Starting phenix.real_space_refine on Mon May 4 10:05:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3m_41006/05_2026/8t3m_41006_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3m_41006/05_2026/8t3m_41006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t3m_41006/05_2026/8t3m_41006_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3m_41006/05_2026/8t3m_41006_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t3m_41006/05_2026/8t3m_41006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3m_41006/05_2026/8t3m_41006.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 72 5.16 5 Na 2 4.78 5 C 6719 2.51 5 N 1530 2.21 5 O 1765 1.98 5 H 10104 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20196 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 5077 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 298} Chain: "D" Number of atoms: 5048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 5048 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 5020 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 294} Chain breaks: 1 Chain: "C" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4929 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 289} Chain breaks: 2 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {' NA': 2, '85R': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.83, per 1000 atoms: 0.19 Number of scatterers: 20196 At special positions: 0 Unit cell: (111.89, 112.725, 85.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 72 16.00 P 4 15.00 Na 2 11.00 O 1765 8.00 N 1530 7.00 C 6719 6.00 H 10104 1.00 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: 1.88 Conformation dependent library (CDL) restraints added in 514.9 milliseconds 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.797A pdb=" N VAL A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.996A pdb=" N MET A 412 " --> pdb=" O ASN A 408 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 408 through 413' Processing helix chain 'A' and resid 415 through 454 removed outlier: 5.197A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 removed outlier: 3.554A pdb=" N LEU A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.671A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 536 through 552 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 559 through 574 Processing helix chain 'A' and resid 577 through 599 removed outlier: 4.118A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 629 removed outlier: 4.201A pdb=" N SER A 629 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 640 through 643 Processing helix chain 'A' and resid 655 through 684 Processing helix chain 'A' and resid 690 through 711 removed outlier: 4.274A pdb=" N ILE A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.621A pdb=" N LEU D 421 " --> pdb=" O PRO D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.503A pdb=" N TYR D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.539A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 5.748A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 655 through 681 removed outlier: 3.502A pdb=" N PHE D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 711 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 408 through 413 removed outlier: 4.190A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.513A pdb=" N ASN B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.627A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 removed outlier: 3.575A pdb=" N TYR B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.530A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 556 removed outlier: 4.809A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 576 through 599 removed outlier: 3.978A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 684 removed outlier: 4.048A pdb=" N PHE B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 711 removed outlier: 3.536A pdb=" N SER B 693 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.608A pdb=" N TYR C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 470 through 500 Processing helix chain 'C' and resid 510 through 531 Processing helix chain 'C' and resid 536 through 552 Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.695A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 5.506A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 628 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 