Starting phenix.real_space_refine on Fri Jul 3 03:30:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xci_33121/07_2026/7xci_33121.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xci_33121/07_2026/7xci_33121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2026/7xci_33121.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2026/7xci_33121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2026/7xci_33121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2026/7xci_33121.map" model { file = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2026/7xci_33121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2026/7xci_33121.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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 6463 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 4189 2.51 5 N 1079 2.21 5 O 1241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6547 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 1 Time building chain proxies: 2.48, per 1000 atoms: 0.38 Number of scatterers: 6547 At special positions: 0 Unit cell: (77.22, 99.66, 114.84, 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 1241 8.00 N 1079 7.00 C 4189 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 702 " - " ASN A 432 " " NAG A 703 " - " ASN A 53 " " NAG A 704 " - " ASN A 90 " " NAG A 705 " - " ASN A 322 " " NAG A 706 " - " ASN A 103 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 546 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 408.0 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 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 56.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.598A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.847A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.531A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.807A 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 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.718A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.708A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.601A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.737A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.650A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 466 removed outlier: 3.831A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix 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: 4.531A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (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: 3.854A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.564A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.866A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.680A 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 600 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.087A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.872A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.887A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 305 hydrogen bonds defined for protein. 872 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: 1.10 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.24: 670 1.24 - 1.39: 2133 1.39 - 1.54: 3845 1.54 - 1.69: 25 1.69 - 1.85: 59 Bond restraints: 6732 Sorted by residual: bond pdb=" CG PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 1.503 1.084 0.419 3.40e-02 8.65e+02 1.52e+02 bond pdb=" CG PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.503 1.103 0.400 3.40e-02 8.65e+02 1.39e+02 bond pdb=" N PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.92e+01 bond pdb=" N PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.34e+01 bond pdb=" CB PRO A 469 " pdb=" CG PRO A 469 " ideal model delta sigma weight residual 1.492 1.704 -0.212 5.00e-02 4.00e+02 1.81e+01 ... (remaining 6727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 9124 4.17 - 8.34: 24 8.34 - 12.51: 1 12.51 - 16.69: 2 16.69 - 20.86: 2 Bond angle restraints: 9153 Sorted by residual: angle pdb=" N PRO A 263 " pdb=" CD PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 103.20 82.34 20.86 1.50e+00 4.44e-01 