Starting phenix.real_space_refine on Wed Jan 14 03:03:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yhw_33841/01_2026/7yhw_33841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yhw_33841/01_2026/7yhw_33841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yhw_33841/01_2026/7yhw_33841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yhw_33841/01_2026/7yhw_33841.map" model { file = "/net/cci-nas-00/data/ceres_data/7yhw_33841/01_2026/7yhw_33841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yhw_33841/01_2026/7yhw_33841.cif" } resolution = 3.09 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= 0.008 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 6333 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 4194 2.51 5 N 1077 2.21 5 O 1248 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-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6557 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1558 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 1.55, per 1000 atoms: 0.24 Number of scatterers: 6557 At special positions: 0 Unit cell: (82.45, 92.65, 119.85, 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 1248 8.00 N 1077 7.00 C 4194 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=2.03 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 D 1 " - " NAG D 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 207.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 705 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 378 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 54.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.758A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 4.045A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.526A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.706A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.711A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.698A pdb=" N THR A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.504A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.823A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.672A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (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 249 removed outlier: 4.061A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.976A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.597A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.706A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.084A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.599A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.435A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.567A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.905A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.793A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.569A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.570A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.427A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.366A 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 352 removed outlier: 6.097A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 359 removed outlier: 3.601A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (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 474 285 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2054 1.34 - 1.46: 1742 1.46 - 1.59: 2887 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6741 Sorted by residual: bond pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 1.469 1.435 0.034 1.28e-02 6.10e+03 7.05e+00 bond pdb=" N GLU A 35 " pdb=" CA GLU A 35 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.30e-02 5.92e+03 6.04e+00 bond pdb=" N ASP A 355 " pdb=" CA ASP A 355 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.23e-02 6.61e+03 5.67e+00 bond pdb=" CA SER A 19 " pdb=" CB SER A 19 " ideal model delta sigma weight residual 1.530 1.486 