655 through 686 Processing helix chain 'C' and resid 688 through 711 removed outlier: 3.978A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2133 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: 3.93 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10084 1.03 - 1.23: 142 1.23 - 1.43: 4351 1.43 - 1.62: 5729 1.62 - 1.82: 129 Bond restraints: 20435 Sorted by residual: bond pdb=" OAA NKN B 801 " pdb=" PAC NKN B 801 " ideal model delta sigma weight residual 1.667 1.455 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" OAB NKN D 801 " pdb=" PAC NKN D 801 " ideal model delta sigma weight residual 1.668 1.457 0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" OAB NKN C 801 " pdb=" PAC NKN C 801 " ideal model delta sigma weight residual 1.668 1.457 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" OAA NKN D 801 " pdb=" PAC NKN D 801 " ideal model delta sigma weight residual 1.667 1.457 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" OAA NKN C 801 " pdb=" PAC NKN C 801 " ideal model delta sigma weight residual 1.667 1.458 0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 20430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.24: 36716 10.24 - 20.47: 6 20.47 - 30.71: 7 30.71 - 40.94: 0 40.94 - 51.18: 3 Bond angle restraints: 36732 Sorted by residual: angle pdb=" OAA NKN C 801 " pdb=" PAC NKN C 801 " pdb=" OAB NKN C 801 " ideal model delta sigma weight residual 54.49 105.67 -51.18 3.00e+00 1.11e-01 2.91e+02 angle pdb=" OAA NKN D 801 " pdb=" PAC NKN D 801 " pdb=" OAB NKN D 801 " ideal model delta sigma weight residual 54.49 104.32 -49.83 3.00e+00 1.11e-01 2.76e+02 angle pdb=" OAA NKN B 801 " pdb=" PAC NKN B 801 " pdb=" OAB NKN B 801 " ideal model delta sigma weight residual 54.49 103.52 -49.03 3.00e+00 1.11e-01 2.67e+02 angle pdb=" OAB NKN C 801 " pdb=" PAC NKN C 801 " pdb=" OAD NKN C 801 " ideal model delta sigma weight residual 128.49 103.72 24.77 3.00e+00 1.11e-01 6.82e+01 angle pdb=" OAB NKN D 801 " pdb=" PAC NKN D 801 " pdb=" OAD NKN D 801 " ideal model delta sigma weight residual 128.49 104.28 24.21 3.00e+00 1.11e-01 6.51e+01 ... (remaining 36727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.61: 9337 33.61 - 67.21: 338 67.21 - 100.82: 27 100.82 - 134.42: 8 134.42 - 168.03: 8 Dihedral angle restraints: 9718 sinusoidal: 5133 harmonic: 4585 Sorted by residual: dihedral pdb=" CD ARG C 579 " pdb=" NE ARG C 579 " pdb=" CZ ARG C 579 " pdb=" NH1 ARG C 579 " ideal model delta sinusoidal sigma weight residual 0.00 74.79 -74.79 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CD ARG B 420 " pdb=" NE ARG B 420 " pdb=" CZ ARG B 420 " pdb=" NH1 ARG B 420 " ideal model delta sinusoidal sigma weight residual 0.00 -61.09 61.09 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" C3 85R A 801 " pdb=" C1 85R A 801 " pdb=" C2 85R A 801 " pdb=" O1 85R A 801 " ideal model delta sinusoidal sigma weight residual 270.74 102.71 168.03 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 9715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 1560 1.006 - 2.013: 0 2.013 - 3.019: 0 3.019 - 4.026: 0 4.026 - 5.032: 7 Chirality restraints: 1567 Sorted by residual: chirality pdb=" C4 85R A 801 " pdb=" C3 85R A 801 " pdb=" C5 85R A 801 " pdb=" O4 85R A 801 " both_signs ideal model delta sigma weight residual False -2.48 2.55 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C5 85R A 801 " pdb=" C4 85R A 801 " pdb=" C6 85R A 801 " pdb=" O5 85R A 801 " both_signs ideal model delta sigma weight residual False 2.48 -2.49 4.97 2.00e-01 2.50e+01 6.17e+02 chirality pdb=" C3 85R A 801 " pdb=" C2 85R A 801 " pdb=" C4 85R A 801 " pdb=" O3 85R A 801 " both_signs ideal model delta sigma weight residual False 2.48 -2.48 4.95 2.00e-01 2.50e+01 6.13e+02 ... (remaining 1564 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 409 " -0.904 9.50e-02 1.11e+02 4.63e-01 2.88e+03 pdb=" NE ARG C 409 " -0.303 2.00e-02 2.50e+03 pdb=" CZ ARG C 409 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG C 409 " 0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG C 409 " 0.038 2.00e-02 2.50e+03 pdb="HH11 ARG C 409 " 0.356 2.00e-02 2.50e+03 pdb="HH12 ARG C 409 " -0.175 2.00e-02 2.50e+03 pdb="HH21 ARG C 409 " 0.725 2.00e-02 2.50e+03 pdb="HH22 ARG C 409 " -0.575 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 428 " 0.156 9.50e-02 1.11e+02 2.13e-01 9.64e+02 