Starting phenix.real_space_refine on Thu Mar 13 22:15:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n59_24183/03_2025/7n59_24183.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n59_24183/03_2025/7n59_24183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n59_24183/03_2025/7n59_24183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n59_24183/03_2025/7n59_24183.map" model { file = "/net/cci-nas-00/data/ceres_data/7n59_24183/03_2025/7n59_24183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n59_24183/03_2025/7n59_24183.cif" } resolution = 3.6 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= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5892 2.51 5 N 1584 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9238 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4599 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 13, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 4599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4599 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 13, 'TRANS': 576} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'GDS': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" CB1 GDS A 801 " occ=0.50 ... (38 atoms not shown) pdb=" SG5 GDS A 801 " occ=0.50 Time building chain proxies: 6.14, per 1000 atoms: 0.66 Number of scatterers: 9238 At special positions: 0 Unit cell: (81.225, 98.325, 142.785, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1726 8.00 N 1584 7.00 C 5892 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 69.2% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 117 through 133 Processing helix chain 'A' and resid 136 through 175 removed outlier: 4.217A pdb=" N ARG A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.602A pdb=" N PHE A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 243 removed outlier: 3.703A pdb=" N VAL A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.542A pdb=" N HIS A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 279 Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 300 through 348 removed outlier: 3.761A pdb=" N TRP A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 removed outlier: 3.649A pdb=" N VAL A 352 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 412 removed outlier: 3.598A pdb=" N GLU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 431 removed outlier: 3.592A pdb=" N LEU A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 457 Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.811A pdb=" N GLY A 517 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 526 Processing helix chain 'A' and resid 547 through 554 removed outlier: 3.913A pdb=" N LEU A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 575 Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 617 through 633 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 673 through 677 Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 705 through 713 removed outlier: 3.678A pdb=" N GLN A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 3.685A pdb=" N MET B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 175 removed outlier: 4.432A pdb=" N ARG B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 197 through 245 removed outlier: 3.563A pdb=" N VAL B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 245 " --> pdb=" O HIS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.975A pdb=" N HIS B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 279 removed outlier: 4.104A pdb=" N ARG B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 296 Processing helix chain 'B' and resid 300 through 348 removed outlier: 3.654A pdb=" N TRP B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE B 327 " --> pdb=" O TRP B 323 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 removed outlier: 3.519A pdb=" N VAL B 352 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 412 removed outlier: 3.515A pdb=" N LYS B 364 " --> pdb=" O TYR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 431 removed outlier: 3.631A pdb=" N LEU B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 435 through 457 removed outlier: 3.705A pdb=" N LEU B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.865A pdb=" N GLY B 517 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 526 Processing helix chain 'B' and resid 547 through 554 removed outlier: 3.890A pdb=" N LEU B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 575 Processing helix chain 'B' and resid 581 through 592 Processing helix chain 'B' and resid 594 through 600 removed outlier: 3.675A pdb=" N ASN B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 633 Processing helix chain 'B' and resid 647 through 662 Processing helix chain 'B' and resid 673 through 680 removed outlier: 4.204A pdb=" N MET B 678 " --> pdb=" O THR B 675 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 679 " --> pdb=" O THR