Starting phenix.real_space_refine on Fri Jun 13 03:33:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fak_28959/06_2025/8fak_28959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fak_28959/06_2025/8fak_28959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fak_28959/06_2025/8fak_28959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fak_28959/06_2025/8fak_28959.map" model { file = "/net/cci-nas-00/data/ceres_data/8fak_28959/06_2025/8fak_28959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fak_28959/06_2025/8fak_28959.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.500 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 57 5.49 5 S 28 5.16 5 C 4696 2.51 5 N 1434 2.21 5 O 1498 1.98 5 H 7248 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14963 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1519 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "B" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1503 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "G" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 723 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "H" Number of atoms: 10134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 10134 Classifications: {'peptide': 643} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 602} Chain breaks: 1 Chain: "J" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 733 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "Z" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 349 Classifications: {'DNA': 11} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9326 SG CYS H 445 37.544 61.957 59.870 1.00 87.36 S ATOM 9374 SG CYS H 448 37.228 58.300 58.786 1.00 80.81 S ATOM 9626 SG CYS H 463 40.304 59.457 60.738 1.00 91.68 S ATOM 9670 SG CYS H 466 39.744 60.511 57.131 1.00 88.01 S ATOM 9202 SG CYS H 436 36.878 71.412 76.767 1.00 66.12 S ATOM 9241 SG CYS H 439 33.163 71.157 75.929 1.00 60.08 S ATOM 9829 SG CYS H 476 35.613 72.552 73.377 1.00 81.61 S ATOM 9864 SG CYS H 479 34.712 74.555 76.479 1.00 75.40 S Time building chain proxies: 6.79, per 1000 atoms: 0.45 Number of scatterers: 14963 At special positions: 0 Unit cell: (83.083, 103.584, 125.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 28 16.00 P 57 15.00 O 1498 8.00 N 1434 7.00 C 4696 6.00 H 7248 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS B 48 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 801 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 466 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 448 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 463 " pdb="ZN ZN H 801 " - pdb=" SG CYS H 445 " pdb=" ZN H 802 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 439 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 476 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 479 " pdb="ZN ZN H 802 " - pdb=" SG CYS H 436 " Number of angles added : 12 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1562 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 32.4% alpha, 20.7% beta 19 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 6.44 Creating SS restraints... Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.911A pdb=" N ALA A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 62 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 66 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 91 through 99 removed outlier: 3.632A pdb=" N ALA H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 removed outlier: 4.035A pdb=" N GLN H 106 " --> pdb=" O ILE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 213 Processing helix chain 'H' and resid 229 through 243 Processing helix chain 'H' and resid 254 through 256 No H-bonds generated for 'chain 'H' and resid 254 through 256' Processing helix chain 'H' and resid 257 through 269 removed outlier: 3.605A pdb=" N THR H 261 " --> pdb=" O LEU H 257 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG H 264 " --> pdb=" O GLN H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 295 Processing helix chain 'H' and resid 304 through 309 removed outlier: 3.971A pdb=" N PHE H 308 " --> pdb=" O SER H 305 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR H 309 " --> pdb=" O ALA