1.93e+02 angle pdb=" N PRO A 469 " pdb=" CD PRO A 469 " pdb=" CG PRO A 469 " ideal model delta sigma weight residual 103.20 82.45 20.75 1.50e+00 4.44e-01 1.91e+02 angle pdb=" CA PRO A 263 " pdb=" CB PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 104.50 90.21 14.29 1.90e+00 2.77e-01 5.65e+01 angle pdb=" CA PRO A 469 " pdb=" CB PRO A 469 " pdb=" CG PRO A 469 " ideal model delta sigma weight residual 104.50 91.08 13.42 1.90e+00 2.77e-01 4.99e+01 angle pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.38e+01 ... (remaining 9148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3548 17.63 - 35.26: 291 35.26 - 52.89: 57 52.89 - 70.52: 8 70.52 - 88.15: 8 Dihedral angle restraints: 3912 sinusoidal: 1582 harmonic: 2330 Sorted by residual: dihedral pdb=" CA PRO B 337 " pdb=" C PRO B 337 " pdb=" N PHE B 338 " pdb=" CA PHE B 338 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 135.79 -42.79 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 56.69 36.31 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 3909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 669 0.038 - 0.076: 232 0.076 - 0.114: 63 0.114 - 0.152: 12 0.152 - 0.190: 4 Chirality restraints: 980 Sorted by residual: chirality pdb=" C1 NAG A 705 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 705 " pdb=" O5 NAG A 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA PRO B 373 " pdb=" N PRO B 373 " pdb=" C PRO B 373 " pdb=" CB PRO B 373 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 977 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " -0.072 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 469 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 262 " -0.059 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO A 263 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 415 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.031 5.00e-02 4.00e+02 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 43 2.58 - 3.16: 5341 3.16 - 3.74: 9924 3.74 - 4.32: 13728 4.32 - 4.90: 23220 Nonbonded interactions: 52256 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.000 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.265 3.040 nonbonded pdb=" OG SER A 607 " pdb=" OD1 ASP A 609 " model vdw 2.272 3.040 nonbonded pdb=" OG SER A 77 " pdb=" O GLN A 101 " model vdw 2.304 3.040 nonbonded pdb=" OE1 GLU A 189 " pdb=" NH2 ARG A 192 " model vdw 2.310 3.120 ... (remaining 52251 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=0.49 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: 10.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.820 Find NCS groups from input model: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.009 0.419 6749 Z= 0.313 Angle : 0.759 20.857 9191 Z= 0.447 Chirality : 0.043 0.190 980 Planarity : 0.006 0.102 1176 Dihedral : 13.739 88.150 2395 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.30 % Favored : 96.44 % Rotamer: Outliers : 0.14 % Allowed : 0.57 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.30), residues: 788 helix: 1.09 (0.27), residues: 387 sheet: 1.23 (0.73), residues: 50 loop : -0.50 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 192 TYR 0.018 0.001 TYR A 202 PHE 0.022 0.001 PHE A 504 TRP 0.019 0.001 TRP A 165 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.29 ( 6732) covalent geometry : angle 0.75317 / 0.45 ( 9153) SS BOND : bond 0.00551 / 0.28 ( 7) SS BOND : angle 1.52376 / 0.77 ( 14) hydrogen bonds : bond 0.16052 / 10.48 ( 305) hydrogen bonds : angle 6.30357 / 4.51 ( 872) metal coordination : bond 0.20318 / 10.20 ( 2) link_BETA1-4 : bond 0.00183 / 0.10 ( 1) link_BETA1-4 : angle 0.70087 / 0.35 ( 3) link_NAG-ASN : bond 0.00325 / 0.16 ( 7) link_NAG-ASN : angle 1.81815 / 1.