pdb=" NE ARG A 428 " -0.111 2.00e-02 2.50e+03 pdb=" CZ ARG A 428 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG A 428 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG A 428 " 0.051 2.00e-02 2.50e+03 pdb="HH11 ARG A 428 " 0.373 2.00e-02 2.50e+03 pdb="HH12 ARG A 428 " -0.412 2.00e-02 2.50e+03 pdb="HH21 ARG A 428 " -0.074 2.00e-02 2.50e+03 pdb="HH22 ARG A 428 " 0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 499 " -0.537 9.50e-02 1.11e+02 2.35e-01 5.54e+02 pdb=" NE ARG A 499 " -0.126 2.00e-02 2.50e+03 pdb=" CZ ARG A 499 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A 499 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 499 " 0.036 2.00e-02 2.50e+03 pdb="HH11 ARG A 499 " 0.317 2.00e-02 2.50e+03 pdb="HH12 ARG A 499 " -0.287 2.00e-02 2.50e+03 pdb="HH21 ARG A 499 " 0.065 2.00e-02 2.50e+03 pdb="HH22 ARG A 499 " 0.056 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2031 2.23 - 2.82: 44143 2.82 - 3.42: 54043 3.42 - 4.01: 69771 4.01 - 4.60: 107287 Nonbonded interactions: 277275 Sorted by model distance: nonbonded pdb=" O PHE B 638 " pdb=" H THR B 641 " model vdw 1.640 2.450 nonbonded pdb=" OD1 ASP B 654 " pdb=" H PHE B 655 " model vdw 1.659 2.450 nonbonded pdb=" OE1 GLU C 416 " pdb=" H GLU C 416 " model vdw 1.671 2.450 nonbonded pdb=" OH TYR C 401 " pdb=" HZ3 LYS C 710 " model vdw 1.681 2.450 nonbonded pdb=" O ASN C 551 " pdb=" H TYR C 554 " model vdw 1.697 2.450 ... (remaining 277270 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 384 through 456 or resid 461 through 463 or resid 469 thro \ ugh 711)) selection = (chain 'B' and (resid 384 through 463 or resid 469 through 711)) selection = (chain 'C' and resid 384 through 711) selection = (chain 'D' and (resid 384 through 456 or resid 461 through 463 or resid 469 thro \ ugh 711)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.450 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: 0.080 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.260 Find NCS groups from input model: 0.330 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.008 0.212 10331 Z= 0.430 Angle : 1.266 51.179 13943 Z= 0.631 Chirality : 0.328 5.032 1567 Planarity : 0.018 0.466 1680 Dihedral : 19.018 168.026 3813 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.18 % Allowed : 2.36 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1189 helix: 1.68 (0.18), residues: 877 sheet: None (None), residues: 0 loop : -2.34 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 579 TYR 0.025 0.001 TYR D 584 PHE 0.012 0.001 PHE B 522 TRP 0.013 0.001 TRP D 697 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00763 (10331) covalent geometry : angle 1.26599 (13943) hydrogen bonds : bond 0.11371 ( 720) hydrogen bonds : angle 5.13281 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 375 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8489 (m-30) cc_final: 0.8268 (m-30) REVERT: A 419 ASN cc_start: 0.7691 (t0) cc_final: 0.7454 (t0) REVERT: A 446 ILE cc_start: 0.8313 (mm) cc_final: 0.8006 (mt) REVERT: A 682 MET cc_start: 0.5022 (tmm) cc_final: 0.4814 (tmm) REVERT: A 691 GLN cc_start: 0.7200 (tt0) cc_final: 0.6894 (tt0) REVERT: A 707 ASP cc_start: 0.7420 (m-30) cc_final: 0.6871 (m-30) REVERT: D 420 ARG cc_start: 0.7622 (mmt180) cc_final: 0.7393 (mmt90) REVERT: D 432 ARG cc_start: 0.8051 (ttt180) cc_final: 0.7808 (ttm-80) REVERT: D 555 TYR cc_start: 0.8300 (m-80) cc_final: 0.8036 (m-80) REVERT: D 627 TYR cc_start: 0.8559 (m-80) cc_final: 0.8306 (m-80) REVERT: D 677 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6735 (tmm) REVERT: B 438 PHE cc_start: 0.8340 (t80) cc_final: 0.8003 (t80) REVERT: B 571 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8724 (ttpt) REVERT: C 420 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7050 (mtp85) REVERT: C 455 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7480 (ttp-170) REVERT: C 498 GLN cc_start: 0.7500 (mt0) cc_final: 0.7211 (tp40) REVERT: C 512 SER cc_start: 0.8123 (p) cc_final: 0.7476 (t) REVERT: C 513 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7308 (mm-30) REVERT: C 682 MET cc_start: 0.6774 (tmm) cc_final: 0.6333 (ttm) outliers start: 13 outliers final: 5 residues processed: 381 average time/residue: 0.2183 time to fit residues: 117.6164 Evaluate side-chains 301 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 295 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132431 restraints weight = 41754.