B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 705 through 713 removed outlier: 3.586A pdb=" N GLN B 709 " --> pdb=" O GLY B 705 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 removed outlier: 4.878A pdb=" N VAL A 484 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 498 removed outlier: 4.878A pdb=" N VAL A 484 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 484 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER A 533 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 557 removed outlier: 3.554A pdb=" N ILE A 670 " --> pdb=" O CYS A 639 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 508 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER A 507 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 684 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ALA A 509 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU A 686 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 511 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 693 " --> pdb=" O VAL A 685 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 495 through 498 removed outlier: 3.657A pdb=" N LEU B 495 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 486 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 484 " --> pdb=" O GLY B 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 495 through 498 removed outlier: 3.657A pdb=" N LEU B 495 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 486 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 484 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 535 " --> pdb=" O GLU B 482 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 484 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER B 533 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 557 removed outlier: 6.609A pdb=" N LEU B 637 " --> pdb=" O ILE B 668 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE B 670 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N CYS B 639 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 508 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER B 507 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL B 684 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ALA B 509 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B 686 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL B 511 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 683 " --> pdb=" O GLN B 694 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN B 694 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL B 685 " --> pdb=" O VAL B 692 " (cutoff:3.500A) 619 hydrogen bonds defined for protein. 1821 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: 2.78 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 3059 1.37 - 1.55: 6273 1.55 - 1.73: 0 1.73 - 1.92: 64 1.92 - 2.10: 1 Bond restraints: 9397 Sorted by residual: bond pdb=" C5 GDS A 801 " pdb=" N4 GDS A 801 " ideal model delta sigma weight residual 1.333 1.451 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C2 GDS A 801 " pdb=" N3 GDS A 801 " ideal model delta sigma weight residual 1.334 1.450 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" CD1 GDS A 801 " pdb=" N2 GDS A 801 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CD6 GDS A 801 " pdb=" N5 GDS A 801 " ideal model delta sigma weight residual 1.349 1.451 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" CD1 GDS A 801 " pdb=" O1 GDS A 801 " ideal model delta sigma weight residual 1.242 1.184 0.058 2.00e-02 2.50e+03 8.48e+00 ... (remaining 9392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12400 1.64 - 3.28: 239 3.28 - 4.91: 43 4.91 - 6.55: 16 6.55 - 8.19: 10 Bond angle restraints: 12708 Sorted by residual: angle pdb=" CB1 GDS A 801 " pdb=" CG1 GDS A 801 " pdb=" CD1 GDS A 801 " ideal model delta sigma weight residual 117.94 109.75 8.19 3.00e+00 1.11e-01 7.45e+00 angle pdb=" C LEU B 242 " pdb=" N HIS B 243 " pdb=" CA HIS B 243 " ideal model delta sigma weight residual 120.72 116.57 4.15 1.67e+00 3.59e-01 6.18e+00 angle pdb=" OE5 GDS A 801 " pdb=" C4 GDS A 801 " pdb=" OE6 GDS A 801 " ideal model delta sigma weight residual 127.28 120.08 7.20 3.00e+00 1.11e-01 5.76e+00 angle pdb=" CB MET A 121 " pdb=" CG MET A 121 " pdb=" SD MET A 121 " ideal model delta sigma weight residual 112.70 119.79 -7.09 3.00e+00 1.11e-01 5.58e+00 angle pdb=" OE3 GDS A 801 " pdb=" C3 GDS A 801 " pdb=" OE4 GDS A 801 " ideal model delta sigma weight residual 127.19 120.15 7.04 3.00e+00 1.11e-01 5.50e+00 ... (remaining 12703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.66: 5368 26.66 - 53.32: 255 53.32 - 79.98: 20 79.98 - 106.64: 4 106.64 - 133.30: 2 Dihedral angle restraints: 5649 sinusoidal: 2233 harmonic: 3416 Sorted by residual: dihedral pdb=" N4 GDS A 801 " pdb=" C5 GDS A 801 " pdb=" CA5 GDS A 801 " pdb=" N5 GDS A 801 " ideal model delta sinusoidal sigma weight residual 133.37 0.07 133.30 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CB5 