Starting phenix.real_space_refine on Thu Feb 13 19:03:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n59_24183/02_2025/7n59_24183.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n59_24183/02_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_24183/02_2025/7n59_24183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n59_24183/02_2025/7n59_24183.map" model { file = "/net/cci-nas-00/data/ceres_data/7n59_24183/02_2025/7n59_24183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n59_24183/02_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-5592/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: 6.04, per 1000 atoms: 0.65 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: 2.46 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: 1.02 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: 2.90 Time building geometry restraints manager: 2.78 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: 1.170 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.010 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- 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 : 0.982 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: 0.1889 time to fit residues: 35.2958 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 : 1.053 ------------------------------------------------------------------------------- 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 = 58)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.138230 restraints weight = 12714.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142419 restraints weight = 6677.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.145163 restraints weight = 4428.046| |-----------------------------------------------------------------------------| 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: 0.7768 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 : 0.983 Fit side-chains REVERT: A 286 GLU cc_start: 0.8112 (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: 0.7549 (p-80) cc_final: 0.7261 (p-80) REVERT: B 506 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7608 (mmtm) REVERT: B 541 GLN cc_start: 0.7942 (tp40) cc_final: 0.7711 (tp40) REVERT: B 688 ASN cc_start: 0.8214 (m-40) cc_final: 0.7979 (p0) outliers start: 12 outliers final: 6 residues processed: 113 average time/residue: 0.1947 time to fit residues: 32.5574 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 : 1.006 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.4276 r_free = 0.4276 target = 0.181730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135524 restraints weight = 12947.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.139454 restraints weight = 7053.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.141903 restraints weight = 4770.484| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 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 = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1099 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= 0.204 Angle : 0.510 6.048 12708 Z= 0.273 Chirality : 0.039 0.144 1486 Planarity : 0.003 0.056 1614 Dihedral : 8.201 94.504 1319 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.51 % Allowed : 11.85 % Favored : 86.65 % 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: 1.68 (0.76), residues: 48 loop : -1.57 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS B 697 PHE 0.017 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.005 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 : 0.966 Fit side-chains REVERT: A 396 THR cc_start: 0.8855 (t) cc_final: 0.8589 (m) REVERT: A 697 HIS cc_start: 0.7590 (p-80) cc_final: 0.7289 (p-80) REVERT: B 506 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7603 (mmtm) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.1951 time to fit residues: 31.0548 Evaluate side-chains 111 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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: 1.9990 chunk 111 optimal weight: 0.0670 chunk 94 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.182701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136500 restraints weight = 12677.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.140468 restraints weight = 6856.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142993 restraints weight = 4616.841| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1309 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= 0.176 Angle : 0.490 6.995 12708 Z= 0.263 Chirality : 0.039 0.158 1486 Planarity : 0.003 0.055 1614 Dihedral : 7.737 84.583 1319 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.81 % Allowed : 13.65 % Favored : 84.54 % 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 : -1.61 (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 B 142 *********************** 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 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.982 Fit side-chains REVERT: A 396 THR cc_start: 0.8834 (t) cc_final: 0.8589 (m) REVERT: A 541 GLN cc_start: 0.8082 (tp40) cc_final: 0.7801 (tp40) REVERT: A 697 HIS cc_start: 0.7634 (p-80) cc_final: 0.7318 (p-80) REVERT: B 506 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7804 (mmtm) REVERT: B 601 PHE cc_start: 0.6728 (m-80) cc_final: 0.6323 (m-80) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.1878 time to fit residues: 30.6177 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 : 1.062 ------------------------------------------------------------------------------- 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 191 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.184402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.138678 restraints weight = 12847.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.142608 restraints weight = 6985.