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136973 restraints weight = 18888.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.139844 restraints weight = 11386.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141704 restraints weight = 8146.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142912 restraints weight = 6405.343| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10331 Z= 0.151 Angle : 0.578 11.996 13943 Z= 0.305 Chirality : 0.037 0.330 1567 Planarity : 0.004 0.059 1680 Dihedral : 11.299 117.087 1493 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.36 % Allowed : 11.36 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1189 helix: 2.08 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -1.90 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 409 TYR 0.017 0.001 TYR A 627 PHE 0.013 0.001 PHE B 489 TRP 0.009 0.001 TRP D 697 HIS 0.005 0.002 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00329 (10331) covalent geometry : angle 0.57792 (13943) hydrogen bonds : bond 0.04711 ( 720) hydrogen bonds : angle 4.13153 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 312 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 ASN cc_start: 0.7660 (t0) cc_final: 0.7433 (t0) REVERT: A 446 ILE cc_start: 0.8380 (mm) cc_final: 0.8132 (mt) REVERT: D 394 SER cc_start: 0.7377 (p) cc_final: 0.6957 (m) REVERT: D 409 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7567 (ttp-110) REVERT: D 432 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7782 (ttm-80) REVERT: B 438 PHE cc_start: 0.8259 (t80) cc_final: 0.7927 (t80) REVERT: B 571 LYS cc_start: 0.8996 (ttpp) cc_final: 0.8787 (ttpt) REVERT: C 420 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.7075 (mtp85) REVERT: C 498 GLN cc_start: 0.7648 (mt0) cc_final: 0.7246 (tp40) REVERT: C 536 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7332 (mt-10) REVERT: C 601 ASP cc_start: 0.7464 (p0) cc_final: 0.7211 (p0) REVERT: C 682 MET cc_start: 0.6990 (tmm) cc_final: 0.6434 (ttm) outliers start: 15 outliers final: 12 residues processed: 321 average time/residue: 0.2090 time to fit residues: 96.7768 Evaluate side-chains 289 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 277 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 105 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 63 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 GLN D 423 GLN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131171 restraints weight = 42120.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135807 restraints weight = 18563.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138726 restraints weight = 10984.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140551 restraints weight = 7720.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141751 restraints weight = 6054.658| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10331 Z= 0.142 Angle : 0.519 8.337 13943 Z= 0.283 Chirality : 0.035 0.202 1567 Planarity : 0.003 0.037 1680 Dihedral : 10.509 147.867 1484 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.82 % Allowed : 13.00 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.25), residues: 1189 helix: 2.17 (0.17), residues: 881 sheet: None (None), residues: 0 loop : -1.69 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 557 TYR 0.018 0.001 TYR D 495 PHE 0.008 0.001 PHE B 659 TRP 0.007 0.001 TRP C 426 HIS 0.004 0.002 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00310 (10331) covalent geometry : angle 0.51875 (13943) hydrogen bonds : bond 0.04537 ( 720) hydrogen bonds : angle 4.02504 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 303 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ILE cc_start: 0.8390 (mm) cc_final: 0.8171 (mt) REVERT: A 574 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8597 (mp) REVERT: D 394 SER cc_start: 0.7413 (p) cc_final: 0.6951 (m) REVERT: D 432 ARG cc_start: 0.8137 (ttt180) cc_final: 0.7702 (ttm-80) REVERT: D 555 TYR cc_start: 0.8466 (m-80) cc_final: 0.7402 (m-80) REVERT: B 438 PHE cc_start: 0.8175 (t80) cc_final: 0.7804 (t80) REVERT: B 628 ASN cc_start: 0.7837 (t0) cc_final: 0.7585 (t0) REVERT: C 498 GLN cc_start: 0.7785 (mt0) cc_final: 0.7308 (tp40) REVERT: C 512 SER cc_start: 0.8100 (p) cc_final: 0.7389 (t) REVERT: C 523 MET cc_start: 0.8080 (tpp) cc_final: 0.7716 (tpt) REVERT: C 682 MET cc_start: 0.6886 (tmm) cc_final: 0.6379 (ttm) outliers start: 31 outliers final: 26 residues processed: 322 average time/residue: 0.1939 time to fit residues: 90.8393 Evaluate side-chains 305 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 110 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 700 GLN C 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.150645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130365 restraints weight = 41998.