GDS A 801 " pdb=" C5 GDS A 801 " pdb=" CA5 GDS A 801 " pdb=" N4 GDS A 801 " ideal model delta sinusoidal sigma weight residual 106.65 -121.23 -132.12 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CB2 GDS A 801 " pdb=" C2 GDS A 801 " pdb=" CA2 GDS A 801 " pdb=" O2 GDS A 801 " ideal model delta sinusoidal sigma weight residual 95.13 1.49 93.64 1 3.00e+01 1.11e-03 1.13e+01 ... (remaining 5646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1369 0.075 - 0.151: 113 0.151 - 0.226: 3 0.226 - 0.301: 0 0.301 - 0.377: 1 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA2 GDS A 801 " pdb=" CB2 GDS A 801 " pdb=" C2 GDS A 801 " pdb=" N2 GDS A 801 " both_signs ideal model delta sigma weight residual False -2.24 -2.62 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA1 GDS A 801 " pdb=" CB1 GDS A 801 " pdb=" C1 GDS A 801 " pdb=" N1 GDS A 801 " both_signs ideal model delta sigma weight residual False -2.43 -2.61 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CB ILE B 538 " pdb=" CA ILE B 538 " pdb=" CG1 ILE B 538 " pdb=" CG2 ILE B 538 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1483 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 711 " 0.021 2.00e-02 2.50e+03 1.76e-02 7.75e+00 pdb=" CG TRP B 711 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 711 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 711 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 711 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 711 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 711 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 711 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 711 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 711 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 323 " 0.019 2.00e-02 2.50e+03 1.55e-02 6.03e+00 pdb=" CG TRP A 323 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 323 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 323 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 323 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 323 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 323 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 323 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 323 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 323 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 711 " -0.010 2.00e-02 2.50e+03 9.38e-03 2.20e+00 pdb=" CG TRP A 711 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 711 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 711 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 711 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 711 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 711 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 711 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 711 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 711 " 0.001 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1394 2.76 - 3.29: 9460 3.29 - 3.83: 15148 3.83 - 4.36: 15671 4.36 - 4.90: 27867 Nonbonded interactions: 69540 Sorted by model distance: nonbonded pdb=" OE2 GLU A 358 " pdb=" OG SER B 240 " model vdw 2.221 3.040 nonbonded pdb=" ND1 HIS A 243 " pdb=" OE2 GLU B 358 " model vdw 2.261 3.120 nonbonded pdb=" O GLN B 709 " pdb=" OG1 THR B 712 " model vdw 2.287 3.040 nonbonded pdb=" OD2 ASP A 366 " pdb=" NH1 ARG B 236 " model vdw 2.319 3.120 nonbonded pdb=" O LEU B 661 " pdb=" NH2 ARG B 665 " model vdw 2.333 3.120 ... (remaining 69535 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 117 through 716) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.230 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.980 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.004 0.118 9397 Z= 0.260 Angle : 0.616 8.191 12708 Z= 0.309 Chirality : 0.041 0.377 1486 Planarity : 0.003 0.028 1614 Dihedral : 14.741 133.305 3441 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % 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: 1.69 (0.25), residues: 1172 helix: 2.28 (0.18), residues: 780 sheet: 0.15 (0.66), residues: 72 loop : -1.70 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 711 HIS 0.005 0.001 HIS B 241 PHE 0.018 0.001 PHE A 394 TYR 0.020 0.001 TYR B 707 ARG 0.004 0.000 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 1.034 Fit side-chains REVERT: A 121 MET cc_start: 0.7833 (tmm) cc_final: 0.7621 (tpt) REVERT: A 286 GLU cc_start: 0.8134 (tp30) cc_final: 0.7613 (tt0) REVERT: A 396 THR cc_start: 0.8851 (t) cc_final: 0.8596 (m) REVERT: B 506 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7619 (mmtm) REVERT: B 541 GLN cc_start: 0.7751 (tp40) cc_final: 0.7379 (tp40) REVERT: B 688 ASN cc_start: 0.8255 (m-40) cc_final: 0.7903 (p0) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.1938 time to fit residues: 36.1114 Evaluate side-chains 97 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 56 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS A 688 ASN B 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.184590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.138230 restraints weight = 12714.