Starting phenix.real_space_refine on Sat Dec 28 22:52:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n59_24183/12_2024/7n59_24183.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n59_24183/12_2024/7n59_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_24183/12_2024/7n59_24183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n59_24183/12_2024/7n59_24183.map" model { file = "/net/cci-nas-00/data/ceres_data/7n59_24183/12_2024/7n59_24183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n59_24183/12_2024/7n59_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-5532/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: 6.21, per 1000 atoms: 0.67 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: 2.65 Conformation dependent library (CDL) restraints added in 1.3 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: 3.06 Time building geometry restraints manager: 2.98 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: 1.450 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.950 Find NCS groups from input model: 0.370 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.400 ------------------------------------------------------------------------------- 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 : 1.066 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: 0.1937 time to fit residues: 35.9646 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 : 0.995 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 1.060 Fit side-chains REVERT: A 286 GLU cc_start: 0.8117 (tp30) cc_final: 0.7550 (tt0) REVERT: A 396 THR cc_start: 0.8823 (t) cc_final: 0.8575 (m) REVERT: A 697 HIS cc_start: 0.7546 (p-80) cc_final: 0.7269 (p-80) REVERT: B 506 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7564 (mmtm) REVERT: B 541 GLN cc_start: 0.7951 (tp40) cc_final: 0.7714 (tp40) REVERT: B 688 ASN cc_start: 0.8236 (m-40) cc_final: 0.7990 (p0) outliers start: 12 outliers final: 6 residues processed: 113 average time/residue: 0.2018 time to fit residues: 34.0853 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 : 1.085 ------------------------------------------------------------------------------- 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 59 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1111 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= 0.194 Angle : 0.504 5.886 12708 Z= 0.270 Chirality : 0.039 0.141 1486 Planarity : 0.003 0.054 1614 Dihedral : 8.139 93.045 1319 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.41 % Allowed : 11.85 % 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: 2.14 (0.24), residues: 1172 helix: 2.59 (0.18), residues: 780 sheet: 1.67 (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 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.129 Fit side-chains REVERT: A 396 THR cc_start: 0.8810 (t) cc_final: 0.8558 (m) REVERT: A 697 HIS cc_start: 0.7589 (p-80) cc_final: 0.7296 (p-80) REVERT: B 506 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7532 (mmtm) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.1893 time to fit residues: 30.2660 Evaluate side-chains 111 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 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 106 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9397 Z= 0.350 Angle : 0.615 7.895 12708 Z= 0.331 Chirality : 0.043 0.166 1486 Planarity : 0.004 0.056 1614 Dihedral : 7.985 83.349 1319 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.91 % Allowed : 14.06 % Favored : 83.03 % 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: 1.65 (0.24), residues: 1172 helix: 2.22 (0.18), residues: 780 sheet: 1.69 (0.75), residues: 48 loop : -1.79 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 323 HIS 0.005 0.001 HIS A 241 PHE 0.016 0.002 PHE B 164 TYR 0.017 0.002 TYR A 313 ARG 0.005 0.001 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 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.136 Fit side-chains REVERT: A 243 HIS cc_start: 0.9044 (OUTLIER) cc_final: 0.8410 (t-90) REVERT: A 343 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8804 (mt) REVERT: A 541 GLN cc_start: 0.8209 (tp40) cc_final: 0.7892 (tp40) REVERT: A 697 HIS cc_start: 0.7683 (p-80) cc_final: 0.7321 (p-80) REVERT: B 506 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7891 (mmtm) outliers start: 29 outliers final: 22 residues processed: 114 average time/residue: 0.2009 time to fit residues: 33.3623 Evaluate side-chains 118 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 293 ILE 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 603 ASP Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 680 CYS Chi-restraints excluded: chain B residue 691 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1680 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= 0.238 Angle : 0.532 7.870 12708 Z= 0.287 Chirality : 0.040 0.159 1486 Planarity : 0.003 0.054 1614 Dihedral : 7.845 82.018 1319 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.31 % Allowed : 16.06 % Favored : 81.63 % 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: 1.88 (0.24), residues: 1172 helix: 2.40 (0.18), residues: 780 sheet: 1.78 (0.76), residues: 48 loop : -1.72 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 711 HIS 0.011 0.001 HIS B 243 PHE 0.017 0.001 PHE A 394 TYR 0.015 0.001 TYR B 205 ARG 0.007 0.000 ARG A 264 *********************** 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 