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135064 restraints weight = 18605.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138014 restraints weight = 11008.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139894 restraints weight = 7775.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141132 restraints weight = 6085.113| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10331 Z= 0.152 Angle : 0.527 8.635 13943 Z= 0.288 Chirality : 0.035 0.223 1567 Planarity : 0.003 0.042 1680 Dihedral : 10.049 147.302 1484 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.73 % Allowed : 15.00 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1189 helix: 2.23 (0.17), residues: 881 sheet: None (None), residues: 0 loop : -1.66 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 557 TYR 0.014 0.001 TYR A 627 PHE 0.014 0.001 PHE B 489 TRP 0.006 0.001 TRP C 426 HIS 0.004 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00337 (10331) covalent geometry : angle 0.52682 (13943) hydrogen bonds : bond 0.04550 ( 720) hydrogen bonds : angle 4.02718 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8584 (mp) REVERT: D 394 SER cc_start: 0.7403 (p) cc_final: 0.6969 (m) REVERT: D 432 ARG cc_start: 0.8129 (ttt180) cc_final: 0.7719 (ttm-80) REVERT: D 555 TYR cc_start: 0.8443 (m-80) cc_final: 0.7424 (m-80) REVERT: D 582 PHE cc_start: 0.5635 (m-10) cc_final: 0.5417 (m-10) REVERT: D 677 MET cc_start: 0.7357 (tmm) cc_final: 0.6793 (ttt) REVERT: B 438 PHE cc_start: 0.8189 (t80) cc_final: 0.7827 (t80) REVERT: B 656 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7344 (mtpt) REVERT: C 420 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7087 (mtp85) REVERT: C 498 GLN cc_start: 0.7790 (mt0) cc_final: 0.7329 (tp40) REVERT: C 512 SER cc_start: 0.8126 (p) cc_final: 0.7420 (t) REVERT: C 682 MET cc_start: 0.6878 (tmm) cc_final: 0.6384 (ttm) outliers start: 30 outliers final: 27 residues processed: 306 average time/residue: 0.1998 time to fit residues: 88.0287 Evaluate side-chains 311 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 628 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130065 restraints weight = 42097.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.134727 restraints weight = 18704.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137629 restraints weight = 11137.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139488 restraints weight = 7861.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140610 restraints weight = 6156.437| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10331 Z= 0.163 Angle : 0.525 6.519 13943 Z= 0.291 Chirality : 0.036 0.243 1567 Planarity : 0.003 0.034 1680 Dihedral : 9.916 158.254 1484 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.36 % Allowed : 15.00 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.26), residues: 1189 helix: 2.17 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -1.58 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 557 TYR 0.016 0.001 TYR B 555 PHE 0.009 0.001 PHE B 659 TRP 0.007 0.001 TRP C 426 HIS 0.005 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00363 (10331) covalent geometry : angle 0.52535 (13943) hydrogen bonds : bond 0.04688 ( 720) hydrogen bonds : angle 4.04631 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 394 SER cc_start: 0.7422 (p) cc_final: 0.7019 (m) REVERT: D 432 ARG cc_start: 0.8128 (ttt180) cc_final: 0.7727 (ttm-80) REVERT: D 677 MET cc_start: 0.7507 (tmm) cc_final: 0.6948 (ttt) REVERT: B 420 ARG cc_start: 0.7524 (ppt170) cc_final: 0.7152 (ptm-80) REVERT: B 438 PHE cc_start: 0.8205 (t80) cc_final: 0.7909 (t80) REVERT: B 656 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7381 (mttt) REVERT: C 420 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.7046 (mtp85) REVERT: C 498 GLN cc_start: 0.7790 (mt0) cc_final: 0.7334 (tp40) REVERT: C 512 SER cc_start: 0.8232 (p) cc_final: 0.7616 (t) REVERT: C 682 MET cc_start: 0.6903 (tmm) cc_final: 0.6419 (ttm) outliers start: 37 outliers final: 31 residues processed: 314 average time/residue: 0.2148 time to fit residues: 95.9085 Evaluate side-chains 313 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.153914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133454 restraints weight = 41780.