H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 328 removed outlier: 3.697A pdb=" N TYR H 327 " --> pdb=" O ASP H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 349 Processing helix chain 'H' and resid 360 through 369 Processing helix chain 'H' and resid 379 through 384 removed outlier: 3.988A pdb=" N ASN H 383 " --> pdb=" O ARG H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 417 Processing helix chain 'H' and resid 490 through 502 removed outlier: 4.006A pdb=" N ALA H 499 " --> pdb=" O GLU H 495 " (cutoff:3.500A) Proline residue: H 500 - end of helix Processing helix chain 'H' and resid 517 through 530 removed outlier: 3.523A pdb=" N LEU H 521 " --> pdb=" O ARG H 517 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU H 522 " --> pdb=" O LYS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 544 Processing helix chain 'H' and resid 569 through 583 Processing helix chain 'H' and resid 603 through 612 Processing helix chain 'H' and resid 613 through 628 removed outlier: 3.552A pdb=" N PHE H 617 " --> pdb=" O GLY H 613 " (cutoff:3.500A) Processing helix chain 'H' and resid 647 through 662 removed outlier: 4.262A pdb=" N LEU H 651 " --> pdb=" O GLN H 647 " (cutoff:3.500A) Processing helix chain 'H' and resid 697 through 711 Processing helix chain 'H' and resid 712 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 19 removed outlier: 15.809A pdb=" N VAL A 6 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 13.405A pdb=" N GLU A 38 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N SER A 8 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL A 36 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR A 10 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG A 34 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N CYS A 12 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLU A 32 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA A 14 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL A 30 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 48 " --> pdb=" O HIS A 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 42 through 54 current: chain 'A' and resid 96 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 96 through 99 current: chain 'B' and resid 26 through 38 removed outlier: 3.596A pdb=" N HIS B 33 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS B 48 " --> pdb=" O HIS B 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 43 through 48 current: chain 'B' and resid 90 through 97 Processing sheet with id=AA2, first strand: chain 'H' and resid 16 through 19 removed outlier: 6.759A pdb=" N VAL H 3 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL H 49 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS H 5 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN H 40 " --> pdb=" O PHE H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 273 through 276 removed outlier: 6.293A pdb=" N GLU H 274 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN H 247 " --> pdb=" O VAL H 316 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N VAL H 318 " --> pdb=" O GLN H 247 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU H 249 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASP H 320 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET H 251 " --> pdb=" O ASP H 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 388 through 393 removed outlier: 6.048A pdb=" N ILE H 388 " --> pdb=" O VAL H 594 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU H 596 " --> pdb=" O ILE H 388 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS H 390 " --> pdb=" O LEU H 596 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR H 598 " --> pdb=" O HIS H 390 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU H 392 " --> pdb=" O THR H 598 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR H 552 " --> pdb=" O GLU H 593 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL H 595 " --> pdb=" O THR H 552 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL H 554 " --> pdb=" O VAL H 595 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLN H 597 " --> pdb=" O VAL H 554 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU H 556 " --> pdb=" O GLN H 597 