Starting phenix.real_space_refine on Tue Feb 3 21:11:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mt7_48602/02_2026/9mt7_48602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mt7_48602/02_2026/9mt7_48602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mt7_48602/02_2026/9mt7_48602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mt7_48602/02_2026/9mt7_48602.map" model { file = "/net/cci-nas-00/data/ceres_data/9mt7_48602/02_2026/9mt7_48602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mt7_48602/02_2026/9mt7_48602.cif" } resolution = 3.23 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= 0.001 sd= 0.014 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 42 5.16 5 C 4397 2.51 5 N 1105 2.21 5 O 1285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 888, 6829 Classifications: {'peptide': 888} Link IDs: {'PTRANS': 32, 'TRANS': 855} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.41, per 1000 atoms: 0.21 Number of scatterers: 6830 At special positions: 0 Unit cell: (78.12, 83.7, 145.08, 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) S 42 16.00 Mg 1 11.99 O 1285 8.00 N 1105 7.00 C 4397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.67 Conformation dependent library (CDL) restraints added in 262.5 milliseconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 52.5% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 50 through 61 removed outlier: 3.817A pdb=" N GLU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 84 through 101 Processing helix chain 'A' and resid 102 through 105 removed outlier: 3.748A pdb=" N ALA A 105 " --> pdb=" O ILE A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.130A pdb=" N ILE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.580A pdb=" N GLU A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.584A pdb=" N VAL A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.637A pdb=" N ALA A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.768A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.704A pdb=" N GLY A 332 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.777A pdb=" N ASN A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.688A pdb=" N TYR A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 416 Processing helix chain 'A' and resid 453 through 457 removed outlier: 3.632A pdb=" N ALA A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 457 " --> pdb=" O ASN A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 457' Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 488 through 505 removed outlier: 4.199A pdb=" N GLU A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.725A pdb=" N ALA A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 removed outlier: 3.601A pdb=" N THR A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.771A pdb=" N ALA A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.654A pdb=" N ALA A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.715A pdb=" N ALA A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA A 645 " --> pdb=" O ASN A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 676 through 713 removed outlier: 3.816A pdb=" N ASN A 703 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 738 Processing helix chain 'A' and resid 739 through 744 Proline residue: A 742 - end of helix No H-bonds generated for 'chain 'A' and resid 739 through 744' Processing helix chain 'A' and resid 758 through 770 removed outlier: 3.902A pdb=" N VAL A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 787 removed outlier: 4.414A pdb=" N PHE A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 794 Processing helix chain 'A' and resid 803 through 827 removed outlier: 3.808A pdb=" N MET A 822 " --> pdb=" O PHE A 818 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 845 through 865 Proline residue: A 863 - end of helix Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'A' and resid 879 through 907 removed outlier: 4.339A pdb=" N TRP A 883 " --> pdb=" O ASN A 879 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 893 " --> pdb=" O VAL A 889 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N THR A 896 " --> pdb=" O MET A 892 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 897 " --> pdb=" O MET A 893 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 163 removed outlier: 5.250A pdb=" N ASN A 152 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 173 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 242 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 181 removed outlier: 3.700A pdb=" N ASP A 180 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 194 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.191A pdb=" N GLY A 652 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU A 670 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER A 654 