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138412 restraints weight = 17490.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141475 restraints weight = 10080.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.143441 restraints weight = 6975.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144726 restraints weight = 5396.699| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10331 Z= 0.155 Angle : 0.516 5.779 13943 Z= 0.287 Chirality : 0.035 0.207 1567 Planarity : 0.003 0.028 1680 Dihedral : 10.147 176.769 1484 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.36 % Allowed : 16.73 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.26), residues: 1189 helix: 2.23 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -1.62 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 409 TYR 0.015 0.001 TYR B 555 PHE 0.014 0.001 PHE B 489 TRP 0.007 0.001 TRP C 426 HIS 0.004 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00343 (10331) covalent geometry : angle 0.51595 (13943) hydrogen bonds : bond 0.04585 ( 720) hydrogen bonds : angle 4.01898 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 289 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 394 SER cc_start: 0.7360 (p) cc_final: 0.6939 (m) REVERT: D 432 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7727 (ttm-80) REVERT: D 677 MET cc_start: 0.7468 (tmm) cc_final: 0.6951 (ttt) REVERT: B 420 ARG cc_start: 0.7464 (ppt170) cc_final: 0.7121 (ptm-80) REVERT: B 438 PHE cc_start: 0.8220 (t80) cc_final: 0.7928 (t80) REVERT: C 498 GLN cc_start: 0.7774 (mt0) cc_final: 0.7351 (tp40) REVERT: C 568 MET cc_start: 0.8139 (mtp) cc_final: 0.7918 (mtm) REVERT: C 682 MET cc_start: 0.6760 (tmm) cc_final: 0.6290 (ttm) outliers start: 37 outliers final: 32 residues processed: 309 average time/residue: 0.2169 time to fit residues: 95.3705 Evaluate side-chains 311 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134541 restraints weight = 41633.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139495 restraints weight = 17488.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.142527 restraints weight = 10037.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.144470 restraints weight = 6960.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145784 restraints weight = 5382.652| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10331 Z= 0.170 Angle : 0.533 6.374 13943 Z= 0.295 Chirality : 0.035 0.161 1567 Planarity : 0.003 0.028 1680 Dihedral : 9.733 166.882 1484 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.27 % Allowed : 17.27 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.26), residues: 1189 helix: 2.16 (0.17), residues: 883 sheet: None (None), residues: 0 loop : -1.66 (0.40), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.016 0.001 TYR B 555 PHE 0.011 0.001 PHE B 489 TRP 0.008 0.001 TRP C 426 HIS 0.005 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00379 (10331) covalent geometry : angle 0.53323 (13943) hydrogen bonds : bond 0.04733 ( 720) hydrogen bonds : angle 4.07841 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 LEU cc_start: 0.8906 (mm) cc_final: 0.8655 (mm) REVERT: D 394 SER cc_start: 0.7376 (p) cc_final: 0.6938 (m) REVERT: D 432 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7731 (ttm-80) REVERT: D 463 TYR cc_start: 0.7138 (m-80) cc_final: 0.6818 (m-10) REVERT: B 420 ARG cc_start: 0.7471 (ppt170) cc_final: 0.7185 (ptm-80) REVERT: B 438 PHE cc_start: 0.8236 (t80) cc_final: 0.7900 (t80) REVERT: B 513 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: C 420 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.7036 (mtp85) REVERT: C 498 GLN cc_start: 0.7767 (mt0) cc_final: 0.7352 (tp40) REVERT: C 512 SER cc_start: 0.8224 (p) cc_final: 0.7598 (t) REVERT: C 568 MET cc_start: 0.8120 (mtp) cc_final: 0.7915 (mtm) REVERT: C 579 ARG cc_start: 0.7000 (mtp180) cc_final: 0.6761 (ttt180) REVERT: C 682 MET cc_start: 0.6735 (tmm) cc_final: 0.6316 (ttm) outliers start: 36 outliers final: 30 residues processed: 307 average time/residue: 0.2105 time to fit residues: 92.5524 Evaluate side-chains 308 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN B 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129511 restraints weight = 42204.