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN H 420 " --> pdb=" O VAL H 551 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU H 553 " --> pdb=" O GLN H 420 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY H 538 " --> pdb=" O LEU H 423 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 433 through 436 removed outlier: 3.661A pdb=" N ALA H 433 " --> pdb=" O VAL H 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 453 through 455 Processing sheet with id=AA7, first strand: chain 'H' and resid 635 through 643 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 635 through 643 current: chain 'H' and resid 687 through 695 No H-bonds generated for sheet with id=AA7 223 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7240 1.04 - 1.23: 133 1.23 - 1.43: 3340 1.43 - 1.62: 4500 1.62 - 1.82: 38 Bond restraints: 15251 Sorted by residual: bond pdb=" N ARG H 108 " pdb=" CA ARG H 108 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.37e-02 5.33e+03 5.68e+00 bond pdb=" C ASN H 706 " pdb=" N GLY H 707 " ideal model delta sigma weight residual 1.334 1.362 -0.028 1.32e-02 5.74e+03 4.54e+00 bond pdb=" N ALA H 110 " pdb=" CA ALA H 110 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.23e-02 6.61e+03 3.27e+00 bond pdb=" C PRO H 109 " pdb=" O PRO H 109 " ideal model delta sigma weight residual 1.235 1.216 0.019 1.30e-02 5.92e+03 2.12e+00 bond pdb=" O3' DT Z 12 " pdb=" P DC Z 13 " ideal model delta sigma weight residual 1.607 1.586 0.021 1.50e-02 4.44e+03 2.01e+00 ... (remaining 15246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 25143 2.10 - 4.19: 2205 4.19 - 6.29: 281 6.29 - 8.38: 3 8.38 - 10.48: 1 Bond angle restraints: 27633 Sorted by residual: angle pdb=" O4' DA J 35 " pdb=" C4' DA J 35 " pdb=" H4' DA J 35 " ideal model delta sigma weight residual 109.00 115.87 -6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" C4' DA J 35 " pdb=" C3' DA J 35 " pdb=" H3' DA J 35 " ideal model delta sigma weight residual 109.00 115.42 -6.42 1.50e+00 4.44e-01 1.83e+01 angle pdb=" O4' DT J 33 " pdb=" C1' DT J 33 " pdb=" H1' DT J 33 " ideal model delta sigma weight residual 109.00 115.11 -6.11 1.50e+00 4.44e-01 1.66e+01 angle pdb=" C4' DA G 7 " pdb=" C3' DA G 7 " pdb=" H3' DA G 7 " ideal model delta sigma weight residual 109.00 115.03 -6.03 1.50e+00 4.44e-01 1.62e+01 angle pdb=" O4' DT G 13 " pdb=" C4' DT G 13 " pdb=" H4' DT G 13 " ideal model delta sigma weight residual 109.00 114.97 -5.97 1.50e+00 4.44e-01 1.58e+01 ... (remaining 27628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 6375 30.75 - 61.49: 516 61.49 - 92.24: 19 92.24 - 122.98: 0 122.98 - 153.73: 2 Dihedral angle restraints: 6912 sinusoidal: 4120 harmonic: 2792 Sorted by residual: dihedral pdb=" C4' DC J 32 " pdb=" C3' DC J 32 " pdb=" O3' DC J 32 " pdb=" P DT J 33 " ideal model delta sinusoidal sigma weight residual 220.00 66.27 153.73 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" C4' DG J 34 " pdb=" C3' DG J 34 " pdb=" O3' DG J 34 " pdb=" P DA J 35 " ideal model delta sinusoidal sigma weight residual 220.00 80.20 139.80 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA CYS A 80 " pdb=" CB CYS A 80 " pdb=" SG CYS A 80 " pdb=" SG CYS B 48 " ideal model delta sinusoidal sigma weight residual -73.00 -14.90 -58.10 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 6909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 835 0.030 - 0.060: 294 0.060 - 0.091: 55 0.091 - 0.121: 70 0.121 - 0.151: 6 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ARG H 108 " pdb=" N ARG H 108 " pdb=" C ARG H 108 " pdb=" CB ARG H 108 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE H 691 " pdb=" N ILE H 691 " pdb=" C ILE H 691 " pdb=" CB ILE H 691 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA THR H 258 " pdb=" N THR H 258 " pdb=" C THR H 258 " pdb=" CB THR H 258 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1257 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 631 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO H 632 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 632 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 632 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC Z 11 " -0.014 2.00e-02 2.50e+03 1.01e-02 