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A 633 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N ILE A 653 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 635 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N PHE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 564 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 377 removed outlier: 3.688A pdb=" N VAL A 372 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 541 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET A 374 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ALA A 539 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N HIS A 376 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR A 537 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU A 534 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN A 514 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 536 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 512 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER A 446 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 377 removed outlier: 3.688A pdb=" N VAL A 372 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 541 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET A 374 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ALA A 539 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N HIS A 376 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR A 537 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N LEU A 534 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL A 478 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLY A 536 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 10.930A pdb=" N ASP A 480 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 17.075A pdb=" N LEU A 538 " --> pdb=" O ASP A 480 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2167 1.34 - 1.46: 1295 1.46 - 1.58: 3408 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 6948 Sorted by residual: bond pdb=" CB MET A 146 " pdb=" CG MET A 146 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB PHE A 440 " pdb=" CG PHE A 440 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.30e-02 1.89e+03 1.27e+00 bond pdb=" C ILE A 769 " pdb=" O ILE A 769 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.20e+00 bond pdb=" CA HIS A 376 " pdb=" CB HIS A 376 " ideal model delta sigma weight residual 1.524 1.509 0.016 1.46e-02 4.69e+03 1.14e+00 bond pdb=" CA MET A 146 " pdb=" CB MET A 146 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.11e+00 ... (remaining 6943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 9302 2.56 - 5.12: 92 5.12 - 7.69: 16 7.69 - 10.25: 3 10.25 - 12.81: 2 Bond angle restraints: 9415 Sorted by residual: angle pdb=" CA MET A 146 " pdb=" CB MET A 146 " pdb=" CG MET A 146 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" CB MET A 146 " pdb=" CG MET A 146 " pdb=" SD MET A 146 " ideal model delta sigma weight residual 112.70 125.51 -12.81 3.00e+00 1.11e-01 1.82e+01 angle pdb=" CB MET A 445 " pdb=" CG MET A 445 " pdb=" SD MET A 445 " ideal model delta sigma weight residual 112.70 124.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" N MET A 893 " pdb=" CA MET A 893 " pdb=" C MET A 893 " ideal model delta sigma weight residual 114.75 110.37 4.38 1.26e+00 6.30e-01 1.21e+01 angle pdb=" CB MET A 336 " pdb=" CG MET A 336 " pdb=" SD MET A 336 " ideal model delta sigma weight residual 112.70 102.97 9.73 3.00e+00 1.11e-01 1.05e+01 ... (remaining 9410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3538 17.99 - 35.98: 514 35.98 - 53.97: 133 53.97 - 71.95: 19 71.95 - 89.94: 7 Dihedral angle restraints: 4211 sinusoidal: 1642 harmonic: 2569 Sorted by residual: dihedral pdb=" CA LEU A 280 " pdb=" C LEU A 280 " pdb=" N ILE A 281 " pdb=" CA ILE A 281 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PRO A 322 " pdb=" C PRO A 322 " pdb=" N MET A 323 " pdb=" CA MET A 323 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA MET A 707 " pdb=" C MET A 707 " pdb=" N PHE A 708 " pdb=" CA PHE A 708 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 731 0.036 - 0.071: 294 0.071 - 0.107: 83 0.107 - 0.142: 29 0.142 - 0.178: 2 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CA MET A 146 " pdb=" N MET A 146 " pdb=" C MET A 146 " pdb=" CB MET A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA MET A 336 " pdb=" N MET A 336 " pdb=" C MET A 336 " pdb=" CB MET A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA ILE A 510 " pdb=" N ILE A 510 " pdb=" C ILE A 510 " pdb=" CB ILE A 510 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1136 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 327 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C THR A 327 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 327 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS A 328 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 283 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C PHE A 283 " -0.057 2.00e-02 2.50e+03 pdb=" O PHE A 283 " 0.021 2.00e-02 2.50e+03 pdb=" N MET A 284 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 440 " 0.013 2.00e-02 2.50e+03 1.69e-02 4.98e+00 pdb=" CG PHE A 440 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 440 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 440 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 440 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 440 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 440 " 0.000 2.00e-02 2.50e+03 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 46 2.52 - 3.11: 5191 3.11 - 3.71: 10712 3.71 - 4.30: 14420 4.30 - 4.90: 24183 Nonbonded interactions: 54552 Sorted by model distance: nonbonded pdb=" OD1 ASN A 706 " pdb="MG MG A1001 " model vdw 1.923 2.170 nonbonded pdb=" O MET A 445 " pdb=" OG1 THR A 464 " model vdw 2.133 3.040 nonbonded pdb=" OE1 GLN A 132 " pdb=" OG1 THR A 326 " model vdw 2.139 3.040 nonbonded pdb=" N GLN A 595 " pdb=" OE1 GLN A 595 " model vdw 2.196 3.120 nonbonded pdb=" O ASN A 706 " pdb=" OG SER A 709 " model vdw 2.246 3.040 ... (remaining 54547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.440 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.840 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6948 Z= 0.159 Angle : 0.708 12.809 9415 Z= 0.370 Chirality : 0.043 0.178 1139 Planarity : 0.004 0.044 1175 Dihedral : 17.692 89.942 2547 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.67 % Favored : 91.99 % Rotamer: Outliers : 2.36 % Allowed : 33.29 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.73 (0.29), residues: 886 helix: 0.48 (0.27), residues: 420 sheet: -1.00 (0.56), residues: 76 loop : -1.42 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 26 TYR 0.020 0.001 TYR A 806 PHE 0.039 0.002 PHE A 440 TRP 0.005 0.001 TRP A 768 HIS 0.002 0.001 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6948) covalent geometry : angle 0.70764 ( 9415) hydrogen bonds : bond 0.16589 ( 327) hydrogen bonds : angle 6.69759 ( 945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7940 (tpt90) REVERT: A 231 MET cc_start: 0.8267 (ttp) cc_final: 0.7904 (ttp) REVERT: A 376 HIS cc_start: 0.8866 (OUTLIER) cc_final: 0.7545 (p90) REVERT: A 445 MET cc_start: 0.6835 (tpp) cc_final: 0.6290 (tpt) REVERT: A 535 MET cc_start: 0.7221 (mmp) cc_final: 0.6497 (mmm) REVERT: A 537 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.6383 (p90) REVERT: A 843 ARG cc_start: 0.6060 (ptt180) cc_final: 0.5058 (mtm-85) outliers start: 18 outliers final: 15 residues processed: 83 average time/residue: 0.0658 time to fit residues: 7.7990 Evaluate side-chains 84 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 828 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.118420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.077446 restraints weight = 14094.163| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.91 r_work: 0.3083 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6948 Z= 0.148 Angle : 0.613 8.602 9415 Z= 0.316 Chirality : 0.043 0.150 1139 Planarity : 0.004 0.044 1175 Dihedral : 6.992 55.998 963 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.34 % Favored : 92.33 % Rotamer: Outliers : 4.46 % Allowed : 29.36 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.29), residues: 886 helix: 0.60 (0.26), residues: 429 sheet: -0.87 (0.58), residues: 75 loop : -1.37 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.017 0.001 TYR A 806 PHE 0.017 0.001 PHE A 440 TRP 0.007 0.001 TRP A 817 HIS 0.002 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6948) covalent geometry : angle 0.61332 ( 9415) hydrogen bonds : bond 0.04186 ( 327) hydrogen bonds : angle 5.12604 ( 945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8697 (t0) cc_final: 0.8497 (m-40) REVERT: A 532 MET cc_start: 0.6502 (tpt) cc_final: 0.5327 (mmm) REVERT: A 535 MET cc_start: 0.7210 (mmp) cc_final: 0.6510 (mmm) REVERT: A 537 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.6595 (p90) REVERT: A 744 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8476 (t0) REVERT: A 843 ARG cc_start: 0.6006 (ptt180) cc_final: 0.4996 (mtm-85) outliers start: 34 outliers final: 9 residues processed: 99 average time/residue: 0.0604 time to fit residues: 8.4540 Evaluate side-chains 78 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 819 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.118659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077686 restraints weight = 13967.308| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.89 r_work: 0.3089 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6948 Z= 0.133 Angle : 0.583 9.017 9415 Z= 0.299 Chirality : 0.042 0.164 