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134189 restraints weight = 18653.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.137099 restraints weight = 11076.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138951 restraints weight = 7846.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.140109 restraints weight = 6170.394| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10331 Z= 0.160 Angle : 0.527 5.944 13943 Z= 0.291 Chirality : 0.035 0.157 1567 Planarity : 0.003 0.028 1680 Dihedral : 9.296 159.583 1482 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.36 % Allowed : 17.91 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.26), residues: 1189 helix: 2.27 (0.17), residues: 877 sheet: None (None), residues: 0 loop : -1.69 (0.40), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.016 0.001 TYR B 555 PHE 0.010 0.001 PHE B 489 TRP 0.007 0.001 TRP C 426 HIS 0.004 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00355 (10331) covalent geometry : angle 0.52742 (13943) hydrogen bonds : bond 0.04643 ( 720) hydrogen bonds : angle 4.02461 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 LEU cc_start: 0.8970 (mm) cc_final: 0.8725 (mm) REVERT: D 394 SER cc_start: 0.7381 (p) cc_final: 0.6950 (m) REVERT: D 432 ARG cc_start: 0.8072 (ttt180) cc_final: 0.7784 (ttm-80) REVERT: D 463 TYR cc_start: 0.7157 (m-80) cc_final: 0.6846 (m-10) REVERT: B 420 ARG cc_start: 0.7379 (ppt170) cc_final: 0.7140 (ptm-80) REVERT: B 438 PHE cc_start: 0.8249 (t80) cc_final: 0.7925 (t80) REVERT: B 513 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: C 420 ARG cc_start: 0.7376 (ttm-80) cc_final: 0.7009 (mtp85) REVERT: C 498 GLN cc_start: 0.7734 (mt0) cc_final: 0.7358 (tp40) REVERT: C 512 SER cc_start: 0.8204 (p) cc_final: 0.7620 (t) REVERT: C 579 ARG cc_start: 0.7040 (mtp180) cc_final: 0.6830 (ttt180) REVERT: C 682 MET cc_start: 0.6555 (tmm) cc_final: 0.6173 (ttm) outliers start: 37 outliers final: 31 residues processed: 303 average time/residue: 0.2176 time to fit residues: 93.7297 Evaluate side-chains 310 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 104 optimal weight: 0.3980 chunk 116 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN D 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.152291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.131193 restraints weight = 41971.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.136247 restraints weight = 17682.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.139367 restraints weight = 10222.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141337 restraints weight = 7115.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142465 restraints weight = 5532.152| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10331 Z= 0.123 Angle : 0.505 6.208 13943 Z= 0.275 Chirality : 0.034 0.145 1567 Planarity : 0.003 0.027 1680 Dihedral : 8.977 159.142 1482 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.45 % Allowed : 19.18 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.26), residues: 1189 helix: 2.44 (0.17), residues: 879 sheet: None (None), residues: 0 loop : -1.56 (0.40), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 455 TYR 0.012 0.001 TYR B 555 PHE 0.010 0.001 PHE B 489 TRP 0.006 0.001 TRP A 697 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00272 (10331) covalent geometry : angle 0.50529 (13943) hydrogen bonds : bond 0.04215 ( 720) hydrogen bonds : angle 3.91143 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 LEU cc_start: 0.8876 (mm) cc_final: 0.8606 (mm) REVERT: D 394 SER cc_start: 0.7344 (p) cc_final: 0.6919 (m) REVERT: D 432 ARG cc_start: 0.8130 (ttt180) cc_final: 0.7725 (ttm-80) REVERT: D 463 TYR cc_start: 0.7156 (m-80) cc_final: 0.6838 (m-10) REVERT: B 420 ARG cc_start: 0.7479 (ppt170) cc_final: 0.7212 (ptm-80) REVERT: B 438 PHE cc_start: 0.8180 (t80) cc_final: 0.7885 (t80) REVERT: B 513 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: B 600 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7862 (mm-30) REVERT: C 420 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.7033 (mtp85) REVERT: C 498 GLN cc_start: 0.7782 (mt0) cc_final: 0.7323 (tp40) REVERT: C 579 ARG cc_start: 0.6978 (mtp180) cc_final: 0.6751 (ttt180) REVERT: C 682 MET cc_start: 0.6576 (tmm) cc_final: 0.6175 (ttm) REVERT: C 707 ASP cc_start: 0.7059 (t0) cc_final: 0.6836 (m-30) outliers start: 27 outliers final: 25 residues processed: 305 average time/residue: 0.2229 time to fit residues: 97.0808 Evaluate side-chains 310 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 29 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.0170 chunk 72 optimal weight: 0.