124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.090 Fit side-chains REVERT: A 243 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8413 (t-90) REVERT: A 343 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8738 (mt) REVERT: A 541 GLN cc_start: 0.8195 (tp40) cc_final: 0.7916 (tp40) REVERT: A 601 PHE cc_start: 0.7125 (m-80) cc_final: 0.6730 (m-80) REVERT: B 249 TYR cc_start: 0.8150 (t80) cc_final: 0.7850 (t80) REVERT: B 506 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7826 (mmtm) REVERT: B 601 PHE cc_start: 0.6763 (m-80) cc_final: 0.6150 (m-80) outliers start: 23 outliers final: 17 residues processed: 113 average time/residue: 0.1890 time to fit residues: 31.3803 Evaluate side-chains 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 210 THR 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 355 PHE 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 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 Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 680 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 10.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9397 Z= 0.200 Angle : 0.504 7.562 12708 Z= 0.273 Chirality : 0.039 0.167 1486 Planarity : 0.003 0.052 1614 Dihedral : 7.537 81.053 1319 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.31 % Allowed : 17.37 % 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: 2.05 (0.24), residues: 1172 helix: 2.55 (0.18), residues: 780 sheet: 1.78 (0.76), residues: 48 loop : -1.69 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 711 HIS 0.006 0.001 HIS A 697 PHE 0.018 0.001 PHE A 394 TYR 0.016 0.001 TYR B 205 ARG 0.006 0.000 ARG A 264 *********************** 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: 23 poor density : 103 time to evaluate : 1.024 Fit side-chains REVERT: A 243 HIS cc_start: 0.8877 (OUTLIER) cc_final: 0.8277 (t-90) REVERT: A 343 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8690 (mt) REVERT: A 541 GLN cc_start: 0.8290 (tp40) cc_final: 0.8021 (tp40) REVERT: A 601 PHE cc_start: 0.7109 (m-80) cc_final: 0.6711 (m-80) REVERT: B 506 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7791 (mmtm) REVERT: B 541 GLN cc_start: 0.8006 (tp40) cc_final: 0.7708 (tp40) REVERT: B 601 PHE cc_start: 0.6726 (m-80) cc_final: 0.6048 (m-80) REVERT: B 697 HIS cc_start: 0.7424 (p90) cc_final: 0.7011 (p-80) outliers start: 23 outliers final: 20 residues processed: 115 average time/residue: 0.2018 time to fit residues: 33.4858 Evaluate side-chains 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 210 THR 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 355 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 404 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 A residue 711 TRP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 404 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1764 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= 0.188 Angle : 0.501 6.774 12708 Z= 0.269 Chirality : 0.039 0.180 1486 Planarity : 0.003 0.053 1614 Dihedral : 7.263 81.064 1319 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.11 % Allowed : 18.57 % Favored : 79.32 % 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: 2.14 (0.24), residues: 1172 helix: 2.61 (0.18), residues: 780 sheet: 1.72 (0.76), residues: 48 loop : -1.64 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 711 HIS 0.011 0.001 HIS B 243 PHE 0.018 0.001 PHE A 394 TYR 0.016 0.001 TYR B 205 ARG 0.005 0.000 ARG A 264 *********************** 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 124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.068 Fit side-chains REVERT: A 243 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8366 (t-90) REVERT: A 253 ARG cc_start: 0.7172 (mmm-85) cc_final: 0.6889 (mmm-85) REVERT: A 541 GLN cc_start: 0.8273 (tp40) cc_final: 0.8016 (tp40) REVERT: A 601 PHE cc_start: 0.7109 (m-80) cc_final: 0.6726 (m-80) REVERT: B 249 TYR cc_start: 0.8168 (t80) cc_final: 0.7926 (t80) REVERT: B 506 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7785 (mmtm) REVERT: B 541 GLN cc_start: 0.8033 (tp40) cc_final: 0.7754 (tp40) REVERT: B 601 PHE cc_start: 0.6671 (m-80) cc_final: 0.5984 (m-80) REVERT: B 697 HIS cc_start: 0.7403 (p90) cc_final: 0.7013 (p-80) outliers start: 21 outliers final: 19 residues processed: 113 average time/residue: 0.1959 time to fit residues: 32.5847 Evaluate side-chains 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 210 THR 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 355 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 404 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 A residue 711 TRP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1787 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= 0.173 Angle : 0.493 7.011 12708 Z= 0.265 Chirality : 0.039 0.165 1486 Planarity : 0.003 0.052 1614 Dihedral : 7.042 81.569 1319 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.41 % Allowed : 18.88 % Favored : 78.71 % 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 (0.25), residues: 1172 helix: 2.72 (0.18), residues: 778 sheet: 1.70 (0.75), residues: 48 loop : -1.59 (0.27), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 711 HIS 0.012 0.001 HIS A 697 PHE 0.018 0.001 PHE A 394 TYR 0.017 0.001 TYR B 205 ARG 0.005 0.000 ARG B 253 *********************** 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 125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 