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.145153 restraints weight = 4717.594| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 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 = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9397 Z= 0.153 Angle : 0.475 7.059 12708 Z= 0.254 Chirality : 0.038 0.170 1486 Planarity : 0.003 0.054 1614 Dihedral : 7.557 83.269 1319 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.71 % Allowed : 14.76 % 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: 2.41 (0.25), residues: 1172 helix: 2.83 (0.18), residues: 778 sheet: 1.90 (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 130 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.029 Fit side-chains REVERT: A 243 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.8476 (t-90) REVERT: A 286 GLU cc_start: 0.8137 (tp30) cc_final: 0.7712 (tt0) REVERT: A 396 THR cc_start: 0.8872 (t) cc_final: 0.8583 (m) REVERT: A 601 PHE cc_start: 0.6963 (m-80) cc_final: 0.6655 (m-80) REVERT: A 697 HIS cc_start: 0.7607 (p-80) cc_final: 0.7375 (p-80) REVERT: B 506 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7768 (mmtm) REVERT: B 601 PHE cc_start: 0.6683 (m-80) cc_final: 0.6165 (m-80) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 0.1908 time to fit residues: 33.1592 Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 355 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.196914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150178 restraints weight = 12244.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.153847 restraints weight = 6499.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.156255 restraints weight = 4337.967| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1593 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= 0.166 Angle : 0.490 8.905 12708 Z= 0.260 Chirality : 0.038 0.178 1486 Planarity : 0.003 0.054 1614 Dihedral : 7.397 83.032 1319 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.51 % Allowed : 17.07 % Favored : 81.43 % 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: 2.45 (0.25), residues: 1172 helix: 2.85 (0.18), residues: 780 sheet: 1.91 (0.77), residues: 48 loop : -1.52 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.003 0.001 HIS B 241 PHE 0.018 0.001 PHE A 394 TYR 0.018 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 125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.980 Fit side-chains REVERT: A 286 GLU cc_start: 0.8186 (tp30) cc_final: 0.7739 (tt0) REVERT: A 541 GLN cc_start: 0.8080 (tp40) cc_final: 0.7794 (tp40) REVERT: A 601 PHE cc_start: 0.7086 (m-80) cc_final: 0.6756 (m-80) REVERT: A 697 HIS cc_start: 0.7580 (p-80) cc_final: 0.7347 (p-80) REVERT: B 506 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7734 (mmtm) REVERT: B 601 PHE cc_start: 0.6730 (m-80) cc_final: 0.6164 (m-80) outliers start: 15 outliers final: 11 residues processed: 116 average time/residue: 0.1930 time to fit residues: 33.0197 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 191 LEU Chi-restraints excluded: chain B residue 355 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 112 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 46 optimal weight: 0.0970 chunk 111 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.191613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144112 restraints weight = 12487.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147553 restraints weight = 6875.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149708 restraints weight = 4688.592| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9397 Z= 0.246 Angle : 0.534 8.826 12708 Z= 0.285 Chirality : 0.040 0.165 1486 Planarity : 0.003 0.053 1614 Dihedral : 7.190 82.923 1319 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.41 % Allowed : 17.17 % Favored : 80.42 % 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: 2.22 (0.24), residues: 1172 helix: 2.67 (0.18), residues: 780 sheet: 1.87 (0.77), residues: 48 loop : -1.60 (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 A 241 PHE 0.015 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.004 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 125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 1.167 Fit side-chains REVERT: A 243 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8371 (t-90) REVERT: A 541 GLN cc_start: 0.8103 (tp40) cc_final: 0.7834 (tp40) REVERT: A 601 PHE cc_start: 0.7077 (m-80) cc_final: 0.6695 (m-80) REVERT: A 697 HIS cc_start: 0.7598 (p-80) cc_final: 0.7397 (p-80) REVERT: B 133 MET cc_start: 0.7425 (mtm) cc_final: 0.7210 (mtm) REVERT: B 506 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7789 (mmtm) REVERT: B 601 PHE cc_start: 0.6705 (m-80) cc_final: 0.6141 (m-80) REVERT: B 697 HIS cc_start: 0.7365 (p90) cc_final: 0.6966 (p-80) outliers start: 24 outliers final: 18 residues processed: 113 average time/residue: 0.1904 time to fit residues: 31.8936 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 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 = 0.4341 r_free = 0.4341 target = 0.194819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147413 restraints weight = 12576.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.151088 restraints weight = 6625.