2.78e+00 pdb=" N1 DC Z 11 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DC Z 11 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DC Z 11 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC Z 11 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC Z 11 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC Z 11 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC Z 11 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC Z 11 " 0.008 2.00e-02 2.50e+03 pdb=" H5 DC Z 11 " -0.018 2.00e-02 2.50e+03 pdb=" H6 DC Z 11 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 630 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO H 631 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 631 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 631 " -0.022 5.00e-02 4.00e+02 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.82: 69 1.82 - 2.52: 11091 2.52 - 3.21: 43172 3.21 - 3.91: 56309 3.91 - 4.60: 87657 Nonbonded interactions: 198298 Sorted by model distance: nonbonded pdb=" HB3 HIS H 437 " pdb=" HD2 HIS H 483 " model vdw 1.129 2.270 nonbonded pdb=" HE1 HIS B 26 " pdb=" HA HIS H 483 " model vdw 1.286 2.270 nonbonded pdb=" ND1 HIS B 26 " pdb=" HD1 HIS H 483 " model vdw 1.294 2.600 nonbonded pdb=" O ASP H 17 " pdb="HO3' DC Z 13 " model vdw 1.477 2.450 nonbonded pdb=" O GLN B 75 " pdb=" H GLU B 95 " model vdw 1.515 2.450 ... (remaining 198293 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 49 through 98)) selection = (chain 'B' and (resid 2 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 81 through 84 or (resid 87 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 \ or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or n \ ame HD23)) or resid 88 through 98)) } 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 42.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.002 0.039 8012 Z= 0.119 Angle : 0.464 5.623 11121 Z= 0.257 Chirality : 0.039 0.151 1260 Planarity : 0.004 0.055 1238 Dihedral : 19.105 153.728 3075 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.31), residues: 827 helix: 2.49 (0.36), residues: 214 sheet: 1.38 (0.36), residues: 261 loop : -0.37 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.004 0.000 HIS H 460 PHE 0.008 0.001 PHE H 617 TYR 0.003 0.000 TYR H 87 ARG 0.002 0.000 ARG H 509 Details of bonding type rmsd hydrogen bonds : bond 0.16988 ( 274) hydrogen bonds : angle 5.75165 ( 717) metal coordination : bond 0.00227 ( 8) metal coordination : angle 1.01354 ( 12) SS BOND : bond 0.00273 ( 1) SS BOND : angle 2.81692 ( 2) covalent geometry : bond 0.00238 ( 8003) covalent geometry : angle 0.46120 (11107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.5748 (p) cc_final: 0.5335 (p) REVERT: A 90 MET cc_start: 0.6544 (mmp) cc_final: 0.6164 (mmm) REVERT: B 10 THR cc_start: 0.8218 (t) cc_final: 0.7990 (p) REVERT: H 27 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8296 (mtmm) REVERT: H 321 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7738 (mm-30) REVERT: H 472 VAL cc_start: 0.9351 (t) cc_final: 0.9148 (p) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4664 time to fit residues: 82.2686 Evaluate side-chains 93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN H 200 ASN H 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.158856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119115 restraints weight = 37392.224| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.47 r_work: 0.3477 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8012 Z= 0.162 Angle : 0.552 4.953 11121 Z= 0.302 Chirality : 0.044 0.145 1260 Planarity : 0.005 0.045 1238 Dihedral : 21.769 154.414 1510 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.14 % Allowed : 7.39 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.30), residues: 827 helix: 2.30 (0.36), residues: 221 sheet: 0.97 (0.36), residues: 240 loop : -0.46 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.006 0.001 HIS H 465 PHE 0.007 0.001 PHE H 574 TYR 0.006 0.001 TYR H 452 ARG 0.004 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 274) hydrogen bonds : angle 4.37316 ( 717) metal coordination : bond 0.00670 ( 8) metal coordination : angle 1.84517 ( 12) SS BOND : bond 0.00229 ( 1) SS BOND : angle 