1139 Planarity : 0.004 0.045 1175 Dihedral : 5.232 54.529 937 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.45 % Favored : 92.21 % Rotamer: Outliers : 3.67 % Allowed : 28.83 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.44 (0.29), residues: 886 helix: 0.73 (0.26), residues: 429 sheet: -0.85 (0.58), residues: 75 loop : -1.33 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.016 0.001 TYR A 806 PHE 0.011 0.001 PHE A 818 TRP 0.008 0.001 TRP A 817 HIS 0.002 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6948) covalent geometry : angle 0.58294 ( 9415) hydrogen bonds : bond 0.03729 ( 327) hydrogen bonds : angle 4.84217 ( 945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.7840 (p90) REVERT: A 377 LEU cc_start: 0.8951 (mm) cc_final: 0.8298 (mm) REVERT: A 388 LEU cc_start: 0.8973 (mt) cc_final: 0.8772 (mt) REVERT: A 532 MET cc_start: 0.6682 (tpt) cc_final: 0.5534 (mmm) REVERT: A 535 MET cc_start: 0.7229 (mmp) cc_final: 0.6559 (mmm) REVERT: A 537 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6665 (p90) REVERT: A 843 ARG cc_start: 0.5941 (ptt180) cc_final: 0.4982 (mtm-85) outliers start: 28 outliers final: 11 residues processed: 92 average time/residue: 0.0674 time to fit residues: 8.7985 Evaluate side-chains 81 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 788 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 0.0270 chunk 28 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.119543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.077783 restraints weight = 14035.963| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.93 r_work: 0.3110 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6948 Z= 0.115 Angle : 0.567 9.498 9415 Z= 0.291 Chirality : 0.043 0.187 1139 Planarity : 0.004 0.044 1175 Dihedral : 5.187 55.964 937 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.55 % Favored : 93.12 % Rotamer: Outliers : 3.80 % Allowed : 29.23 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.30), residues: 886 helix: 0.87 (0.27), residues: 429 sheet: -0.94 (0.57), residues: 75 loop : -1.33 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.015 0.001 TYR A 806 PHE 0.010 0.001 PHE A 776 TRP 0.008 0.001 TRP A 817 HIS 0.002 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6948) covalent geometry : angle 0.56735 ( 9415) hydrogen bonds : bond 0.03423 ( 327) hydrogen bonds : angle 4.65453 ( 945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8638 (t0) cc_final: 0.8429 (m-40) REVERT: A 270 GLU cc_start: 0.7406 (pp20) cc_final: 0.7037 (pp20) REVERT: A 376 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.7801 (p90) REVERT: A 388 LEU cc_start: 0.9016 (mt) cc_final: 0.8804 (mt) REVERT: A 471 MET cc_start: 0.8558 (ttm) cc_final: 0.8349 (ttm) REVERT: A 532 MET cc_start: 0.6787 (tpt) cc_final: 0.5781 (mmm) REVERT: A 535 MET cc_start: 0.7219 (mmp) cc_final: 0.6529 (mmm) REVERT: A 843 ARG cc_start: 0.5920 (ptt180) cc_final: 0.4970 (mtm-85) outliers start: 29 outliers final: 18 residues processed: 97 average time/residue: 0.0546 time to fit residues: 7.7003 Evaluate side-chains 87 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 865 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.120130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079891 restraints weight = 14099.708| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.86 r_work: 0.3110 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6948 Z= 0.117 Angle : 0.570 10.174 9415 Z= 0.288 Chirality : 0.042 0.239 1139 Planarity : 0.004 0.044 1175 Dihedral : 5.149 55.794 937 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.77 % Favored : 92.89 % Rotamer: Outliers : 4.06 % Allowed : 29.88 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.29), residues: 886 helix: 0.85 (0.26), residues: 435 sheet: -0.96 (0.58), residues: 75 loop : -1.34 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.014 0.001 TYR A 806 PHE 0.013 0.001 PHE A 818 TRP 0.008 0.001 TRP A 817 HIS 0.002 0.000 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6948) covalent geometry : angle 0.57015 ( 9415) hydrogen bonds : bond 0.03363 ( 327) hydrogen bonds : angle 4.57541 ( 945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8637 (t0) cc_final: 0.8428 (m-40) REVERT: A 74 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8601 (tt) REVERT: A 270 GLU cc_start: 0.7388 (pp20) cc_final: 0.6676 (pp20) REVERT: A 376 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.7710 (p90) REVERT: A 388 LEU cc_start: 0.9028 (mt) cc_final: 0.8801 (mt) REVERT: A 445 MET cc_start: 0.7773 (tpp) cc_final: 0.7435 (tpp) REVERT: A 532 MET cc_start: 0.6770 (tpt) cc_final: 0.5770 (mmm) REVERT: A 535 MET cc_start: 0.7243 (mmp) cc_final: 0.6569 (mmm) REVERT: A 537 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.6606 (p90) REVERT: A 843 ARG