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153516 restraints weight = 4390.145| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9397 Z= 0.175 Angle : 0.500 9.915 12708 Z= 0.265 Chirality : 0.038 0.166 1486 Planarity : 0.003 0.050 1614 Dihedral : 6.883 83.760 1319 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.91 % Allowed : 17.97 % 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: 2.38 (0.25), residues: 1172 helix: 2.82 (0.18), residues: 780 sheet: 0.49 (0.66), residues: 74 loop : -1.52 (0.29), residues: 318 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 A 394 TYR 0.016 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: 19 poor density : 102 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8488 (t-90) REVERT: A 541 GLN cc_start: 0.8149 (tp40) cc_final: 0.7878 (tp40) REVERT: A 601 PHE cc_start: 0.7120 (m-80) cc_final: 0.6729 (m-80) REVERT: A 697 HIS cc_start: 0.7574 (p-80) cc_final: 0.7287 (p-80) REVERT: B 506 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7762 (mmtm) REVERT: B 601 PHE cc_start: 0.6698 (m-80) cc_final: 0.6039 (m-80) REVERT: B 697 HIS cc_start: 0.7322 (p90) cc_final: 0.6948 (p-80) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.1843 time to fit residues: 30.1819 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 680 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 0.2980 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.187122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.145077 restraints weight = 12111.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145977 restraints weight = 6861.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146473 restraints weight = 5682.028| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 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 = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1800 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= 0.172 Angle : 0.504 10.134 12708 Z= 0.265 Chirality : 0.038 0.191 1486 Planarity : 0.003 0.049 1614 Dihedral : 6.670 85.064 1319 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.81 % Allowed : 18.17 % Favored : 80.02 % 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: 2.42 (0.25), residues: 1172 helix: 2.86 (0.18), residues: 780 sheet: 0.47 (0.66), residues: 74 loop : -1.50 (0.29), residues: 318 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 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 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 243 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.8524 (t-90) REVERT: A 601 PHE cc_start: 0.7118 (m-80) cc_final: 0.6778 (m-80) REVERT: A 697 HIS cc_start: 0.7450 (p-80) cc_final: 0.7175 (p-80) REVERT: B 506 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7917 (mmtm) REVERT: B 601 PHE cc_start: 0.6795 (m-80) cc_final: 0.6193 (m-80) REVERT: B 697 HIS cc_start: 0.7129 (p90) cc_final: 0.6886 (p-80) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.1924 time to fit residues: 31.2043 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 147 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.184944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142441 restraints weight = 12423.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142958 restraints weight = 6729.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.143665 restraints weight = 4817.880| |-----------------------------------------------------------------------------| 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) = 0.139 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3815 r_free = 0.3815 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1857 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= 0.214 Angle : 0.529 9.758 12708 Z= 0.278 Chirality : 0.039 0.181 1486 Planarity : 0.003 0.049 1614 Dihedral : 6.628 86.234 1319 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.61 % Allowed : 18.57 % Favored : 79.82 % 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 (0.25), residues: 1172 helix: 2.81 (0.18), residues: 778 sheet: 0.54 (0.65), residues: 74 loop : -1.57 (0.28), residues: 320 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 0.016 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.004 0.000 ARG A 547 ********************** 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 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 601 PHE cc_start: 0.7162 (m-80) cc_final: 0.6778 (m-80) REVERT: A 697 HIS cc_start: 0.7495 (p-80) cc_final: 0.7246 (p-80) REVERT: B 506 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7904 (mmtm) REVERT: B 601 PHE cc_start: 0.6785 (m-80) cc_final: 0.6088 (m-80) REVERT: B 697 HIS cc_start: 0.7113 (p90) cc_final: 0.6893 (p-80) outliers start: 16 outliers final: 15 residues processed: 108 average time/residue: 0.1943 time to fit residues: 31.1124 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 191 LEU Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 680 CYS 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: 0.6980 chunk 94 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4304 r_free = 0.4304 target = 0.185003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143347 restraints weight = 12250.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.143286 restraints weight = 6918.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143732 restraints weight = 5496.734| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 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 = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1910 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= 0.208 Angle : 0.527 9.741 12708 Z= 0.278 Chirality : 0.039 0.180 1486 Planarity : 0.003 0.048 1614 Dihedral : 6.582 87.881 1319 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.51 % Allowed : 18.98 % Favored : 79.52 % 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: 2.35 (0.25), residues: 1172 helix: 2.81 (0.18), residues: 778 sheet: 0.59 (0.65), residues: 74 loop : -1.57 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 711 HIS 0.004 0.001 HIS A 241 PHE 0.016 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.003 0.000 ARG A 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.88 seconds wall clock time: 53 minutes 44.48 seconds (3224.48 seconds total)