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142476 restraints weight = 6677.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145219 restraints weight = 4416.691| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9397 Z= 0.170 Angle : 0.527 7.088 12708 Z= 0.280 Chirality : 0.039 0.139 1486 Planarity : 0.004 0.050 1614 Dihedral : 9.020 114.821 1319 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.20 % Allowed : 7.93 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.25), residues: 1172 helix: 2.54 (0.18), residues: 780 sheet: 0.20 (0.66), residues: 74 loop : -1.59 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 323 HIS 0.003 0.001 HIS A 485 PHE 0.017 0.001 PHE B 394 TYR 0.018 0.001 TYR B 205 ARG 0.008 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.218 Fit side-chains REVERT: A 286 GLU cc_start: 0.8115 (tp30) cc_final: 0.7553 (tt0) REVERT: A 396 THR cc_start: 0.8824 (t) cc_final: 0.8575 (m) REVERT: A 697 HIS cc_start: 0.7550 (p-80) cc_final: 0.7266 (p-80) REVERT: B 506 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7587 (mmtm) REVERT: B 541 GLN cc_start: 0.7944 (tp40) cc_final: 0.7710 (tp40) REVERT: B 688 ASN cc_start: 0.8226 (m-40) cc_final: 0.7985 (p0) outliers start: 12 outliers final: 6 residues processed: 113 average time/residue: 0.2318 time to fit residues: 38.6026 Evaluate side-chains 104 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 158 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.181887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135683 restraints weight = 12918.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139621 restraints weight = 7027.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142127 restraints weight = 4749.748| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9397 Z= 0.201 Angle : 0.508 6.000 12708 Z= 0.272 Chirality : 0.039 0.140 1486 Planarity : 0.003 0.056 1614 Dihedral : 8.173 93.676 1319 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.51 % Allowed : 11.75 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.24), residues: 1172 helix: 2.58 (0.18), residues: 780 sheet: 1.66 (0.76), residues: 48 loop : -1.56 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 323 HIS 0.004 0.001 HIS B 697 PHE 0.017 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.687 Fit side-chains REVERT: A 396 THR cc_start: 0.8855 (t) cc_final: 0.8589 (m) REVERT: A 697 HIS cc_start: 0.7596 (p-80) cc_final: 0.7290 (p-80) REVERT: B 506 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7613 (mmtm) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.2381 time to fit residues: 37.4781 Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 0.0570 chunk 94 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.183019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136935 restraints weight = 12664.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.140858 restraints weight = 6841.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.143425 restraints weight = 4609.448| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9397 Z= 0.175 Angle : 0.489 6.971 12708 Z= 0.262 Chirality : 0.039 0.164 1486 Planarity : 0.003 0.055 1614 Dihedral : 7.722 84.419 1319 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.81 % Allowed : 13.25 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.24), residues: 1172 helix: 2.71 (0.18), residues: 780 sheet: 1.86 (0.76), residues: 48 loop : -1.60 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 323 HIS 0.004 0.001 HIS B 697 PHE 0.017 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.988 Fit side-chains REVERT: A 286 GLU cc_start: 0.8166 (tp30) cc_final: 0.7722 (tt0) REVERT: A 396 THR cc_start: 0.8835 (t) cc_final: 0.8589 (m) REVERT: A 541 GLN cc_start: 0.8071 (tp40) cc_final: 0.7791 (tp40) REVERT: A 697 HIS cc_start: 0.7629 (p-80) cc_final: 0.7308 (p-80) REVERT: B 506 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7806 (mmtm) REVERT: B 601 PHE cc_start: 0.6728 (m-80) cc_final: 0.6326 (m-80) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 0.1848 time to fit residues: 30.7176 Evaluate side-chains 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 355 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 0.0770 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.184079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138224 restraints weight = 12845.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.142187 restraints weight = 6986.