Starting phenix.real_space_refine on Sat Jul 4 10:55:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3m_41006/07_2026/8t3m_41006_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3m_41006/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3m_41006/07_2026/8t3m_41006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3m_41006/07_2026/8t3m_41006.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3m_41006/07_2026/8t3m_41006_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3m_41006/07_2026/8t3m_41006_trim.cif" } 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-dev-6108/lib/python3.11/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, 45 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'85R': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.51, per 1000 atoms: 0.17 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: 2.38 Conformation dependent library (CDL) restraints added in 736.6 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: 0.37 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: 4.47 Time building geometry restraints manager: 3.13 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: 5.570 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.370 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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/Z covalent geometry : bond 0.00763 / 0.43 (10331) covalent geometry : angle 1.26599 / 0.63 (13943) hydrogen bonds : bond 0.11371 / 7.52 ( 720) hydrogen bonds : angle 5.13281 / 3.63 ( 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: 0.2012 time to fit residues: 109.1843 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 : 0.340 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.152155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.132230 restraints weight = 41830.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136736 restraints weight = 18873.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.139615 restraints weight = 11386.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141419 restraints weight = 8099.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142599 restraints weight = 6410.131| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2203 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= 0.160 Angle : 0.584 13.897 13943 Z= 0.307 Chirality : 0.037 0.481 1567 Planarity : 0.004 0.056 1680 Dihedral : 11.126 117.266 1493 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.36 % Allowed : 11.27 % Favored : 87.36 % 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: 1.64 (0.25), residues: 1189 helix: 2.06 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -1.91 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 499 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/Z covalent geometry : bond 0.00347 / 0.16 (10331) covalent geometry : angle 0.58446 / 0.31 (13943) hydrogen bonds : bond 0.04805 / 3.15 ( 720) hydrogen bonds : angle 4.14854 / 2.93 ( 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 331 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 316 time to evaluate : 0.588 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 446 ILE cc_start: 0.8391 (mm) cc_final: 0.8146 (mt) REVERT: A 691 GLN cc_start: 0.7118 (tt0) cc_final: 0.6911 (tt0) REVERT: D 394 SER cc_start: 0.7396 (p) cc_final: 0.6959 (m) REVERT: D 409 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7579 (ttp-110) REVERT: D 432 ARG cc_start: 0.8062 (ttt180) cc_final: 0.7784 (ttm-80) REVERT: B 438 PHE cc_start: 0.8268 (t80) cc_final: 0.7938 (t80) REVERT: B 571 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8788 (ttpt) REVERT: C 420 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7076 (mtp85) REVERT: C 498 GLN cc_start: 0.7646 (mt0) cc_final: 0.7248 (tp40) REVERT: C 536 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7342 (mt-10) REVERT: C 601 ASP cc_start: 0.7482 (p0) cc_final: 0.7190 (p0) REVERT: C 682 MET cc_start: 0.6930 (tmm) cc_final: 0.6387 (ttm) outliers start: 15 outliers final: 12 residues processed: 325 average time/residue: 0.2015 time to fit residues: 94.3157 Evaluate side-chains 293 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 281 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 423 GLN ** C 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.149878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129860 restraints weight = 42279.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134445 restraints weight = 18574.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137303 restraints weight = 11014.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139127 restraints weight = 7807.