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.170 Fit side-chains REVERT: A 383 MET cc_start: 0.8242 (mtp) cc_final: 0.7894 (mtp) REVERT: B 420 ASP cc_start: 0.8031 (m-30) cc_final: 0.7576 (m-30) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.0616 time to fit residues: 8.6353 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134054 restraints weight = 8455.033| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.21 r_work: 0.3216 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6749 Z= 0.133 Angle : 0.570 9.404 9191 Z= 0.291 Chirality : 0.043 0.235 980 Planarity : 0.005 0.056 1176 Dihedral : 4.309 25.581 863 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.80 % Favored : 96.95 % Rotamer: Outliers : 0.86 % Allowed : 6.03 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.30), residues: 788 helix: 1.18 (0.26), residues: 387 sheet: 1.18 (0.72), residues: 50 loop : -0.43 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 192 TYR 0.015 0.001 TYR A 385 PHE 0.028 0.001 PHE A 504 TRP 0.019 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 6732) covalent geometry : angle 0.56036 / 0.29 ( 9153) SS BOND : bond 0.00589 / 0.30 ( 7) SS BOND : angle 1.02511 / 0.53 ( 14) hydrogen bonds : bond 0.05083 / 3.50 ( 305) hydrogen bonds : angle 4.85557 / 3.42 ( 872) metal coordination : bond 0.00192 / 0.10 ( 2) link_BETA1-4 : bond 0.00070 / 0.04 ( 1) link_BETA1-4 : angle 1.15114 / 0.58 ( 3) link_NAG-ASN : bond 0.00254 / 0.14 ( 7) link_NAG-ASN : angle 2.09846 / 1.32 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.155 Fit side-chains REVERT: A 265 HIS cc_start: 0.6035 (p90) cc_final: 0.5822 (p-80) REVERT: A 435 GLU cc_start: 0.7277 (mp0) cc_final: 0.7037 (mp0) REVERT: B 420 ASP cc_start: 0.8520 (m-30) cc_final: 0.8119 (m-30) outliers start: 6 outliers final: 2 residues processed: 97 average time/residue: 0.0713 time to fit residues: 9.5257 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 0.0030 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.176969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120556 restraints weight = 15370.564| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.35 r_work: 0.3202 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6749 Z= 0.124 Angle : 0.537 9.450 9191 Z= 0.272 Chirality : 0.042 0.242 980 Planarity : 0.004 0.046 1176 Dihedral : 4.361 29.875 863 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 1.29 % Allowed : 8.75 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.30), residues: 788 helix: 1.35 (0.27), residues: 383 sheet: 0.50 (0.65), residues: 55 loop : -0.41 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 192 TYR 0.018 0.001 TYR A 381 PHE 0.024 0.001 PHE A 504 TRP 0.018 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6732) covalent geometry : angle 0.52732 / 0.27 ( 9153) SS BOND : bond 0.00260 / 0.13 ( 7) SS BOND : angle 1.01303 / 0.52 ( 14) hydrogen bonds : bond 0.04920 / 3.41 ( 305) hydrogen bonds : angle 4.59623 / 3.24 ( 872) metal coordination : bond 0.00248 / 0.12 ( 2) link_BETA1-4 : bond 0.00234 / 0.12 ( 1) link_BETA1-4 : angle 1.16492 / 0.59 ( 3) link_NAG-ASN : bond 0.00283 / 0.15 ( 7) link_NAG-ASN : angle 2.02516 / 1.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.167 Fit side-chains REVERT: A 383 MET cc_start: 0.8788 (mtp) cc_final: 0.8574 (mtp) REVERT: A 435 GLU cc_start: 0.7312 (mp0) cc_final: 0.7072 (mp0) REVERT: B 420 ASP cc_start: 0.8550 (m-30) cc_final: 0.8237 (m-30) REVERT: B 443 SER cc_start: 0.8769 (m) cc_final: 0.8351 (m) outliers start: 9 outliers final: 5 residues processed: 98 average time/residue: 0.0681 time to fit residues: 9.1921 Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.0270 chunk 52 optimal weight: 0.0070 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.0770 chunk 68 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.179545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122447 restraints weight = 10501.237| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.81 r_work: 0.3251 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6749 Z= 0.105 Angle : 0.531 9.428 9191 Z= 0.266 Chirality : 0.042 0.282 980 Planarity : 0.004 0.045 1176 Dihedral : 4.223 24.419 863 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 0.72 % Allowed : 10.47 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.30), residues: 788 helix: 1.55 (0.27), residues: 375 sheet: 0.53 (0.65), residues: 