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" N HIS A 34 " pdb=" CA HIS A 34 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.44e+00 ... (remaining 6736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 8774 1.53 - 3.07: 329 3.07 - 4.60: 47 4.60 - 6.13: 11 6.13 - 7.66: 2 Bond angle restraints: 9163 Sorted by residual: angle pdb=" N THR B 500 " pdb=" CA THR B 500 " pdb=" C THR B 500 " ideal model delta sigma weight residual 114.16 106.50 7.66 1.48e+00 4.57e-01 2.68e+01 angle pdb=" CA ASN B 487 " pdb=" C ASN B 487 " pdb=" O ASN B 487 " ideal model delta sigma weight residual 121.28 117.09 4.19 1.19e+00 7.06e-01 1.24e+01 angle pdb=" CA THR A 20 " pdb=" C THR A 20 " pdb=" O THR A 20 " ideal model delta sigma weight residual 122.01 118.40 3.61 1.05e+00 9.07e-01 1.18e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 112.43 109.47 2.96 9.20e-01 1.18e+00 1.04e+01 angle pdb=" N GLN A 42 " pdb=" CA GLN A 42 " pdb=" C GLN A 42 " ideal model delta sigma weight residual 111.82 108.17 3.65 1.16e+00 7.43e-01 9.90e+00 ... (remaining 9158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3657 17.92 - 35.83: 355 35.83 - 53.75: 73 53.75 - 71.67: 14 71.67 - 89.58: 3 Dihedral angle restraints: 4102 sinusoidal: 1780 harmonic: 2322 Sorted by residual: 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 50.19 42.81 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -128.02 42.02 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA CYS B 391 " pdb=" C CYS B 391 " pdb=" N PHE B 392 " pdb=" CA PHE B 392 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 4099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 702 0.047 - 0.094: 234 0.094 - 0.142: 45 0.142 - 0.189: 2 0.189 - 0.236: 1 Chirality restraints: 984 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 981 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO B 479 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 521 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 402 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" CD GLU A 402 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 402 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 402 " -0.011 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 38 2.58 - 3.16: 5149 3.16 - 3.74: 9341 3.74 - 4.32: 13213 4.32 - 4.90: 22742 Nonbonded interactions: 50483 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 705 " model vdw 2.001 2.230 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 199 " pdb=" OD2 ASP A 509 " model vdw 2.298 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.315 3.120 nonbonded pdb=" O GLY A 268 " pdb=" ND2 ASN A 277 " model vdw 2.319 3.120 ... (remaining 50478 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: 17.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.830 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.007 0.209 6760 Z= 0.284 Angle : 0.691 7.664 9207 Z= 0.396 Chirality : 0.046 0.236 984 Planarity : 0.004 0.050 1176 Dihedral : 14.210 89.582 2591 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.29 % Allowed : 1.15 % Favored : 98.56 % 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: -0.31 (0.30), residues: 787 helix: 0.49 (0.28), residues: 375 sheet: 1.71 (0.78), residues: 44 loop : -1.17 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.020 0.002 TYR A 385 PHE 0.017 0.002 PHE A 512 TRP 0.011 0.001 TRP B 436 HIS 0.010 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 6741) covalent geometry : angle 0.68105 ( 9163) SS BOND : bond 0.00405 ( 7) SS BOND : angle 0.96623 ( 14) hydrogen bonds : bond 0.22891 ( 285) hydrogen bonds : angle 6.51716 ( 801) metal coordination : bond 0.20132 ( 2) link_BETA1-4 : bond 0.00225 ( 2) link_BETA1-4 : angle 1.25966 ( 6) link_BETA1-6 : bond 0.00091 ( 1) link_BETA1-6 : angle 1.68321 ( 3) link_NAG-ASN : bond 0.00443 ( 7) link_NAG-ASN : angle 2.36802 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7548 (m-40) cc_final: 0.7066 (m-40) REVERT: A 63 ASN cc_start: 0.7895 (m110) cc_final: 0.7694 (m110) REVERT: A 98 GLN cc_start: 0.7502 (tt0) cc_final: 0.7022 (tt0) REVERT: A 102 GLN cc_start: 0.7185 (mp10) cc_final: 0.6848 (mp10) REVERT: A 150 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7610 (tp30) REVERT: A 206 ASP cc_start: 0.7202 (t0) cc_final: 0.6854 (t0) REVERT: A 232 GLU cc_start: 0.7376 (tp30) cc_final: 0.7033 (tp30) REVERT: A 313 LYS cc_start: 0.8280 (ttmm) cc_final: 0.8044 (ttmm) REVERT: B 405 ASN cc_start: 0.7905 (m-40) cc_final: 0.7590 (m-40) REVERT: B 438 SER cc_start: 0.7479 (p) cc_final: 0.7101 (p) REVERT: B 500 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7580 (p) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.0726 time to fit residues: 17.5673 Evaluate side-chains 174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 chunk 74 optimal weight: 0.5980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101856 restraints weight = 9611.641| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.12 r_work: 0.3156 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6760 Z= 0.206 Angle : 0.567 6.589 9207 Z= 0.295 Chirality : 0.045 0.257 984 Planarity : 0.005 0.049 1176 Dihedral : 6.825 53.888 1067 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.87 % Allowed : 9.38 % Favored : 89.75 % 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: -0.05 (0.31), residues: 787 helix: 0.81 (0.28), residues: 384 sheet: 1.54 (0.79), residues: 44 loop : -1.18 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.019 0.002 TYR A 385 PHE 0.010 0.001 PHE A 285 TRP 0.016 0.001 TRP B 436 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 6741) covalent geometry : angle 0.55508 ( 9163) SS BOND : bond 0.00421 ( 7) SS BOND : angle 0.97357 ( 14) hydrogen bonds : bond 0.06332 ( 285) hydrogen bonds : angle 4.71437 ( 801) metal coordination : bond 0.00982 ( 2) link_BETA1-4 : bond 0.00504 ( 2) link_BETA1-4 : angle 1.23342 ( 6) link_BETA1-6 : bond 0.00086 ( 1) link_BETA1-6 : angle 1.52896 ( 3) link_NAG-ASN : bond 0.00411 ( 7) link_NAG-ASN : angle 2.26591 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 0.264 Fit side-chains REVERT: A 35 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 61 ASN cc_start: 0.7847 (m-40) cc_final: 0.7335 (m-40) REVERT: A 98 GLN cc_start: 0.8269 (tt0) cc_final: 0.7761 (tt0) REVERT: A 102 GLN cc_start: 0.7610 (mp10) cc_final: 0.7239 (mp10) REVERT: A 152 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.7101 (mtp) REVERT: A 206 ASP cc_start: 0.7840 (t0) cc_final: 0.7430 (t0) REVERT: A 232 GLU cc_start: 0.8154 (tp30) cc_final: 0.7781 (tp30) REVERT: A 360 MET cc_start: 0.8403 (ttt) cc_final: 0.8062 (ttp) REVERT: A 455 MET cc_start: 0.8297 (tmm) cc_final: 0.7613 (tmm) REVERT: B 405 ASN cc_start: 0.8287 (m-40) cc_final: 0.7944 (m-40) REVERT: B 468 ILE cc_start: 0.8661 (pt) cc_final: 0.8419 (mt) outliers start: 6 outliers final: 3 residues processed: 180 average time/residue: 0.0779 time to fit residues: 18.9543 Evaluate side-chains 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 283 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 0.0470 chunk 35 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 68 optimal weight: 0.2980 overall best weight: 0.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102955 restraints weight = 9513.774| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.93 r_work: 0.3183 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6760 Z= 0.160 Angle : 0.519 6.399 9207 Z= 0.267 Chirality : 0.043 0.245 984 Planarity : 0.004 0.046 1176 Dihedral : 5.992 53.307 1066 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.88 % Allowed : 12.84 % Favored : 85.28 % 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: 0.08 (0.31), residues: 787 helix: 0.95 (0.28), residues: 390 sheet: 1.37 (0.79), residues: 44 loop : -1.15 