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.140172 restraints weight = 6127.564| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10331 Z= 0.159 Angle : 0.528 8.164 13943 Z= 0.291 Chirality : 0.035 0.198 1567 Planarity : 0.003 0.040 1680 Dihedral : 10.653 152.786 1484 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.73 % Allowed : 13.00 % Favored : 84.27 % 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: 1.73 (0.25), residues: 1189 helix: 2.09 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -1.76 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 557 TYR 0.015 0.001 TYR D 495 PHE 0.009 0.001 PHE B 522 TRP 0.007 0.001 TRP C 426 HIS 0.004 0.002 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (10331) covalent geometry : angle 0.52773 / 0.29 (13943) hydrogen bonds : bond 0.04740 / 3.12 ( 720) hydrogen bonds : angle 4.07636 / 2.87 ( 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 332 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 302 time to evaluate : 0.713 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 446 ILE cc_start: 0.8468 (mm) cc_final: 0.8252 (mt) REVERT: A 574 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8569 (mp) REVERT: D 394 SER cc_start: 0.7426 (p) cc_final: 0.6986 (m) REVERT: D 432 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7762 (ttm-80) REVERT: D 555 TYR cc_start: 0.8466 (m-80) cc_final: 0.7460 (m-80) REVERT: B 438 PHE cc_start: 0.8265 (t80) cc_final: 0.7882 (t80) REVERT: B 628 ASN cc_start: 0.7851 (t0) cc_final: 0.7606 (t0) REVERT: C 498 GLN cc_start: 0.7747 (mt0) cc_final: 0.7311 (tp40) REVERT: C 512 SER cc_start: 0.8145 (p) cc_final: 0.7507 (t) REVERT: C 523 MET cc_start: 0.8040 (tpp) cc_final: 0.7727 (tpt) REVERT: C 576 ASP cc_start: 0.8189 (m-30) cc_final: 0.7986 (m-30) REVERT: C 682 MET cc_start: 0.6890 (tmm) cc_final: 0.6393 (ttm) outliers start: 30 outliers final: 27 residues processed: 322 average time/residue: 0.1903 time to fit residues: 89.7753 Evaluate side-chains 302 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 553 LEU 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 494 GLN Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 634 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 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: 0.9990 chunk 41 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3678 r_free = 0.3678 target = 0.152062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131455 restraints weight = 41855.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136280 restraints weight = 17958.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139313 restraints weight = 10496.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141152 restraints weight = 7344.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142427 restraints weight = 5782.436| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3137 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= 0.141 Angle : 0.515 8.586 13943 Z= 0.282 Chirality : 0.035 0.221 1567 Planarity : 0.003 0.034 1680 Dihedral : 10.003 154.464 1484 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.00 % Allowed : 15.18 % Favored : 81.82 % 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 : -1.63 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 557 TYR 0.013 0.001 TYR D 495 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/Z covalent geometry : bond 0.00309 / 0.14 (10331) covalent geometry : angle 0.51482 / 0.28 (13943) hydrogen bonds : bond 0.04491 / 2.95 ( 720) hydrogen bonds : angle 4.01080 / 2.82 ( 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 325 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 0.534 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: A 574 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8592 (mp) REVERT: D 394 SER cc_start: 0.7422 (p) cc_final: 0.6972 (m) REVERT: D 432 ARG cc_start: 0.8149 (ttt180) cc_final: 0.7707 (ttm-80) REVERT: D 555 TYR cc_start: 0.8431 (m-80) cc_final: 0.7405 (m-80) REVERT: B 438 PHE cc_start: 0.8174 (t80) cc_final: 0.7863 (t80) REVERT: C 420 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7093 (mtp85) REVERT: C 498 GLN cc_start: 0.7809 (mt0) cc_final: 0.7329 (tp40) REVERT: C 512 SER cc_start: 0.8152 (p) cc_final: 0.7442 (t) REVERT: C 536 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7447 (mt-10) REVERT: C 576 ASP cc_start: 0.8304 (m-30) cc_final: 0.8028 (m-30) REVERT: C 651 GLU cc_start: 0.6398 (tp30) cc_final: 0.6186 (tp30) REVERT: C 682 MET cc_start: 0.6871 (tmm) cc_final: 0.6382 (ttm) outliers start: 33 outliers final: 29 residues processed: 312 average time/residue: 0.1976 time to fit residues: 88.8305 Evaluate side-chains 321 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 547 MET Chi-restraints excluded: chain D residue 573 ILE 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 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 556 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130177 restraints weight = 42073.