55 loop : -0.39 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 192 TYR 0.017 0.001 TYR A 202 PHE 0.021 0.001 PHE A 504 TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 6732) covalent geometry : angle 0.52011 / 0.26 ( 9153) SS BOND : bond 0.00394 / 0.21 ( 7) SS BOND : angle 1.67288 / 1.00 ( 14) hydrogen bonds : bond 0.04278 / 2.99 ( 305) hydrogen bonds : angle 4.52391 / 3.19 ( 872) metal coordination : bond 0.00071 / 0.04 ( 2) link_BETA1-4 : bond 0.00302 / 0.16 ( 1) link_BETA1-4 : angle 0.87971 / 0.46 ( 3) link_NAG-ASN : bond 0.00239 / 0.12 ( 7) link_NAG-ASN : angle 1.92869 / 1.19 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.214 Fit side-chains REVERT: A 181 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7324 (mp0) REVERT: A 435 GLU cc_start: 0.7295 (mp0) cc_final: 0.6802 (mp0) REVERT: B 360 ASN cc_start: 0.7454 (m-40) cc_final: 0.7200 (m-40) REVERT: B 420 ASP cc_start: 0.8482 (m-30) cc_final: 0.8137 (m-30) REVERT: B 443 SER cc_start: 0.8668 (m) cc_final: 0.8258 (m) outliers start: 5 outliers final: 2 residues processed: 92 average time/residue: 0.0635 time to fit residues: 8.1395 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.0770 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 68 optimal weight: 0.0270 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.178446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119441 restraints weight = 10617.618| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.66 r_work: 0.3255 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6749 Z= 0.105 Angle : 0.518 9.500 9191 Z= 0.259 Chirality : 0.041 0.245 980 Planarity : 0.004 0.043 1176 Dihedral : 4.063 23.010 863 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 1.15 % Allowed : 10.62 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.30), residues: 788 helix: 1.52 (0.27), residues: 383 sheet: 1.06 (0.68), residues: 45 loop : -0.42 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 192 TYR 0.018 0.001 TYR A 202 PHE 0.023 0.001 PHE A 504 TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 6732) covalent geometry : angle 0.50940 / 0.26 ( 9153) SS BOND : bond 0.00387 / 0.20 ( 7) SS BOND : angle 1.01364 / 0.54 ( 14) hydrogen bonds : bond 0.04238 / 2.97 ( 305) hydrogen bonds : angle 4.40309 / 3.11 ( 872) metal coordination : bond 0.00125 / 0.06 ( 2) link_BETA1-4 : bond 0.00220 / 0.12 ( 1) link_BETA1-4 : angle 0.97812 / 0.50 ( 3) link_NAG-ASN : bond 0.00263 / 0.14 ( 7) link_NAG-ASN : angle 1.87184 / 1.15 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.149 Fit side-chains REVERT: A 435 GLU cc_start: 0.7331 (mp0) cc_final: 0.6989 (mp0) REVERT: B 360 ASN cc_start: 0.7628 (m-40) cc_final: 0.7342 (m-40) REVERT: B 420 ASP cc_start: 0.8744 (m-30) cc_final: 0.8447 (m-30) REVERT: B 443 SER cc_start: 0.8722 (m) cc_final: 0.8281 (m) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 0.0630 time to fit residues: 8.2883 Evaluate side-chains 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116988 restraints weight = 16995.989| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.93 r_work: 0.3117 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6749 Z= 0.132 Angle : 0.540 9.577 9191 Z= 0.272 Chirality : 0.042 0.239 980 Planarity : 0.004 0.042 1176 Dihedral : 4.195 22.407 863 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.15 % Allowed : 10.76 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.31), residues: 788 helix: 1.48 (0.27), residues: 384 sheet: 0.54 (0.67), residues: 60 loop : -0.38 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 192 TYR 0.020 0.001 TYR A 381 PHE 0.021 0.001 PHE A 504 TRP 0.017 0.001 TRP A 165 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6732) covalent geometry : angle 0.53096 / 0.27 ( 9153) SS BOND : bond 0.00554 / 0.28 ( 7) SS BOND : angle 1.05798 / 0.57 ( 14) hydrogen bonds : bond 0.05017 / 3.48 ( 305) hydrogen bonds : angle 4.45714 / 3.15 ( 872) metal coordination : bond 0.00224 / 0.12 ( 2) link_BETA1-4 : bond 0.00236 / 0.12 ( 1) link_BETA1-4 : angle 1.47371 / 0.74 ( 3) link_NAG-ASN : bond 