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 559 TYR 0.016 0.001 TYR A 385 PHE 0.008 0.001 PHE A 285 TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6741) covalent geometry : angle 0.50712 ( 9163) SS BOND : bond 0.00385 ( 7) SS BOND : angle 0.96503 ( 14) hydrogen bonds : bond 0.05458 ( 285) hydrogen bonds : angle 4.40830 ( 801) metal coordination : bond 0.00396 ( 2) link_BETA1-4 : bond 0.00336 ( 2) link_BETA1-4 : angle 1.25819 ( 6) link_BETA1-6 : bond 0.00296 ( 1) link_BETA1-6 : angle 1.52988 ( 3) link_NAG-ASN : bond 0.00413 ( 7) link_NAG-ASN : angle 2.14466 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.236 Fit side-chains REVERT: A 35 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 61 ASN cc_start: 0.7805 (m-40) cc_final: 0.7278 (m-40) REVERT: A 63 ASN cc_start: 0.8018 (m-40) cc_final: 0.7795 (m-40) REVERT: A 98 GLN cc_start: 0.8284 (tt0) cc_final: 0.7996 (tt0) REVERT: A 102 GLN cc_start: 0.7588 (mp10) cc_final: 0.7249 (mp10) REVERT: A 152 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6775 (mtp) REVERT: A 232 GLU cc_start: 0.8073 (tp30) cc_final: 0.7698 (tp30) REVERT: A 355 ASP cc_start: 0.7942 (t0) cc_final: 0.7548 (m-30) REVERT: A 360 MET cc_start: 0.8294 (ttt) cc_final: 0.8025 (ttp) REVERT: B 405 ASN cc_start: 0.8252 (m-40) cc_final: 0.7898 (m-40) REVERT: B 468 ILE cc_start: 0.8695 (pt) cc_final: 0.8426 (mt) outliers start: 13 outliers final: 7 residues processed: 171 average time/residue: 0.0824 time to fit residues: 18.7132 Evaluate side-chains 170 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.0670 chunk 55 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.0370 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 417 ASN B 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101822 restraints weight = 9627.086| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.01 r_work: 0.3180 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6760 Z= 0.155 Angle : 0.513 6.366 9207 Z= 0.263 Chirality : 0.043 0.240 984 Planarity : 0.004 0.045 1176 Dihedral : 5.569 53.570 1066 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.16 % Allowed : 14.57 % Favored : 83.26 % 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: 0.15 (0.31), residues: 787 helix: 1.02 (0.28), residues: 393 sheet: 1.32 (0.78), residues: 44 loop : -1.13 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 559 TYR 0.015 0.001 TYR A 385 PHE 0.007 0.001 PHE A 285 TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6741) covalent geometry : angle 0.50124 ( 9163) SS BOND : bond 0.00371 ( 7) SS BOND : angle 0.93706 ( 14) hydrogen bonds : bond 0.05196 ( 285) hydrogen bonds : angle 4.29798 ( 801) metal coordination : bond 0.00211 ( 2) link_BETA1-4 : bond 0.00314 ( 2) link_BETA1-4 : angle 1.24197 ( 6) link_BETA1-6 : bond 0.00202 ( 1) link_BETA1-6 : angle 1.49843 ( 3) link_NAG-ASN : bond 0.00408 ( 7) link_NAG-ASN : angle 2.15031 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.209 Fit side-chains REVERT: A 35 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7715 (mt-10) REVERT: A 61 ASN cc_start: 0.7847 (m-40) cc_final: 0.7347 (m-40) REVERT: A 63 ASN cc_start: 0.8094 (m-40) cc_final: 0.7863 (m-40) REVERT: A 98 GLN cc_start: 0.8449 (tt0) cc_final: 0.8181 (tt0) REVERT: A 102 GLN cc_start: 0.7640 (mp10) cc_final: 0.7270 (mp10) REVERT: A 152 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6828 (mtp) REVERT: A 232 GLU cc_start: 0.8116 (tp30) cc_final: 0.7747 (tp30) REVERT: A 355 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: A 402 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7112 (mm-30) REVERT: B 405 ASN cc_start: 0.8230 (m-40) cc_final: 0.7911 (m-40) REVERT: B 468 ILE cc_start: 0.8716 (pt) cc_final: 0.8433 (mt) outliers start: 15 outliers final: 8 residues processed: 170 average time/residue: 0.0813 time to fit residues: 18.5118 Evaluate side-chains 