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134810 restraints weight = 18770.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137709 restraints weight = 11241.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.139566 restraints weight = 7958.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140788 restraints weight = 6255.090| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10331 Z= 0.162 Angle : 0.522 7.810 13943 Z= 0.289 Chirality : 0.035 0.227 1567 Planarity : 0.003 0.034 1680 Dihedral : 10.145 170.129 1484 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.00 % Allowed : 15.91 % Favored : 81.09 % 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: 1.89 (0.26), residues: 1189 helix: 2.19 (0.17), residues: 881 sheet: None (None), residues: 0 loop : -1.65 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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/Z covalent geometry : bond 0.00361 / 0.16 (10331) covalent geometry : angle 0.52157 / 0.29 (13943) hydrogen bonds : bond 0.04643 / 3.06 ( 720) hydrogen bonds : angle 4.03883 / 2.83 ( 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 323 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 290 time to evaluate : 0.570 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: A 636 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6958 (mt-10) REVERT: D 394 SER cc_start: 0.7390 (p) cc_final: 0.6946 (m) REVERT: D 432 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7734 (ttm-80) REVERT: D 463 TYR cc_start: 0.7065 (m-80) cc_final: 0.6657 (m-10) REVERT: D 677 MET cc_start: 0.7447 (tmm) cc_final: 0.6899 (ttt) REVERT: B 438 PHE cc_start: 0.8225 (t80) cc_final: 0.7921 (t80) REVERT: B 656 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7375 (mttt) REVERT: C 420 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.7067 (mtp85) REVERT: C 498 GLN cc_start: 0.7777 (mt0) cc_final: 0.7342 (tp40) REVERT: C 576 ASP cc_start: 0.8325 (m-30) cc_final: 0.8111 (m-30) REVERT: C 682 MET cc_start: 0.6846 (tmm) cc_final: 0.6375 (ttm) outliers start: 33 outliers final: 28 residues processed: 311 average time/residue: 0.2103 time to fit residues: 94.4109 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 : 0.525 ------------------------------------------------------------------------------- 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 570 GLU 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 553 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 THR 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: 0.9980 chunk 49 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 78 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.151555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131145 restraints weight = 41972.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135879 restraints weight = 18886.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138823 restraints weight = 11251.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140648 restraints weight = 7993.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141834 restraints weight = 6311.953| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10331 Z= 0.134 Angle : 0.500 7.732 13943 Z= 0.275 Chirality : 0.034 0.159 1567 Planarity : 0.003 0.028 1680 Dihedral : 9.873 175.553 1484 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.36 % Allowed : 16.36 % Favored : 80.27 % 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: 2.09 (0.26), residues: 1189 helix: 2.36 (0.17), residues: 877 sheet: None (None), residues: 0 loop : -1.61 (0.39), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 409 TYR 0.016 0.001 TYR D 495 PHE 0.013 0.001 PHE B 489 TRP 0.006 0.001 TRP C 426 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10331) covalent geometry : angle 0.50041 / 0.27 (13943) hydrogen bonds : bond 0.04338 / 2.86 ( 720) hydrogen bonds : angle 3.94276 / 2.77 ( 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 334 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 0.563 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 523 MET cc_start: 0.8138 (tpp) cc_final: 0.7537 (ttm) REVERT: D 394 SER cc_start: 0.7361 (p) cc_final: 0.6922 (m) REVERT: D 432 ARG cc_start: 