1.036 Fit side-chains REVERT: A 243 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8393 (t-90) REVERT: A 253 ARG cc_start: 0.7182 (mmm-85) cc_final: 0.6926 (mmm-85) REVERT: A 541 GLN cc_start: 0.8272 (tp40) cc_final: 0.8023 (tp40) REVERT: A 601 PHE cc_start: 0.7133 (m-80) cc_final: 0.6753 (m-80) REVERT: B 506 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7794 (mmtm) REVERT: B 541 GLN cc_start: 0.8027 (tp40) cc_final: 0.7759 (tp40) REVERT: B 601 PHE cc_start: 0.6687 (m-80) cc_final: 0.5991 (m-80) REVERT: B 697 HIS cc_start: 0.7406 (p90) cc_final: 0.7047 (p-80) outliers start: 24 outliers final: 20 residues processed: 112 average time/residue: 0.1927 time to fit residues: 31.9292 Evaluate side-chains 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 404 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 243 HIS Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 0.0270 chunk 100 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9397 Z= 0.148 Angle : 0.484 7.059 12708 Z= 0.258 Chirality : 0.038 0.164 1486 Planarity : 0.003 0.051 1614 Dihedral : 6.562 84.422 1319 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.10 % Allowed : 20.38 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.25), residues: 1172 helix: 2.90 (0.19), residues: 778 sheet: 0.46 (0.65), residues: 74 loop : -1.50 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.011 0.001 HIS A 697 PHE 0.019 0.001 PHE A 394 TYR 0.018 0.001 TYR B 205 ARG 0.004 0.000 ARG A 264 *********************** 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 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 286 GLU cc_start: 0.8142 (tp30) cc_final: 0.7722 (tt0) REVERT: A 396 THR cc_start: 0.8885 (t) cc_final: 0.8597 (m) REVERT: A 541 GLN cc_start: 0.8255 (tp40) cc_final: 0.8038 (tp40) REVERT: A 582 GLU cc_start: 0.7802 (mp0) cc_final: 0.7591 (mp0) REVERT: A 601 PHE cc_start: 0.7197 (m-80) cc_final: 0.6873 (m-80) REVERT: B 506 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7764 (mmtm) REVERT: B 541 GLN cc_start: 0.8018 (tp40) cc_final: 0.7787 (tp40) REVERT: B 601 PHE cc_start: 0.6603 (m-80) cc_final: 0.5911 (m-80) REVERT: B 697 HIS cc_start: 0.7282 (p90) cc_final: 0.6993 (p-80) outliers start: 11 outliers final: 9 residues processed: 115 average time/residue: 0.2076 time to fit residues: 34.4675 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 568 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 711 TRP Chi-restraints excluded: chain B residue 243 HIS 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 68 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1966 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= 0.179 Angle : 0.511 7.419 12708 Z= 0.269 Chirality : 0.039 0.197 1486 Planarity : 0.003 0.051 1614 Dihedral : 6.547 85.846 1319 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.20 % Allowed : 20.78 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.44 (0.25), residues: 1172 helix: 2.86 (0.18), residues: 778 sheet: 1.75 (0.75), residues: 48 loop : -1.50 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.011 0.001 HIS A 697 PHE 0.018 0.001 PHE A 394 TYR 0.018 0.001 TYR B 205 ARG 0.006 0.000 ARG A 253 ********************** 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 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 541 GLN cc_start: 0.8272 (tp40) cc_final: 0.8050 (tp40) REVERT: A 601 PHE cc_start: 0.7204 (m-80) cc_final: 0.6838 (m-80) REVERT: B 506 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7766 (mmtm) REVERT: B 541 GLN cc_start: 0.8014 (tp40) cc_final: 0.7801 (tp40) REVERT: B 601 PHE cc_start: 0.6609 (m-80) cc_final: 0.5909 (m-80) REVERT: B 697 HIS cc_start: 0.7308 (p90) cc_final: 0.7041 (p-80) outliers start: 12 outliers final: 12 residues processed: 107 average time/residue: 0.2036 time to fit residues: 32.0820 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 : 1.100 ------------------------------------------------------------------------------- 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 325 THR Chi-restraints excluded: chain A residue 343 ILE 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 147 LEU Chi-restraints excluded: chain B residue 243 HIS 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 28 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 39 optimal weight: 0.0370 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.4368 r_free = 0.4368 target = 0.197427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150126 restraints weight = 12283.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.153869 restraints weight = 6512.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156311 restraints weight = 4336.462| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9397 Z= 0.155 Angle : 0.493 7.458 12708 Z= 0.260 Chirality : 0.038 0.192 1486 Planarity : 0.003 0.051 1614 Dihedral : 6.459 87.495 1319 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.51 % Allowed : 20.58 % Favored : 77.91 % 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: 2.90 (0.18), residues: 778 sheet: 0.60 (0.66), residues: 74 loop : -1.47 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 711 HIS 0.014 0.002 HIS A 697 PHE 0.018 0.001 PHE A 394 TYR 0.018 0.001 TYR B 205 ARG 0.004 0.000 ARG B 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1833.39 seconds wall clock time: 34 minutes 26.81 seconds (2066.81 seconds total)