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 54 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.0170 chunk 31 optimal weight: 0.0030 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 250 ASN A 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101859 restraints weight = 9762.910| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.03 r_work: 0.3174 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6760 Z= 0.165 Angle : 0.515 6.372 9207 Z= 0.265 Chirality : 0.043 0.240 984 Planarity : 0.004 0.044 1176 Dihedral : 5.424 53.098 1066 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.45 % Allowed : 15.73 % Favored : 81.82 % 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: 0.19 (0.31), residues: 787 helix: 1.06 (0.28), residues: 393 sheet: 1.21 (0.78), residues: 44 loop : -1.10 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 559 TYR 0.015 0.001 TYR A 385 PHE 0.019 0.001 PHE B 375 TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6741) covalent geometry : angle 0.50304 ( 9163) SS BOND : bond 0.00537 ( 7) SS BOND : angle 0.80413 ( 14) hydrogen bonds : bond 0.05223 ( 285) hydrogen bonds : angle 4.22929 ( 801) metal coordination : bond 0.00279 ( 2) link_BETA1-4 : bond 0.00306 ( 2) link_BETA1-4 : angle 1.21925 ( 6) link_BETA1-6 : bond 0.00166 ( 1) link_BETA1-6 : angle 1.48142 ( 3) link_NAG-ASN : bond 0.00418 ( 7) link_NAG-ASN : angle 2.11537 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7838 (m-40) cc_final: 0.7350 (m-40) REVERT: A 63 ASN cc_start: 0.8102 (m-40) cc_final: 0.7877 (m-40) REVERT: A 98 GLN cc_start: 0.8515 (tt0) cc_final: 0.8244 (tt0) REVERT: A 102 GLN cc_start: 0.7688 (mp10) cc_final: 0.7308 (mp10) REVERT: A 152 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6650 (mtp) REVERT: A 232 GLU cc_start: 0.8116 (tp30) cc_final: 0.7745 (tp30) REVERT: A 355 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: A 402 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: B 405 ASN cc_start: 0.8181 (m-40) cc_final: 0.7913 (m-40) REVERT: B 468 ILE cc_start: 0.8736 (pt) cc_final: 0.8444 (mt) outliers start: 17 outliers final: 9 residues processed: 176 average time/residue: 0.0819 time to fit residues: 19.2998 Evaluate side-chains 180 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.4980 chunk 71 optimal weight: 0.0970 chunk 40 optimal weight: 0.0770 chunk 25 optimal weight: 0.0570 chunk 36 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 43 optimal weight: 0.0970 chunk 41 optimal weight: 0.4980 chunk 59 optimal weight: 0.0370 chunk 5 optimal weight: 0.3980 overall best weight: 0.0730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105215 restraints weight = 9694.037| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.99 r_work: 0.3213 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6760 Z= 0.097 Angle : 0.479 6.151 9207 Z= 0.245 Chirality : 0.041 0.214 984 Planarity : 0.004 0.042 1176 Dihedral : 5.119 52.324 1066 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.88 % Allowed : 16.74 % Favored : 81.39 % 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: 0.46 (0.32), residues: 787 helix: 1.32 (0.28), residues: 386 sheet: 1.06 (0.77), residues: 46 loop : -0.95 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 559 TYR 0.012 0.001 TYR A 183 PHE 0.025 0.001 PHE B 375 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 6741) covalent geometry : angle 0.46816 ( 9163) SS BOND : bond 0.00427 ( 7) SS BOND : angle 0.77667 ( 14) hydrogen bonds : bond 0.04086 ( 285) hydrogen bonds : angle 4.14491 ( 801) metal coordination : bond 0.00081 ( 2) link_BETA1-4 : bond 0.00361 ( 2) link_BETA1-4 : angle 1.01215 ( 6) link_BETA1-6 : bond 0.00334 ( 1) link_BETA1-6 : angle 1.51441 ( 3) link_NAG-ASN : bond 0.00390 ( 7) link_NAG-ASN : angle 1.95003 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7701 (m-40) cc_final: 0.7179 (m-40) REVERT: A 63 ASN cc_start: 0.7966 (m-40) cc_final: 