592 distance: 95 - 123: 15.906 distance: 96 - 97: 14.087 distance: 97 - 98: 7.089 distance: 97 - 100: 14.382 distance: 98 - 99: 14.987 distance: 98 - 107: 11.880 distance: 99 - 130: 21.844 distance: 100 - 101: 5.191 distance: 101 - 102: 7.704 distance: 101 - 103: 6.219 distance: 102 - 104: 13.078 distance: 103 - 105: 17.153 distance: 104 - 106: 4.661 distance: 105 - 106: 4.937