0.00303 / 0.17 ( 7) link_NAG-ASN : angle 1.94257 / 1.19 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.171 Fit side-chains REVERT: A 435 GLU cc_start: 0.7352 (mp0) cc_final: 0.6942 (mp0) REVERT: B 360 ASN cc_start: 0.7644 (m-40) cc_final: 0.6968 (t0) REVERT: B 420 ASP cc_start: 0.8644 (m-30) cc_final: 0.8301 (m-30) REVERT: B 443 SER cc_start: 0.8806 (m) cc_final: 0.8370 (m) outliers start: 8 outliers final: 7 residues processed: 91 average time/residue: 0.0655 time to fit residues: 8.3075 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118608 restraints weight = 10431.523| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.85 r_work: 0.3214 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6749 Z= 0.136 Angle : 0.549 9.562 9191 Z= 0.277 Chirality : 0.042 0.242 980 Planarity : 0.004 0.045 1176 Dihedral : 4.220 22.310 863 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.15 % Allowed : 11.19 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.30), residues: 788 helix: 1.55 (0.27), residues: 382 sheet: 0.54 (0.68), residues: 60 loop : -0.45 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 192 TYR 0.020 0.001 TYR A 381 PHE 0.020 0.001 PHE A 504 TRP 0.016 0.001 TRP A 165 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 6732) covalent geometry : angle 0.53996 / 0.28 ( 9153) SS BOND : bond 0.00406 / 0.21 ( 7) SS BOND : angle 1.04574 / 0.55 ( 14) hydrogen bonds : bond 0.04967 / 3.45 ( 305) hydrogen bonds : angle 4.46588 / 3.16 ( 872) metal coordination : bond 0.00264 / 0.13 ( 2) link_BETA1-4 : bond 0.00163 / 0.09 ( 1) link_BETA1-4 : angle 1.25791 / 0.64 ( 3) link_NAG-ASN : bond 0.00271 / 0.15 ( 7) link_NAG-ASN : angle 1.93952 / 1.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.209 Fit side-chains REVERT: A 435 GLU cc_start: 0.7365 (mp0) cc_final: 0.6974 (mp0) REVERT: B 360 ASN cc_start: 0.7574 (m-40) cc_final: 0.6944 (t0) REVERT: B 420 ASP cc_start: 0.8494 (m-30) cc_final: 0.8140 (m-30) REVERT: B 443 SER cc_start: 0.8715 (m) cc_final: 0.8293 (m) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.0610 time to fit residues: 7.7036 Evaluate side-chains 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 73 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.177124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118910 restraints weight = 10510.337| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.66 r_work: 0.3239 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6749 Z= 0.121 Angle : 0.538 9.532 9191 Z= 0.272 Chirality : 0.042 0.242 980 Planarity : 0.004 0.046 1176 Dihedral : 4.158 22.105 863 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.15 % Allowed : 11.33 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.31), residues: 788 helix: 1.67 (0.27), residues: 376 sheet: 0.59 (0.68), residues: 60 loop : -0.38 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 192 TYR 0.018 0.001 TYR A 202 PHE 0.019 0.001 PHE A 504 TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6732) covalent geometry : angle 0.53025 / 0.27 ( 9153) SS BOND : bond 0.00382 / 0.20 ( 7) SS BOND : angle 0.98516 / 0.52 ( 14) hydrogen bonds : bond 0.04703 / 3.27 ( 305) hydrogen bonds : angle 4.42651 / 3.12 ( 872) metal coordination : bond 0.00191 / 0.10 ( 2) link_BETA1-4 : bond 0.00183 / 0.10 ( 1) link_BETA1-4 : angle 1.05855 / 0.54 ( 3) link_NAG-ASN : bond 0.00255 / 0.14 ( 7) link_NAG-ASN : angle 1.88033 / 1.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7222 (mp0) REVERT: A 435 GLU cc_start: 0.7495 (mp0) cc_final: 0.7078 (mp0) REVERT: B 360 ASN cc_start: 0.7689 (m-40) cc_final: 0.7071 (t0) REVERT: B 420 ASP cc_start: 0.8645 (m-30) cc_final: 0.8332 (m-30) REVERT: B 443 SER cc_start: 0.8705 (m) cc_final: 0.8279 (m) outliers start: 8 outliers final: 8 residues processed: 89 average time/residue: 0.0660 time to fit residues: 8.2168 Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145546 restraints weight = 20245.036| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 5.61 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6749 Z= 0.117 Angle : 0.530 