0.8076 (ttt180) cc_final: 0.7778 (ttm-80) REVERT: D 677 MET cc_start: 0.7301 (tmm) cc_final: 0.6817 (ttt) REVERT: B 438 PHE cc_start: 0.8271 (t80) cc_final: 0.7927 (t80) REVERT: C 420 ARG cc_start: 0.7401 (ttm-80) cc_final: 0.7033 (mtp85) REVERT: C 498 GLN cc_start: 0.7769 (mt0) cc_final: 0.7356 (tp40) REVERT: C 568 MET cc_start: 0.8081 (mtp) cc_final: 0.7859 (mtm) REVERT: C 576 ASP cc_start: 0.8516 (m-30) cc_final: 0.8195 (m-30) REVERT: C 682 MET cc_start: 0.6721 (tmm) cc_final: 0.6265 (ttm) outliers start: 37 outliers final: 28 residues processed: 316 average time/residue: 0.2198 time to fit residues: 100.0322 Evaluate side-chains 310 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 494 GLN Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 THR 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 668 ILE Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 38 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.150497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129386 restraints weight = 42306.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134345 restraints weight = 17901.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137443 restraints weight = 10414.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.139423 restraints weight = 7250.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140723 restraints weight = 5644.450| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10331 Z= 0.166 Angle : 0.533 6.534 13943 Z= 0.294 Chirality : 0.035 0.165 1567 Planarity : 0.003 0.030 1680 Dihedral : 9.524 162.575 1484 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.09 % Allowed : 17.18 % Favored : 79.73 % 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: 1.94 (0.26), residues: 1189 helix: 2.23 (0.17), residues: 883 sheet: None (None), residues: 0 loop : -1.66 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 409 TYR 0.016 0.001 TYR B 555 PHE 0.011 0.001 PHE B 489 TRP 0.007 0.001 TRP C 426 HIS 0.005 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (10331) covalent geometry : angle 0.53290 / 0.29 (13943) hydrogen bonds : bond 0.04651 / 3.07 ( 720) hydrogen bonds : angle 4.02870 / 2.83 ( 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: 34 poor density : 291 time to evaluate : 0.551 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: A 523 MET cc_start: 0.8164 (tpp) cc_final: 0.7608 (ttm) REVERT: A 585 LEU cc_start: 0.8879 (mm) cc_final: 0.8629 (mm) REVERT: D 394 SER cc_start: 0.7376 (p) cc_final: 0.6937 (m) REVERT: D 432 ARG cc_start: 0.8131 (ttt180) cc_final: 0.7715 (ttm-80) REVERT: D 463 TYR cc_start: 0.7131 (m-80) cc_final: 0.6787 (m-10) REVERT: B 438 PHE cc_start: 0.8222 (t80) cc_final: 0.7929 (t80) REVERT: B 513 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: C 498 GLN cc_start: 0.7818 (mt0) cc_final: 0.7365 (tp40) REVERT: C 568 MET cc_start: 0.8129 (mtp) cc_final: 0.7896 (mtm) REVERT: C 576 ASP cc_start: 0.8592 (m-30) cc_final: 0.8308 (m-30) REVERT: C 682 MET cc_start: 0.6704 (tmm) cc_final: 0.6273 (ttm) outliers start: 34 outliers final: 28 residues processed: 309 average time/residue: 0.2033 time to fit residues: 91.2261 Evaluate side-chains 316 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 573 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain B residue 411 ASP 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 556 THR 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 668 ILE 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: 0.1980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130229 restraints weight = 42484.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135081 restraints weight = 18365.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138012 restraints weight = 10782.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139976 restraints weight = 7641.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141154 restraints weight = 5956.689| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3805 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= 0.148 Angle : 0.517 5.811 13943 Z= 0.286 Chirality : 0.034 0.155 1567 Planarity : 0.003 0.028 1680 Dihedral : 9.209 158.481 1482 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.82 % Allowed : 17.82 % Favored : 79.36 % 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: 2.06 (0.26), residues: 1189 helix: 2.35 (0.17), residues: 878 sheet: None (None), residues: 0 loop : -1.66 (0.40), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 409 TYR 0.014 0.001 TYR B 555 PHE 0.011 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/Z covalent geometry : bond 0.00329 / 