3.30246 ( 2) covalent geometry : bond 0.00371 ( 8003) covalent geometry : angle 0.54681 (11107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7428 (m-80) cc_final: 0.7150 (m-80) REVERT: A 80 CYS cc_start: 0.5351 (p) cc_final: 0.4582 (p) REVERT: A 89 LYS cc_start: 0.7190 (mmmm) cc_final: 0.6886 (mmmm) REVERT: A 90 MET cc_start: 0.6334 (mmp) cc_final: 0.5970 (mmt) REVERT: B 89 LYS cc_start: 0.7236 (ptpp) cc_final: 0.6866 (pttp) REVERT: H 27 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8195 (mtmm) REVERT: H 321 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7778 (mm-30) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 0.4586 time to fit residues: 58.7739 Evaluate side-chains 87 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain H residue 542 LEU Chi-restraints excluded: chain H residue 644 HIS Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.157968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118011 restraints weight = 37022.989| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.45 r_work: 0.3460 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8012 Z= 0.137 Angle : 0.508 4.870 11121 Z= 0.278 Chirality : 0.043 0.143 1260 Planarity : 0.004 0.041 1238 Dihedral : 21.605 155.885 1510 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.14 % Allowed : 9.09 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.30), residues: 827 helix: 2.44 (0.36), residues: 221 sheet: 0.58 (0.35), residues: 247 loop : -0.55 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.012 0.001 HIS H 483 PHE 0.007 0.001 PHE H 617 TYR 0.005 0.001 TYR H 578 ARG 0.002 0.000 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 274) hydrogen bonds : angle 4.09116 ( 717) metal coordination : bond 0.00581 ( 8) metal coordination : angle 1.67651 ( 12) SS BOND : bond 0.00021 ( 1) SS BOND : angle 3.14976 ( 2) covalent geometry : bond 0.00313 ( 8003) covalent geometry : angle 0.50346 (11107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7514 (m-80) cc_final: 0.7252 (m-80) REVERT: A 80 CYS cc_start: 0.5637 (p) cc_final: 0.4561 (p) REVERT: A 89 LYS cc_start: 0.7337 (mmmm) cc_final: 0.6869 (mmmm) REVERT: A 90 MET cc_start: 0.6678 (mmp) cc_final: 0.6410 (mmt) REVERT: B 95 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7254 (mm-30) REVERT: H 321 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7935 (mm-30) outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.4553 time to fit residues: 53.9770 Evaluate side-chains 89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 644 HIS Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.152855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113460 restraints weight = 36275.049| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.39 r_work: 0.3357 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8012 Z= 0.180 Angle : 0.542 5.346 11121 Z= 0.297 Chirality : 0.044 0.148 1260 Planarity : 0.005 0.043 1238 Dihedral : 21.542 156.463 1510 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.14 % Allowed : 9.52 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.29), residues: 827 helix: 2.02 (0.36), residues: 226 sheet: 0.05 (0.34), residues: 235 loop : -0.81 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 289 HIS 0.008 0.001 HIS H 483 PHE 0.008 0.001 PHE H 617 TYR 0.007 0.001 TYR H 578 ARG 0.004 0.000 ARG H 264 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 274) hydrogen bonds : angle 4.10677 ( 717) metal coordination : bond 0.00763 ( 8) metal coordination : angle 2.02703 ( 12) SS BOND : bond 0.00112 ( 1) SS BOND : angle 3.19168 ( 2) covalent geometry : bond 0.00414 ( 8003) covalent geometry : angle 0.53654 (11107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7598 (m-80) cc_final: 0.7367 (m-80) REVERT: A 80 CYS cc_start: 0.5837 (p) cc_final: 0.5052 (p) REVERT: A 89 LYS cc_start: 0.7347 (mmmm) cc_final: 0.6979 (mmmm) REVERT: A 90 MET cc_start: 0.7182 (mmp) cc_final: 0.6788 (mmt) REVERT: B 95 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7102 (mm-30) REVERT: B 96 GLN cc_start: 0.6381 (mp-120) cc_final: 0.6038 (mp10) REVERT: H 254 GLU cc_start: 0.8669 (pm20) cc_final: 0.8361 (pt0) REVERT: H 321 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8007 (mm-30) REVERT: H 513 ASP cc_start: 0.8342 (m-30) cc_final: 0.8140 (m-30) outliers start: 8 outliers final: 5 residues processed: 88 average time/residue: 0.4349 time to fit residues: 51.6976 Evaluate side-chains 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.153930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114543 restraints weight = 36481.776| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.40 r_work: 0.3379 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8012 Z= 0.120 Angle : 0.499 4.753 11121 Z= 0.274 Chirality : 0.042 0.150 1260 Planarity : 0.004 0.045 1238 Dihedral : 21.412 156.416 1510 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.99 % Allowed : 10.94 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.30), residues: 827 helix: 2.22 (0.36), residues: 226 sheet: 0.03 (0.34), residues: 244 loop : -0.75 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 289 HIS 0.007 0.001 HIS H 483 PHE 0.007 0.001 PHE H 617 TYR 0.004 0.001 TYR H 343 ARG 0.009 0.000 ARG H 686 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 274) hydrogen bonds : angle 3.86972 ( 717) metal coordination : bond 0.00420 ( 8) metal coordination : angle 1.33351 ( 12) SS BOND : bond 0.00014 ( 1) SS BOND : angle 2.93262 ( 2) covalent geometry : bond 0.00274 ( 8003) covalent geometry : angle 0.49594 (11107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7418 (m-80) cc_final: 0.7149 (m-80) REVERT: A 80 CYS cc_start: 0.5514 (p) cc_final: 0.4603 (p) REVERT: A 90 MET cc_start: 0.7028 (mmp) cc_final: 0.6599 (mmt) REVERT: B 28 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7415 (mm-40) REVERT: B 95 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7051 (mm-30) REVERT: H 51 ASP cc_start: 0.7813 (t0) cc_final: 0.7511 (t0) REVERT: H 321 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7789 (mm-30) REVERT: H 593 GLU cc_start: 0.7996 (mp0) cc_final: 0.7694 (mp0) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.4450 time to fit residues: 55.4412 Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 542 LEU Chi-restraints excluded: chain H residue 717 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.151246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111487 restraints weight = 36578.368| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.41 r_work: 0.3334 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8012 Z= 0.200 Angle : 0.554 5.675 11121 Z= 0.304 Chirality : 0.044 0.149 1260 Planarity : 0.005 0.048 1238 Dihedral : 21.471 157.404 1510 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.28 % Allowed : 11.22 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.29), residues: 827 helix: 1.86 (0.35), residues: 226 sheet: -0.50 (0.33), residues: 241 loop : -0.99 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 289 HIS 0.006 0.001 HIS H 483 PHE 0.009 0.001 PHE H 502 TYR 0.007 0.001 TYR H 452 ARG 0.011 0.001 ARG H 686 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 274) hydrogen bonds : angle 4.06565 ( 717) metal coordination : bond 0.00797 ( 8) metal coordination : angle 2.05663 ( 12) SS BOND : bond 0.00210 ( 1) SS BOND : angle 2.96061 ( 2) covalent geometry : bond 0.00460 ( 8003) covalent geometry : angle 0.54842 (11107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7684 (m-80) cc_final: 0.7483 (m-80) REVERT: A 80 CYS cc_start: 0.5917 (p) cc_final: 0.5200 (p) REVERT: A 89 LYS cc_start: 0.7366 (mmmm) cc_final: 0.6920 (mmmm) REVERT: A 90 MET cc_start: 0.7209 (mmp) cc_final: 0.6688 (mmt) REVERT: B 95 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7142 (mm-30) REVERT: H 51 ASP cc_start: 0.8079 (t0) cc_final: 0.7812 (t0) REVERT: H 254 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8412 (pt0) REVERT: H 321 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8041 (mm-30) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.4635 time to fit residues: 55.2813 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.150824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110874 restraints weight = 36492.130| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.44 r_work: 0.3328 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8012 Z= 0.188 Angle : 0.548 5.372 