9.534 9191 Z= 0.267 Chirality : 0.041 0.243 980 Planarity : 0.004 0.046 1176 Dihedral : 4.096 21.894 863 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.29 % Allowed : 11.62 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.31), residues: 788 helix: 1.71 (0.27), residues: 376 sheet: 0.58 (0.68), residues: 60 loop : -0.34 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 192 TYR 0.018 0.001 TYR A 202 PHE 0.019 0.001 PHE A 504 TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6732) covalent geometry : angle 0.52191 / 0.26 ( 9153) SS BOND : bond 0.00366 / 0.19 ( 7) SS BOND : angle 0.95382 / 0.50 ( 14) hydrogen bonds : bond 0.04541 / 3.16 ( 305) hydrogen bonds : angle 4.38001 / 3.09 ( 872) metal coordination : bond 0.00162 / 0.08 ( 2) link_BETA1-4 : bond 0.00186 / 0.10 ( 1) link_BETA1-4 : angle 1.03657 / 0.53 ( 3) link_NAG-ASN : bond 0.00254 / 0.13 ( 7) link_NAG-ASN : angle 1.86796 / 1.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8141 (m-30) cc_final: 0.7769 (m-30) REVERT: B 443 SER cc_start: 0.8205 (m) cc_final: 0.7963 (m) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.0735 time to fit residues: 9.0625 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.0020 chunk 64 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.176646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120163 restraints weight = 15445.939| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.67 r_work: 0.3215 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6749 Z= 0.122 Angle : 0.544 9.552 9191 Z= 0.275 Chirality : 0.042 0.242 980 Planarity : 0.004 0.046 1176 Dihedral : 4.127 21.928 863 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.29 % Allowed : 12.05 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.31), residues: 788 helix: 1.67 (0.27), residues: 376 sheet: 0.57 (0.68), residues: 60 loop : -0.36 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 192 TYR 0.018 0.001 TYR A 202 PHE 0.019 0.001 PHE A 504 TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6732) covalent geometry : angle 0.53612 / 0.27 ( 9153) SS BOND : bond 0.00378 / 0.19 ( 7) SS BOND : angle 0.96867 / 0.51 ( 14) hydrogen bonds : bond 0.04647 / 3.23 ( 305) hydrogen bonds : angle 4.39339 / 3.11 ( 872) metal coordination : bond 0.00181 / 0.09 ( 2) link_BETA1-4 : bond 0.00190 / 0.10 ( 1) link_BETA1-4 : angle 1.08597 / 0.55 ( 3) link_NAG-ASN : bond 0.00243 / 0.13 ( 7) link_NAG-ASN : angle 1.86149 / 1.17 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8469 (m-30) cc_final: 0.8127 (m-30) REVERT: B 443 SER cc_start: 0.8657 (m) cc_final: 0.8244 (m) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 0.0664 time to fit residues: 7.7432 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 73 optimal weight: 0.0020 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118846 restraints weight = 16775.661| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.78 r_work: 0.3193 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6749 Z= 0.128 Angle : 0.553 9.567 9191 Z= 0.279 Chirality : 0.042 0.243 980 Planarity : 0.004 0.046 1176 Dihedral : 4.165 21.851 863 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.72 % Allowed : 11.76 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.31), residues: 788 helix: 1.67 (0.27), residues: 376 sheet: 0.53 (0.68), residues: 60 loop : -0.39 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 192 TYR 0.020 0.001 TYR A 381 PHE 0.018 0.001 PHE A 504 TRP 0.017 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6732) covalent geometry : angle 0.54450 / 0.28 ( 9153) SS BOND : bond 0.00389 / 0.20 ( 7) SS BOND : angle 0.99769 / 0.53 ( 14) hydrogen bonds : bond 0.04825 / 3.35 ( 305) hydrogen bonds : angle 4.41550 / 3.13 ( 872) metal coordination : bond 0.00209 / 0.11 ( 2) link_BETA1-4 : bond 0.00129 / 0.07 ( 1) link_BETA1-4 : angle 1.19692 / 0.60 ( 3) link_NAG-ASN : bond 0.00273 / 0.15 ( 7) link_NAG-ASN : angle 1.90585 / 1.20 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.38 seconds wall clock time: 34 minutes 31.20 seconds (2071.20 seconds total)