0.15 (10331) covalent geometry : angle 0.51708 / 0.29 (13943) hydrogen bonds : bond 0.04466 / 2.94 ( 720) hydrogen bonds : angle 3.96694 / 2.79 ( 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 324 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 0.488 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 523 MET cc_start: 0.8111 (tpp) cc_final: 0.7634 (ttm) REVERT: A 585 LEU cc_start: 0.8927 (mm) cc_final: 0.8680 (mm) REVERT: D 394 SER cc_start: 0.7358 (p) cc_final: 0.6919 (m) REVERT: D 412 MET cc_start: 0.6981 (ttm) cc_final: 0.6764 (ttm) REVERT: D 432 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7756 (ttm-80) REVERT: D 463 TYR cc_start: 0.7134 (m-80) cc_final: 0.6812 (m-10) REVERT: B 438 PHE cc_start: 0.8249 (t80) cc_final: 0.7915 (t80) REVERT: B 513 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: C 420 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.7023 (mtp85) REVERT: C 498 GLN cc_start: 0.7754 (mt0) cc_final: 0.7336 (tp40) REVERT: C 536 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7450 (mt-10) REVERT: C 572 MET cc_start: 0.8388 (tmm) cc_final: 0.8179 (tmm) REVERT: C 576 ASP cc_start: 0.8567 (m-30) cc_final: 0.8354 (m-30) REVERT: C 682 MET cc_start: 0.6600 (tmm) cc_final: 0.6222 (ttm) outliers start: 31 outliers final: 29 residues processed: 310 average time/residue: 0.2002 time to fit residues: 89.6351 Evaluate side-chains 313 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 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 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 573 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain B residue 411 ASP 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 556 THR 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 668 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.154933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134326 restraints weight = 41653.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139344 restraints weight = 17381.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142491 restraints weight = 9999.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144508 restraints weight = 6882.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145821 restraints weight = 5304.809| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10331 Z= 0.183 Angle : 0.549 6.440 13943 Z= 0.306 Chirality : 0.036 0.193 1567 Planarity : 0.003 0.028 1680 Dihedral : 9.210 153.565 1482 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.00 % Allowed : 18.55 % Favored : 78.45 % 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: 1.81 (0.26), residues: 1189 helix: 2.18 (0.17), residues: 877 sheet: None (None), residues: 0 loop : -1.80 (0.39), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.018 0.001 TYR B 555 PHE 0.012 0.001 PHE B 489 TRP 0.008 0.001 TRP C 426 HIS 0.005 0.002 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (10331) covalent geometry : angle 0.54922 / 0.31 (13943) hydrogen bonds : bond 0.04866 / 3.20 ( 720) hydrogen bonds : angle 4.09233 / 2.87 ( 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 316 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 0.543 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 523 MET cc_start: 0.8133 (tpp) cc_final: 0.7675 (ttm) REVERT: A 585 LEU cc_start: 0.8877 (mm) cc_final: 0.8607 (mm) REVERT: D 394 SER cc_start: 0.7383 (p) cc_final: 0.6956 (m) REVERT: D 412 MET cc_start: 0.7090 (ttm) cc_final: 0.6861 (ttm) REVERT: D 432 ARG cc_start: 0.8129 (ttt180) cc_final: 0.7719 (ttm-80) REVERT: D 463 TYR cc_start: 0.7138 (m-80) cc_final: 0.6887 (m-10) REVERT: B 438 PHE cc_start: 0.8202 (t80) cc_final: 0.7925 (t80) REVERT: B 513 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7128 (mm-30) REVERT: B 600 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7887 (mm-30) REVERT: C 420 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.7040 (mtp85) REVERT: C 498 GLN cc_start: 0.7791 (mt0) cc_final: 0.7351 (tp40) REVERT: C 512 SER cc_start: 0.8190 (p) cc_final: 0.7597 (t) REVERT: C 576 ASP cc_start: 0.8616 (m-30) cc_final: 0.8388 (m-30) REVERT: C 603 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7721 (ptpt) REVERT: C 682 MET cc_start: 0.6521 (tmm) cc_final: 0.6200 (ttm) outliers start: 33 outliers final: 31 residues processed: 300 average time/residue: 0.2055 time to fit residues: 89.5044 Evaluate side-chains 311 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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 437 ASN 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 494 GLN Chi-restraints excluded: chain B residue 513 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 THR 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 668 ILE 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: 0.9980 chunk 94 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 628 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.149153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129076 restraints weight = 42684.