0.7738 (m-40) REVERT: A 98 GLN cc_start: 0.8418 (tt0) cc_final: 0.8137 (tt0) REVERT: A 102 GLN cc_start: 0.7673 (mp10) cc_final: 0.7256 (mp10) REVERT: A 150 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7639 (tp30) REVERT: A 152 MET cc_start: 0.7030 (mtp) cc_final: 0.6688 (mtp) REVERT: A 167 SER cc_start: 0.8516 (m) cc_final: 0.8221 (p) REVERT: A 232 GLU cc_start: 0.8073 (tp30) cc_final: 0.7652 (tp30) REVERT: A 355 ASP cc_start: 0.7915 (t0) cc_final: 0.7539 (m-30) REVERT: A 402 GLU cc_start: 0.7543 (tt0) cc_final: 0.7279 (mm-30) REVERT: B 405 ASN cc_start: 0.8186 (m-40) cc_final: 0.7829 (m-40) REVERT: B 468 ILE cc_start: 0.8741 (pt) cc_final: 0.8432 (mt) outliers start: 13 outliers final: 3 residues processed: 174 average time/residue: 0.0832 time to fit residues: 19.4702 Evaluate side-chains 174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.0670 chunk 53 optimal weight: 0.4980 chunk 60 optimal weight: 0.0970 chunk 59 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 0.0770 chunk 10 optimal weight: 0.3980 overall best weight: 0.1452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104131 restraints weight = 9628.822| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.03 r_work: 0.3197 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6760 Z= 0.116 Angle : 0.507 12.106 9207 Z= 0.254 Chirality : 0.041 0.215 984 Planarity : 0.004 0.042 1176 Dihedral : 5.074 52.762 1066 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.01 % Allowed : 18.33 % Favored : 80.66 % 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: 0.56 (0.32), residues: 787 helix: 1.44 (0.28), residues: 384 sheet: 1.03 (0.77), residues: 46 loop : -0.91 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 559 TYR 0.012 0.001 TYR A 385 PHE 0.018 0.001 PHE B 375 TRP 0.009 0.001 TRP A 168 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6741) covalent geometry : angle 0.49673 ( 9163) SS BOND : bond 0.00350 ( 7) SS BOND : angle 0.79359 ( 14) hydrogen bonds : bond 0.04345 ( 285) hydrogen bonds : angle 4.09414 ( 801) metal coordination : bond 0.00148 ( 2) link_BETA1-4 : bond 0.00340 ( 2) link_BETA1-4 : angle 1.08916 ( 6) link_BETA1-6 : bond 0.00267 ( 1) link_BETA1-6 : angle 1.40004 ( 3) link_NAG-ASN : bond 0.00378 ( 7) link_NAG-ASN : angle 2.00474 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 0.255 Fit side-chains REVERT: A 61 ASN cc_start: 0.7785 (m-40) cc_final: 0.7276 (m-40) REVERT: A 63 ASN cc_start: 0.8042 (m-40) cc_final: 0.7827 (m-40) REVERT: A 98 GLN cc_start: 0.8506 (tt0) cc_final: 0.8197 (tt0) REVERT: A 102 GLN cc_start: 0.7693 (mp10) cc_final: 0.7258 (mp10) REVERT: A 167 SER cc_start: 0.8553 (m) cc_final: 0.8308 (p) REVERT: A 232 GLU cc_start: 0.8103 (tp30) cc_final: 0.7698 (tp30) REVERT: A 276 THR cc_start: 0.8609 (m) cc_final: 0.8356 (p) REVERT: A 355 ASP cc_start: 0.7832 (t0) cc_final: 0.7472 (m-30) REVERT: A 402 GLU cc_start: 0.7688 (tt0) cc_final: 0.7475 (mm-30) REVERT: B 405 ASN cc_start: 0.8154 (m-40) cc_final: 0.7873 (m-40) REVERT: B 468 ILE cc_start: 0.8722 (pt) cc_final: 0.8416 (mt) outliers start: 7 outliers final: 6 residues processed: 172 average time/residue: 0.0808 time to fit residues: 18.7213 Evaluate side-chains 173 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 167 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 0.0770 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 63 optimal weight: 0.1980 chunk 58 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103322 restraints weight = 9674.031| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.03 r_work: 0.3187 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6760 Z= 0.141 Angle : 0.519 11.010 9207 Z= 0.263 Chirality : 0.042 0.222 984 Planarity : 0.004 0.042 1176 Dihedral : 5.114 52.948 1066 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.73 % Allowed : 17.17 % Favored : 81.10 % 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: 