cc_start: 0.5936 (ptt180) cc_final: 0.4984 (mtm-85) outliers start: 31 outliers final: 16 residues processed: 97 average time/residue: 0.0715 time to fit residues: 9.5555 Evaluate side-chains 87 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 788 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.118943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.078271 restraints weight = 14021.083| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.84 r_work: 0.3100 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6948 Z= 0.131 Angle : 0.569 8.588 9415 Z= 0.292 Chirality : 0.043 0.192 1139 Planarity : 0.004 0.044 1175 Dihedral : 5.185 58.162 936 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.88 % Favored : 92.78 % Rotamer: Outliers : 3.67 % Allowed : 30.01 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.29), residues: 886 helix: 0.84 (0.26), residues: 435 sheet: -1.01 (0.58), residues: 75 loop : -1.33 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.014 0.001 TYR A 806 PHE 0.014 0.001 PHE A 818 TRP 0.008 0.001 TRP A 817 HIS 0.002 0.000 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6948) covalent geometry : angle 0.56925 ( 9415) hydrogen bonds : bond 0.03422 ( 327) hydrogen bonds : angle 4.56677 ( 945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 376 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.7705 (p90) REVERT: A 532 MET cc_start: 0.6844 (tpt) cc_final: 0.5860 (mmm) REVERT: A 535 MET cc_start: 0.7267 (mmp) cc_final: 0.6735 (mmm) outliers start: 28 outliers final: 21 residues processed: 93 average time/residue: 0.0579 time to fit residues: 7.8083 Evaluate side-chains 92 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 865 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 0.0980 chunk 46 optimal weight: 0.0670 chunk 42 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 43 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.124484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.082608 restraints weight = 14024.071| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.84 r_work: 0.3129 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6948 Z= 0.104 Angle : 0.571 10.854 9415 Z= 0.288 Chirality : 0.042 0.169 1139 Planarity : 0.004 0.044 1175 Dihedral : 5.080 58.968 936 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.66 % Favored : 93.00 % Rotamer: Outliers : 3.28 % Allowed : 30.67 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.29), residues: 886 helix: 0.90 (0.26), residues: 435 sheet: -1.14 (0.57), residues: 75 loop : -1.26 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.014 0.001 TYR A 806 PHE 0.019 0.001 PHE A 818 TRP 0.009 0.001 TRP A 817 HIS 0.002 0.000 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6948) covalent geometry : angle 0.57126 ( 9415) hydrogen bonds : bond 0.03154 ( 327) hydrogen bonds : angle 4.49789 ( 945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 270 GLU cc_start: 0.7314 (pp20) cc_final: 0.6768 (pp20) REVERT: A 376 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.7862 (p90) REVERT: A 377 LEU cc_start: 0.8948 (mm) cc_final: 0.8747 (mm) REVERT: A 471 MET cc_start: 0.8387 (ttm) cc_final: 0.8162 (ptm) REVERT: A 532 MET cc_start: 0.6884 (tpt) cc_final: 0.5942 (mmm) REVERT: A 535 MET cc_start: 0.7347 (mmp) cc_final: 0.6739 (mmm) outliers start: 25 outliers final: 21 residues processed: 94 average time/residue: 0.0710 time to fit residues: 9.1943 Evaluate side-chains 91 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 865 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.0060 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.074244 restraints weight = 14058.279| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.89 r_work: 0.3039 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6948 Z= 0.189 Angle : 0.622 11.781 9415 Z= 0.315 Chirality : 0.044 0.184 1139 Planarity : 0.004 0.043 1175 Dihedral : 5.309 59.931 936 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.67 % Favored : 91.99 % Rotamer: Outliers : 3.67 % Allowed : 30.93 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.29), residues: 886 helix: 0.72 (0.26), residues: 441 sheet: -1.28 (0.57), residues: 76 loop : -1.33 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 686 TYR 0.014 0.001 TYR A 806 PHE 0.017 0.002 PHE A 818 TRP 0.007 0.001 TRP A 278 HIS 0.002 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6948) covalent geometry : angle 0.62214 ( 9415) hydrogen bonds : bond 0.03768 ( 327) hydrogen bonds : angle 4.59021 ( 945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8652 (m-40) cc_final: 0.8116 (m-40) REVERT: A 74 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8640 (tt) REVERT: A 376 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8336 (p90) REVERT: A 471 MET cc_start: 0.8552 (ttm) cc_final: 