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.144760 restraints weight = 4718.834| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9397 Z= 0.159 Angle : 0.476 6.989 12708 Z= 0.255 Chirality : 0.038 0.167 1486 Planarity : 0.003 0.053 1614 Dihedral : 7.549 82.996 1319 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.61 % Allowed : 14.86 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.25), residues: 1172 helix: 2.81 (0.18), residues: 778 sheet: 1.88 (0.77), residues: 48 loop : -1.53 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.003 0.001 HIS B 697 PHE 0.018 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.003 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.156 Fit side-chains REVERT: A 243 HIS cc_start: 0.8827 (OUTLIER) cc_final: 0.8441 (t-90) REVERT: A 286 GLU cc_start: 0.8140 (tp30) cc_final: 0.7723 (tt0) REVERT: A 396 THR cc_start: 0.8882 (t) cc_final: 0.8592 (m) REVERT: A 541 GLN cc_start: 0.8148 (tp40) cc_final: 0.7898 (tp40) REVERT: A 601 PHE cc_start: 0.6971 (m-80) cc_final: 0.6654 (m-80) REVERT: A 697 HIS cc_start: 0.7604 (p-80) cc_final: 0.7379 (p-80) REVERT: B 506 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7765 (mmtm) REVERT: B 601 PHE cc_start: 0.6685 (m-80) cc_final: 0.6161 (m-80) outliers start: 16 outliers final: 10 residues processed: 117 average time/residue: 0.2175 time to fit residues: 37.7445 Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 47 optimal weight: 0.0010 chunk 3 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.193998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146457 restraints weight = 12331.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150195 restraints weight = 6540.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152569 restraints weight = 4337.596| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9397 Z= 0.189 Angle : 0.502 8.940 12708 Z= 0.267 Chirality : 0.039 0.175 1486 Planarity : 0.003 0.053 1614 Dihedral : 7.272 82.850 1319 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.91 % Allowed : 16.77 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.25), residues: 1172 helix: 2.79 (0.18), residues: 780 sheet: 1.86 (0.77), residues: 48 loop : -1.55 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.004 0.001 HIS B 241 PHE 0.017 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.942 Fit side-chains REVERT: A 243 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.8549 (t-90) REVERT: A 601 PHE cc_start: 0.7056 (m-80) cc_final: 0.6687 (m-80) REVERT: A 697 HIS cc_start: 0.7611 (p-80) cc_final: 0.7394 (p-80) REVERT: B 506 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7695 (mmtm) REVERT: B 601 PHE cc_start: 0.6719 (m-80) cc_final: 0.6116 (m-80) REVERT: B 697 HIS cc_start: 0.7333 (p90) cc_final: 0.6915 (p-80) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.2119 time to fit residues: 36.3900 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 112 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.184624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.142680 restraints weight = 12224.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142275 restraints weight = 7015.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.143079 restraints weight = 5580.455| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9397 Z= 0.201 Angle : 0.510 9.315 12708 Z= 0.271 Chirality : 0.039 0.165 1486 Planarity : 0.003 0.050 1614 Dihedral : 7.038 83.357 1319 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.41 % Allowed : 16.97 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.24), residues: 1172 helix: 2.77 (0.18), residues: 780 sheet: 1.79 (0.76), residues: 48 loop : -1.56 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 711 HIS 0.003 0.001 HIS A 241 PHE 0.017 0.001 PHE B 139 TYR 0.017 0.001 TYR B 205 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8882 (OUTLIER) cc_final: 0.8506 (t-90) REVERT: A 541 GLN cc_start: 0.8059 (tp40) cc_final: 0.7782 (tp40) REVERT: A 601 PHE cc_start: 0.7026 (m-80) cc_final: 0.6660 (m-80) REVERT: A 697 HIS cc_start: 0.7546 (p-80) cc_final: 0.7333 (p-80) REVERT: B 506 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7814 (mmtm) REVERT: B 601 PHE cc_start: 0.6664 (m-80) cc_final: 0.6084 (m-80) REVERT: B 697 HIS cc_start: 0.7232 (p90) cc_final: 0.6878 (p-80) outliers start: 24 outliers final: 19 residues processed: 114 average time/residue: 0.2004 time to fit residues: 33.7730 Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 680 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 23 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.183988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138205 restraints weight = 13046.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142207 restraints weight = 7063.