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.150875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130561 restraints weight = 41835.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.135262 restraints weight = 18586.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138148 restraints weight = 11054.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139928 restraints weight = 7837.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141183 restraints weight = 6224.418| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10331 Z= 0.148 Angle : 0.526 5.903 13943 Z= 0.289 Chirality : 0.035 0.148 1567 Planarity : 0.003 0.027 1680 Dihedral : 8.945 156.304 1482 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.82 % Allowed : 18.91 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.26), residues: 1189 helix: 2.35 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -1.66 (0.40), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.017 0.001 TYR D 495 PHE 0.010 0.001 PHE B 489 TRP 0.007 0.001 TRP C 426 HIS 0.004 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00330 (10331) covalent geometry : angle 0.52615 (13943) hydrogen bonds : bond 0.04431 ( 720) hydrogen bonds : angle 3.96918 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 LEU cc_start: 0.8897 (mm) cc_final: 0.8638 (mm) REVERT: D 394 SER cc_start: 0.7373 (p) cc_final: 0.6949 (m) REVERT: D 432 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7740 (ttm-80) REVERT: D 463 TYR cc_start: 0.7157 (m-80) cc_final: 0.6825 (m-10) REVERT: B 420 ARG cc_start: 0.7439 (ppt170) cc_final: 0.7182 (ptm-80) REVERT: B 438 PHE cc_start: 0.8213 (t80) cc_final: 0.7899 (t80) REVERT: B 513 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: B 600 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7911 (mm-30) REVERT: C 420 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7034 (mtp85) REVERT: C 498 GLN cc_start: 0.7763 (mt0) cc_final: 0.7355 (tp40) REVERT: C 512 SER cc_start: 0.8216 (p) cc_final: 0.7597 (t) REVERT: C 579 ARG cc_start: 0.6968 (mtp180) cc_final: 0.6763 (ttt180) REVERT: C 603 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7565 (ptpt) REVERT: C 682 MET cc_start: 0.6551 (tmm) cc_final: 0.6195 (ttm) outliers start: 31 outliers final: 26 residues processed: 302 average time/residue: 0.2155 time to fit residues: 92.7893 Evaluate side-chains 311 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 84 optimal weight: 0.0060 chunk 117 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.155851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.134796 restraints weight = 41524.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.139927 restraints weight = 17359.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143094 restraints weight = 9995.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.145070 restraints weight = 6914.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.146414 restraints weight = 5347.831| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10331 Z= 0.124 Angle : 0.509 5.892 13943 Z= 0.277 Chirality : 0.034 0.142 1567 Planarity : 0.003 0.026 1680 Dihedral : 8.828 157.540 1482 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.27 % Allowed : 19.45 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.26), residues: 1189 helix: 2.45 (0.17), residues: 877 sheet: None (None), residues: 0 loop : -1.56 (0.40), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.017 0.001 TYR D 495 PHE 0.008 0.001 PHE B 659 TRP 0.006 0.001 TRP A 697 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00276 (10331) covalent geometry : angle 0.50906 (13943) hydrogen bonds : bond 0.04144 ( 720) hydrogen bonds : angle 3.90707 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3633.33 seconds wall clock time: 62 minutes 37.82 seconds (3757.82 seconds total)