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133705 restraints weight = 18952.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136604 restraints weight = 11304.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138413 restraints weight = 8011.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.139640 restraints weight = 6314.905| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10331 Z= 0.178 Angle : 0.545 6.508 13943 Z= 0.303 Chirality : 0.035 0.206 1567 Planarity : 0.003 0.029 1680 Dihedral : 9.150 152.420 1482 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.00 % Allowed : 18.91 % Favored : 78.09 % 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: 1.80 (0.26), residues: 1189 helix: 2.16 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -1.81 (0.40), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.018 0.001 TYR B 555 PHE 0.012 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/Z covalent geometry : bond 0.00397 / 0.18 (10331) covalent geometry : angle 0.54475 / 0.30 (13943) hydrogen bonds : bond 0.04809 / 3.17 ( 720) hydrogen bonds : angle 4.11237 / 2.88 ( 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 318 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 0.575 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 523 MET cc_start: 0.8085 (tpp) cc_final: 0.7673 (ttm) REVERT: A 585 LEU cc_start: 0.8977 (mm) cc_final: 0.8727 (mm) REVERT: D 394 SER cc_start: 0.7391 (p) cc_final: 0.6973 (m) REVERT: D 432 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7791 (ttm-80) REVERT: D 463 TYR cc_start: 0.7134 (m-80) cc_final: 0.6912 (m-10) REVERT: B 438 PHE cc_start: 0.8277 (t80) cc_final: 0.7958 (t80) REVERT: B 513 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: B 600 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7817 (mm-30) REVERT: C 420 ARG cc_start: 0.7375 (ttm-80) cc_final: 0.7006 (mtp85) REVERT: C 498 GLN cc_start: 0.7725 (mt0) cc_final: 0.7351 (tp40) REVERT: C 512 SER cc_start: 0.8209 (p) cc_final: 0.7690 (t) REVERT: C 576 ASP cc_start: 0.8591 (m-30) cc_final: 0.8365 (m-30) REVERT: C 603 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7628 (ptpt) REVERT: C 682 MET cc_start: 0.6495 (tmm) cc_final: 0.6173 (ttm) outliers start: 33 outliers final: 31 residues processed: 303 average time/residue: 0.2082 time to fit residues: 91.2080 Evaluate side-chains 316 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 573 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain B residue 411 ASP 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 556 THR 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 628 ASN Chi-restraints excluded: chain C residue 668 ILE 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: 0.9990 chunk 117 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 chunk 108 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.150410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130226 restraints weight = 42362.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.134992 restraints weight = 18383.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137967 restraints weight = 10792.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139852 restraints weight = 7555.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141060 restraints weight = 5898.360| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10331 Z= 0.188 Angle : 0.845 59.200 13943 Z= 0.504 Chirality : 0.035 0.191 1567 Planarity : 0.003 0.029 1680 Dihedral : 9.151 152.409 1482 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.18 % Allowed : 18.73 % Favored : 78.09 % Cbeta Deviations : 0.09 % 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: 1.81 (0.26), residues: 1189 helix: 2.17 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -1.82 (0.40), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.015 0.001 TYR B 555 PHE 0.011 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/Z covalent geometry : bond 0.00399 / 0.19 (10331) covalent geometry : angle 0.84504 / 0.50 (13943) hydrogen bonds : bond 0.04773 / 3.15 ( 720) hydrogen bonds : angle 4.10926 / 2.88 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3535.02 seconds wall clock time: 61 minutes 3.93 seconds (3663.93 seconds total)