11121 Z= 0.302 Chirality : 0.044 0.150 1260 Planarity : 0.005 0.055 1238 Dihedral : 21.491 157.608 1510 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.28 % Allowed : 11.79 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.29), residues: 827 helix: 1.70 (0.35), residues: 226 sheet: -0.71 (0.33), residues: 235 loop : -1.15 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 289 HIS 0.005 0.001 HIS H 483 PHE 0.009 0.001 PHE H 502 TYR 0.007 0.001 TYR H 578 ARG 0.011 0.001 ARG H 686 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 274) hydrogen bonds : angle 4.11208 ( 717) metal coordination : bond 0.00780 ( 8) metal coordination : angle 1.70875 ( 12) SS BOND : bond 0.00179 ( 1) SS BOND : angle 2.90801 ( 2) covalent geometry : bond 0.00428 ( 8003) covalent geometry : angle 0.54400 (11107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 CYS cc_start: 0.5792 (p) cc_final: 0.5164 (p) REVERT: A 90 MET cc_start: 0.7273 (mmp) cc_final: 0.6791 (mmt) REVERT: B 95 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7235 (mm-30) REVERT: H 51 ASP cc_start: 0.8043 (t0) cc_final: 0.7705 (t0) REVERT: H 254 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: H 321 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8065 (mm-30) outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.4556 time to fit residues: 54.3031 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 542 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.152991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113439 restraints weight = 36420.458| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.41 r_work: 0.3375 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8012 Z= 0.107 Angle : 0.503 4.626 11121 Z= 0.276 Chirality : 0.042 0.144 1260 Planarity : 0.005 0.058 1238 Dihedral : 21.290 159.416 1510 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.57 % Allowed : 12.36 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.30), residues: 827 helix: 2.18 (0.36), residues: 225 sheet: -0.53 (0.33), residues: 252 loop : -0.94 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 289 HIS 0.004 0.001 HIS H 483 PHE 0.005 0.001 PHE H 617 TYR 0.003 0.001 TYR H 343 ARG 0.014 0.000 ARG H 686 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 274) hydrogen bonds : angle 3.77035 ( 717) metal coordination : bond 0.00313 ( 8) metal coordination : angle 1.20189 ( 12) SS BOND : bond 0.00028 ( 1) SS BOND : angle 2.75750 ( 2) covalent geometry : bond 0.00244 ( 8003) covalent geometry : angle 0.50031 (11107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7358 (mmmm) cc_final: 0.7003 (mmmm) REVERT: A 90 MET cc_start: 0.7186 (mmp) cc_final: 0.6791 (tpp) REVERT: B 95 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7295 (mm-30) REVERT: H 51 ASP cc_start: 0.7995 (t0) cc_final: 0.7660 (t0) REVERT: H 230 LYS cc_start: 0.8715 (mttm) cc_final: 0.8292 (mttp) REVERT: H 254 GLU cc_start: 0.8736 (pm20) cc_final: 0.8426 (pt0) REVERT: H 321 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7886 (mm-30) REVERT: H 593 GLU cc_start: 0.8281 (mp0) cc_final: 0.7767 (mp0) outliers start: 4 outliers final: 4 residues processed: 89 average time/residue: 0.4647 time to fit residues: 55.5652 Evaluate side-chains 90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain H residue 542 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.0270 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.154104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114419 restraints weight = 36453.605| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.43 r_work: 0.3391 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8012 Z= 0.103 Angle : 0.500 4.789 11121 Z= 0.272 Chirality : 0.042 0.136 1260 Planarity : 0.005 0.069 1238 Dihedral : 21.154 161.172 1510 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.71 % Allowed : 12.78 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.30), residues: 827 helix: 2.41 (0.36), residues: 226 sheet: -0.28 (0.34), residues: 246 loop : -0.76 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 289 HIS 0.003 0.000 HIS H 336 PHE 0.005 0.001 PHE H 617 TYR 0.003 0.000 TYR H 614 ARG 0.014 0.000 ARG H 686 Details of bonding type rmsd hydrogen