0.56 (0.32), residues: 787 helix: 1.45 (0.28), residues: 384 sheet: 1.03 (0.75), residues: 46 loop : -0.93 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 559 TYR 0.014 0.001 TYR A 385 PHE 0.007 0.001 PHE A 523 TRP 0.010 0.001 TRP A 168 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6741) covalent geometry : angle 0.50858 ( 9163) SS BOND : bond 0.00361 ( 7) SS BOND : angle 0.78614 ( 14) hydrogen bonds : bond 0.04737 ( 285) hydrogen bonds : angle 4.12681 ( 801) metal coordination : bond 0.00221 ( 2) link_BETA1-4 : bond 0.00404 ( 2) link_BETA1-4 : angle 1.18838 ( 6) link_BETA1-6 : bond 0.00202 ( 1) link_BETA1-6 : angle 1.40337 ( 3) link_NAG-ASN : bond 0.00391 ( 7) link_NAG-ASN : angle 2.01468 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7803 (m-40) cc_final: 0.7307 (m-40) REVERT: A 63 ASN cc_start: 0.8088 (m-40) cc_final: 0.7858 (m-40) REVERT: A 98 GLN cc_start: 0.8561 (tt0) cc_final: 0.8297 (tt0) REVERT: A 102 GLN cc_start: 0.7710 (mp10) cc_final: 0.7296 (mp10) REVERT: A 167 SER cc_start: 0.8565 (m) cc_final: 0.8297 (p) REVERT: A 232 GLU cc_start: 0.8108 (tp30) cc_final: 0.7714 (tp30) REVERT: A 355 ASP cc_start: 0.7838 (t0) cc_final: 0.7499 (m-30) REVERT: A 402 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: B 405 ASN cc_start: 0.8152 (m-40) cc_final: 0.7883 (m-40) REVERT: B 468 ILE cc_start: 0.8746 (pt) cc_final: 0.8432 (mt) outliers start: 12 outliers final: 7 residues processed: 174 average time/residue: 0.0770 time to fit residues: 18.0924 Evaluate side-chains 177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 0.0980 chunk 64 optimal weight: 0.0020 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 45 optimal weight: 0.0980 chunk 17 optimal weight: 0.1980 overall best weight: 0.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105007 restraints weight = 9731.748| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.04 r_work: 0.3210 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6760 Z= 0.100 Angle : 0.494 10.776 9207 Z= 0.248 Chirality : 0.041 0.208 984 Planarity : 0.004 0.041 1176 Dihedral : 4.959 52.693 1066 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.15 % Allowed : 17.75 % Favored : 81.10 % 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: 0.68 (0.32), residues: 787 helix: 1.51 (0.28), residues: 386 sheet: 1.02 (0.75), residues: 46 loop : -0.81 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 559 TYR 0.012 0.001 TYR A 183 PHE 0.006 0.001 PHE A 315 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6741) covalent geometry : angle 0.48368 ( 9163) SS BOND : bond 0.00329 ( 7) SS BOND : angle 0.79215 ( 14) hydrogen bonds : bond 0.04054 ( 285) hydrogen bonds : angle 4.07719 ( 801) metal coordination : bond 0.00086 ( 2) link_BETA1-4 : bond 0.00424 ( 2) link_BETA1-4 : angle 1.05192 ( 6) link_BETA1-6 : bond 0.00214 ( 1) link_BETA1-6 : angle 1.40174 ( 3) link_NAG-ASN : bond 0.00376 ( 7) link_NAG-ASN : angle 1.92327 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7774 (m-40) cc_final: 0.7284 (m-40) REVERT: A 98 GLN cc_start: 0.8530 (tt0) cc_final: 0.8243 (tt0) REVERT: A 102 GLN cc_start: 0.7710 (mp10) cc_final: 0.7303 (mp10) REVERT: A 167 SER cc_start: 0.8561 (m) cc_final: 0.8301 (p) REVERT: A 232 GLU cc_start: 0.8107 (tp30) cc_final: 0.7709 (tp30) REVERT: A 276 THR cc_start: 0.8615 (m) cc_final: 0.8378 (p) REVERT: A 402 GLU cc_start: 0.7771 (tt0) cc_final: 0.7540 (tp30) REVERT: B 405 ASN cc_start: 0.8147 (m-40) cc_final: 0.7874 (m-40) REVERT: B 468 ILE cc_start: 0.8732 (pt) cc_final: 0.8425 (mt) outliers start: 8 outliers final: 7 residues processed: 174 average time/residue: 0.0787 time to fit residues: 18.5724 Evaluate side-chains 176 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.0670 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 19 optimal weight: 0.2980 chunk 73 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102989 