0.8310 (ptm) REVERT: A 532 MET cc_start: 0.6946 (tpt) cc_final: 0.5987 (mmm) REVERT: A 744 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8381 (t0) outliers start: 28 outliers final: 19 residues processed: 91 average time/residue: 0.0575 time to fit residues: 7.4583 Evaluate side-chains 90 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 865 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 0.0270 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.122820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080199 restraints weight = 14226.464| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.83 r_work: 0.3085 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6948 Z= 0.125 Angle : 0.602 14.688 9415 Z= 0.301 Chirality : 0.042 0.195 1139 Planarity : 0.004 0.044 1175 Dihedral : 5.150 57.503 936 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.00 % Favored : 92.66 % Rotamer: Outliers : 2.88 % Allowed : 31.72 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.29), residues: 886 helix: 0.82 (0.26), residues: 439 sheet: -1.28 (0.57), residues: 75 loop : -1.26 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 686 TYR 0.013 0.001 TYR A 806 PHE 0.014 0.001 PHE A 818 TRP 0.007 0.001 TRP A 817 HIS 0.001 0.000 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6948) covalent geometry : angle 0.60202 ( 9415) hydrogen bonds : bond 0.03407 ( 327) hydrogen bonds : angle 4.52400 ( 945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8600 (tt) REVERT: A 133 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7949 (pp20) REVERT: A 376 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.6919 (p90) REVERT: A 471 MET cc_start: 0.8428 (ttm) cc_final: 0.8190 (ptm) REVERT: A 532 MET cc_start: 0.6954 (tpt) cc_final: 0.6053 (mmm) REVERT: A 535 MET cc_start: 0.7129 (mmp) cc_final: 0.6794 (mmm) REVERT: A 843 ARG cc_start: 0.5895 (ptt180) cc_final: 0.4950 (mtm-85) outliers start: 22 outliers final: 17 residues processed: 88 average time/residue: 0.0586 time to fit residues: 7.3647 Evaluate side-chains 90 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 865 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.121390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078801 restraints weight = 14257.330| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.82 r_work: 0.3052 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6948 Z= 0.164 Angle : 0.642 15.732 9415 Z= 0.318 Chirality : 0.043 0.201 1139 Planarity : 0.004 0.043 1175 Dihedral : 5.239 56.513 936 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.34 % Favored : 92.33 % Rotamer: Outliers : 2.88 % Allowed : 32.11 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.29), residues: 886 helix: 0.73 (0.26), residues: 442 sheet: -1.31 (0.57), residues: 74 loop : -1.30 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 686 TYR 0.014 0.001 TYR A 806 PHE 0.015 0.001 PHE A 818 TRP 0.006 0.001 TRP A 278 HIS 0.002 0.000 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6948) covalent geometry : angle 0.64184 ( 9415) hydrogen bonds : bond 0.03612 ( 327) hydrogen bonds : angle 4.58188 ( 945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8622 (tt) REVERT: A 376 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.7089 (p-80) REVERT: A 471 MET cc_start: 0.8444 (ttm) cc_final: 0.8191 (ptm) REVERT: A 532 MET cc_start: 0.6964 (tpt) cc_final: 0.6067 (mmm) REVERT: A 535 MET cc_start: 0.7101 (mmp) cc_final: 0.6630 (mmm) outliers start: 22 outliers final: 16 residues processed: 86 average time/residue: 0.0531 time to fit residues: 6.6110 Evaluate side-chains 86 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 865 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.122219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079859 restraints weight = 14125.220| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.80 r_work: 0.3076 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6948 Z= 0.130 Angle : 0.611 12.613 9415 Z= 0.307 Chirality : 0.043 0.264 1139 Planarity : 0.004 0.044 1175 Dihedral : 5.228 55.041 936 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.43 % Favored : 93.23 % Rotamer: Outliers : 2.75 % Allowed : 31.72 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.29), residues: 886 helix: 0.85 (0.26), residues: 436 sheet: -1.24 (0.59), residues: 69 loop : -1.27 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 686 TYR 0.013 0.001 TYR A 806 PHE 0.013 0.001 PHE A 776 TRP 0.006 0.001 TRP A 817 HIS 0.001 0.000 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6948) covalent geometry : angle 0.61066 ( 9415) hydrogen bonds : bond 0.03417 ( 327) hydrogen bonds : angle 4.53095 ( 945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1502.08 seconds wall clock time: 26 minutes 25.30 seconds (1585.30 seconds total)