bonds : bond 0.02685 ( 274) hydrogen bonds : angle 3.58181 ( 717) metal coordination : bond 0.00311 ( 8) metal coordination : angle 1.35067 ( 12) SS BOND : bond 0.00091 ( 1) SS BOND : angle 2.72455 ( 2) covalent geometry : bond 0.00237 ( 8003) covalent geometry : angle 0.49698 (11107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7211 (mmmm) cc_final: 0.6839 (mmmm) REVERT: A 90 MET cc_start: 0.6904 (mmp) cc_final: 0.6593 (mmt) REVERT: B 95 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7164 (mm-30) REVERT: H 51 ASP cc_start: 0.7856 (t0) cc_final: 0.7511 (t0) REVERT: H 230 LYS cc_start: 0.8671 (mttm) cc_final: 0.8297 (mttp) REVERT: H 254 GLU cc_start: 0.8554 (pm20) cc_final: 0.8207 (pt0) REVERT: H 321 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7811 (mm-30) REVERT: H 593 GLU cc_start: 0.8024 (mp0) cc_final: 0.7524 (mp0) REVERT: H 611 TYR cc_start: 0.7779 (m-10) cc_final: 0.7531 (m-80) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.4566 time to fit residues: 54.9834 Evaluate side-chains 91 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.0770 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.152717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112535 restraints weight = 36713.034| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.49 r_work: 0.3362 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8012 Z= 0.127 Angle : 0.511 4.998 11121 Z= 0.280 Chirality : 0.043 0.139 1260 Planarity : 0.005 0.069 1238 Dihedral : 21.178 160.757 1510 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.57 % Allowed : 13.21 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 827 helix: 2.32 (0.36), residues: 226 sheet: -0.34 (0.34), residues: 245 loop : -0.82 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.004 0.001 HIS H 460 PHE 0.008 0.001 PHE H 502 TYR 0.005 0.001 TYR H 452 ARG 0.014 0.000 ARG H 686 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 274) hydrogen bonds : angle 3.65171 ( 717) metal coordination : bond 0.00489 ( 8) metal coordination : angle 1.41017 ( 12) SS BOND : bond 0.00044 ( 1) SS BOND : angle 2.68051 ( 2) covalent geometry : bond 0.00293 ( 8003) covalent geometry : angle 0.50749 (11107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7249 (mmmm) cc_final: 0.6938 (mmmm) REVERT: A 90 MET cc_start: 0.7133 (mmp) cc_final: 0.6782 (tpp) REVERT: B 95 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7232 (mm-30) REVERT: H 51 ASP cc_start: 0.7906 (t0) cc_final: 0.7561 (t0) REVERT: H 230 LYS cc_start: 0.8672 (mttm) cc_final: 0.8260 (mttp) REVERT: H 254 GLU cc_start: 0.8570 (pm20) cc_final: 0.8274 (pt0) REVERT: H 321 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7846 (mm-30) REVERT: H 593 GLU cc_start: 0.8065 (mp0) cc_final: 0.7533 (mp0) outliers start: 4 outliers final: 4 residues processed: 91 average time/residue: 0.4594 time to fit residues: 56.0996 Evaluate side-chains 92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain H residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.153415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113297 restraints weight = 36440.851| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.48 r_work: 0.3379 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8012 Z= 0.107 Angle : 0.500 4.760 11121 Z= 0.273 Chirality : 0.042 0.138 1260 Planarity : 0.005 0.071 1238 Dihedral : 21.142 161.513 1510 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.57 % Allowed : 13.21 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.30), residues: 827 helix: 2.38 (0.36), residues: 227 sheet: -0.28 (0.34), residues: 246 loop : -0.84 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.003 0.001 HIS H 483 PHE 0.007 0.001 PHE B 77 TYR 0.004 0.001 TYR H 452 ARG 0.015 0.000 ARG H 686 Details of bonding type rmsd hydrogen bonds : bond 0.02777 ( 274) hydrogen bonds : angle 3.57192 ( 717) metal coordination : bond 0.00365 ( 8) metal coordination : angle 1.08933 ( 12) SS BOND : bond 0.00093 ( 1) SS BOND : angle 2.65691 ( 2) covalent geometry : bond 0.00249 ( 8003) covalent geometry : angle 0.49732 (11107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8175.67 seconds wall clock time: 140 minutes 15.46 seconds (8415.46 seconds total)