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144771 restraints weight = 4745.285| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9397 Z= 0.162 Angle : 0.494 10.005 12708 Z= 0.261 Chirality : 0.038 0.159 1486 Planarity : 0.003 0.049 1614 Dihedral : 6.712 84.837 1319 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.61 % Allowed : 17.77 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.25), residues: 1172 helix: 2.92 (0.18), residues: 778 sheet: 1.81 (0.76), residues: 48 loop : -1.51 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 711 HIS 0.003 0.001 HIS A 241 PHE 0.018 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8801 (OUTLIER) cc_final: 0.8511 (t-90) REVERT: A 286 GLU cc_start: 0.8165 (tp30) cc_final: 0.7690 (tt0) REVERT: A 541 GLN cc_start: 0.8028 (tp40) cc_final: 0.7784 (tp40) REVERT: A 601 PHE cc_start: 0.7128 (m-80) cc_final: 0.6787 (m-80) REVERT: A 697 HIS cc_start: 0.7564 (p-80) cc_final: 0.7274 (p-80) REVERT: B 506 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7768 (mmtm) REVERT: B 601 PHE cc_start: 0.6664 (m-80) cc_final: 0.6080 (m-80) REVERT: B 697 HIS cc_start: 0.7323 (p90) cc_final: 0.6952 (p-80) outliers start: 16 outliers final: 11 residues processed: 114 average time/residue: 0.1815 time to fit residues: 30.8154 Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.187503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.145786 restraints weight = 12144.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146437 restraints weight = 7163.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146611 restraints weight = 5196.542| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9397 Z= 0.174 Angle : 0.501 9.896 12708 Z= 0.264 Chirality : 0.038 0.158 1486 Planarity : 0.003 0.050 1614 Dihedral : 6.586 86.000 1319 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.51 % Allowed : 18.17 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.25), residues: 1172 helix: 2.91 (0.18), residues: 778 sheet: 0.49 (0.66), residues: 74 loop : -1.48 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.003 0.001 HIS A 241 PHE 0.017 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 541 GLN cc_start: 0.7953 (tp40) cc_final: 0.7750 (tp40) REVERT: A 601 PHE cc_start: 0.7164 (m-80) cc_final: 0.6822 (m-80) REVERT: A 697 HIS cc_start: 0.7406 (p-80) cc_final: 0.7140 (p-80) REVERT: B 506 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7852 (mmtm) REVERT: B 601 PHE cc_start: 0.6765 (m-80) cc_final: 0.6120 (m-80) REVERT: B 697 HIS cc_start: 0.7116 (p90) cc_final: 0.6884 (p-80) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.2025 time to fit residues: 31.7771 Evaluate side-chains 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.188614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147415 restraints weight = 12352.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147884 restraints weight = 6468.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148167 restraints weight = 5139.065| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9397 Z= 0.160 Angle : 0.497 10.003 12708 Z= 0.261 Chirality : 0.038 0.159 1486 Planarity : 0.003 0.048 1614 Dihedral : 6.414 88.871 1319 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.31 % Allowed : 18.57 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.25), residues: 1172 helix: 2.98 (0.18), residues: 778 sheet: 0.60 (0.66), residues: 74 loop : -1.46 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.003 0.001 HIS A 241 PHE 0.017 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.003 0.000 ARG A 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 286 GLU cc_start: 0.8138 (tp30) cc_final: 0.7651 (tt0) REVERT: A 601 PHE cc_start: 0.7155 (m-80) cc_final: 0.6806 (m-80) REVERT: A 697 HIS cc_start: 0.7424 (p-80) cc_final: 0.7188 (p-80) REVERT: B 506 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7795 (mmtm) REVERT: B 601 PHE cc_start: 0.6651 (m-80) cc_final: 0.6007 (m-80) outliers start: 13 outliers final: 13 residues processed: 110 average time/residue: 0.2160 time to fit residues: 35.0833 Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 7 optimal weight: 0.5980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.188591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147408 restraints weight = 12240.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148096 restraints weight = 6427.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.148417 restraints weight = 4894.589| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9397 Z= 0.165 Angle : 0.509 9.782 12708 Z= 0.266 Chirality : 0.038 0.159 1486 Planarity : 0.003 0.048 1614 Dihedral : 6.394 90.074 1319 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.31 % Allowed : 19.08 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.25), residues: 1172 helix: 2.97 (0.18), residues: 778 sheet: 0.66 (0.66), residues: 74 loop : -1.52 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.003 0.000 HIS A 241 PHE 0.017 0.001 PHE A 394 TYR 0.018 0.001 TYR B 205 ARG 0.003 0.000 ARG B 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.94 seconds wall clock time: 59 minutes 7.77 seconds (3547.77 seconds total)