restraints weight = 9646.160| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.01 r_work: 0.3177 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6760 Z= 0.177 Angle : 0.540 10.439 9207 Z= 0.275 Chirality : 0.043 0.227 984 Planarity : 0.004 0.042 1176 Dihedral : 5.113 53.359 1066 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.15 % Allowed : 18.90 % Favored : 79.94 % 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: 0.53 (0.31), residues: 787 helix: 1.42 (0.28), residues: 384 sheet: 0.90 (0.73), residues: 46 loop : -0.91 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 559 TYR 0.016 0.001 TYR A 385 PHE 0.009 0.001 PHE A 400 TRP 0.023 0.001 TRP A 168 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6741) covalent geometry : angle 0.52916 ( 9163) SS BOND : bond 0.00370 ( 7) SS BOND : angle 0.87955 ( 14) hydrogen bonds : bond 0.05073 ( 285) hydrogen bonds : angle 4.12008 ( 801) metal coordination : bond 0.00303 ( 2) link_BETA1-4 : bond 0.00241 ( 2) link_BETA1-4 : angle 1.22990 ( 6) link_BETA1-6 : bond 0.00201 ( 1) link_BETA1-6 : angle 1.38512 ( 3) link_NAG-ASN : bond 0.00413 ( 7) link_NAG-ASN : angle 2.07487 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.249 Fit side-chains REVERT: A 61 ASN cc_start: 0.7817 (m-40) cc_final: 0.7326 (m-40) REVERT: A 63 ASN cc_start: 0.8115 (m-40) cc_final: 0.7897 (m-40) REVERT: A 98 GLN cc_start: 0.8575 (tt0) cc_final: 0.8291 (tt0) REVERT: A 102 GLN cc_start: 0.7728 (mp10) cc_final: 0.7287 (mp10) REVERT: A 167 SER cc_start: 0.8593 (m) cc_final: 0.8290 (p) REVERT: A 232 GLU cc_start: 0.8112 (tp30) cc_final: 0.7713 (tp30) REVERT: A 402 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7519 (tp30) REVERT: A 564 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8068 (mt-10) REVERT: A 571 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7633 (tt0) REVERT: B 405 ASN cc_start: 0.8172 (m-40) cc_final: 0.7906 (m-40) REVERT: B 468 ILE cc_start: 0.8756 (pt) cc_final: 0.8443 (mt) outliers start: 8 outliers final: 7 residues processed: 170 average time/residue: 0.0754 time to fit residues: 17.4240 Evaluate side-chains 175 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.1980 chunk 65 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 73 optimal weight: 0.0870 chunk 7 optimal weight: 0.5980 chunk 77 optimal weight: 0.0770 chunk 21 optimal weight: 0.0980 chunk 29 optimal weight: 0.4980 chunk 59 optimal weight: 0.0030 overall best weight: 0.0926 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.116513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104909 restraints weight = 9700.051| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.06 r_work: 0.3212 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6760 Z= 0.102 Angle : 0.504 10.370 9207 Z= 0.254 Chirality : 0.041 0.206 984 Planarity : 0.004 0.042 1176 Dihedral : 4.937 52.649 1066 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.15 % Allowed : 18.76 % Favored : 80.09 % 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: 0.69 (0.32), residues: 787 helix: 1.49 (0.28), residues: 386 sheet: 0.90 (0.73), residues: 46 loop : -0.76 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 559 TYR 0.012 0.001 TYR A 183 PHE 0.006 0.001 PHE B 400 TRP 0.013 0.001 TRP A 168 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6741) covalent geometry : angle 0.49444 ( 9163) SS BOND : bond 0.00319 ( 7) SS BOND : angle 0.77850 ( 14) hydrogen bonds : bond 0.04040 ( 285) hydrogen bonds : angle 4.05822 ( 801) metal coordination : bond 0.00098 ( 2) link_BETA1-4 : bond 0.00404 ( 2) link_BETA1-4 : angle 1.02152 ( 6) link_BETA1-6 : bond 0.00283 ( 1) link_BETA1-6 : angle 1.44438 ( 3) link_NAG-ASN : bond 0.00384 ( 7) link_NAG-ASN : angle 1.94436 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2144.38 seconds wall clock time: 37 minutes 22.78 seconds (2242.78 seconds total)