Starting phenix.real_space_refine on Sat Jul 4 10:53:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t10_40951/07_2026/8t10_40951_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t10_40951/07_2026/8t10_40951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t10_40951/07_2026/8t10_40951_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t10_40951/07_2026/8t10_40951_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t10_40951/07_2026/8t10_40951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t10_40951/07_2026/8t10_40951.map" } resolution = 3.7 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 68 5.16 5 Na 2 4.78 5 C 6728 2.51 5 N 1522 2.21 5 O 1758 1.98 5 H 10070 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 20152 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4971 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 291} Chain breaks: 2 Chain: "A" Number of atoms: 5034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 5034 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4971 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 291} Chain breaks: 2 Chain: "C" Number of atoms: 5034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 5034 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 294} Chain breaks: 1 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 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: 3.99, per 1000 atoms: 0.20 Number of scatterers: 20152 At special positions: 0 Unit cell: (114.395, 111.89, 80.16, 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 68 16.00 P 4 15.00 Na 2 11.00 O 1758 8.00 N 1522 7.00 C 6728 6.00 H 10070 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: 2.00 Conformation dependent library (CDL) restraints added in 821.8 milliseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.741A pdb=" N LEU B 413 " --> pdb=" O HIS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 removed outlier: 4.053A pdb=" N VAL B 430 " --> pdb=" O TRP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 3.805A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 504 through 508 removed outlier: 3.589A pdb=" N PHE B 507 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.500A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.864A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 4.077A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.845A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) 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 670 Processing helix chain 'B' and resid 673 through 689 removed outlier: 4.013A pdb=" N ILE B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 711 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 415 through 427 Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 532 removed outlier: 3.607A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 552 removed outlier: 4.208A pdb=" N ALA A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.893A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.799A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 689 through 712 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 Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 555 Processing helix chain 'D' and resid 559 through 599 removed outlier: 4.275A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 640 through 643 Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 712 removed outlier: 4.299A pdb=" N ALA D 690 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 429 through 450 removed outlier: 3.561A pdb=" N PHE C 448 " --> pdb=" O TYR C 444 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA C 450 " --> pdb=" O ILE C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 removed outlier: 4.175A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 556 removed outlier: 4.637A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 575 removed outlier: 3.533A pdb=" N LEU C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.948A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 689 through 711 removed outlier: 3.531A pdb=" N SER C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2139 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: 4.81 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 6626 1.02 - 1.22: 3466 1.22 - 1.42: 4441 1.42 - 1.62: 5735 1.62 - 1.82: 126 Bond restraints: 20394 Sorted by residual: bond pdb=" OAA NKN A 901 " pdb=" PAC NKN A 901 " ideal model delta sigma weight residual 1.667 1.442 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" NE1 TRP A 549 " pdb=" HE1 TRP A 549 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 697 " pdb=" HE1 TRP D 697 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP B 697 " pdb=" HE1 TRP B 697 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" OAB NKN C 901 " pdb=" PAC NKN C 901 " ideal model delta sigma weight residual 1.668 1.455 0.213 2.00e-02 2.50e+03 1.14e+02 ... (remaining 20389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.07: 36604 10.07 - 20.13: 20 20.13 - 30.20: 12 30.20 - 40.27: 0 40.27 - 50.33: 2 Bond angle restraints: 36638 Sorted by residual: angle pdb=" OAA NKN C 901 " pdb=" PAC NKN C 901 " pdb=" OAB NKN C 901 " ideal model delta sigma weight residual 54.49 104.82 -50.33 3.00e+00 1.11e-01 2.81e+02 angle pdb=" OAA NKN A 901 " pdb=" PAC NKN A 901 " pdb=" OAB NKN A 901 " ideal model delta sigma weight residual 54.49 101.96 -47.47 3.00e+00 1.11e-01 2.50e+02 angle pdb=" CA SER A 505 " pdb=" CB SER A 505 " pdb=" OG SER A 505 " ideal model delta sigma weight residual 111.10 134.39 -23.29 2.00e+00 2.50e-01 1.36e+02 angle pdb=" CA SER A 505 " pdb=" CB SER A 505 " pdb=" HB2 SER A 505 " ideal model delta sigma weight residual 109.00 78.81 30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" OG SER A 505 " pdb=" CB SER A 505 " pdb=" HB2 SER A 505 " ideal model delta sigma weight residual 109.00 78.88 30.12 3.00e+00 1.11e-01 1.01e+02 ... (remaining 36633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.29: 9204 30.29 - 60.57: 464 60.57 - 90.86: 42 90.86 - 121.14: 18 121.14 - 151.43: 2 Dihedral angle restraints: 9730 sinusoidal: 5146 harmonic: 4584 Sorted by residual: dihedral pdb=" C ILE D 689 " pdb=" N ILE D 689 " pdb=" CA ILE D 689 " pdb=" CB ILE D 689 " ideal model delta harmonic sigma weight residual -122.00 -141.42 19.42 0 2.50e+00 1.60e-01 6.03e+01 dihedral pdb=" CD ARG D 474 " pdb=" NE ARG D 474 " pdb=" CZ ARG D 474 " pdb=" NH1 ARG D 474 " ideal model delta sinusoidal sigma weight residual 0.00 62.83 -62.83 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CD ARG A 428 " pdb=" NE ARG A 428 " pdb=" CZ ARG A 428 " pdb=" NH1 ARG A 428 " ideal model delta sinusoidal sigma weight residual 0.00 -58.52 58.52 1 1.00e+01 1.00e-02 4.59e+01 ... (remaining 9727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1354 0.123 - 0.245: 211 0.245 - 0.368: 2 0.368 - 0.491: 0 0.491 - 0.613: 1 Chirality restraints: 1568 Sorted by residual: chirality pdb=" CA ILE D 689 " pdb=" N ILE D 689 " pdb=" C ILE D 689 " pdb=" CB ILE D 689 " both_signs ideal model delta sigma weight residual False 2.43 1.82 0.61 2.00e-01 2.50e+01 9.41e+00 chirality pdb=" CA ARG C 557 " pdb=" N ARG C 557 " pdb=" C ARG C 557 " pdb=" CB ARG C 557 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA SER A 505 " pdb=" N SER A 505 " pdb=" C SER A 505 " pdb=" CB SER A 505 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1565 not shown) Planarity restraints: 2842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 420 " -0.471 9.50e-02 1.11e+02 2.55e-01 9.28e+02 pdb=" NE ARG C 420 " -0.121 2.00e-02 2.50e+03 pdb=" CZ ARG C 420 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG C 420 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG C 420 " 0.046 2.00e-02 2.50e+03 pdb="HH11 ARG C 420 " 0.401 2.00e-02 2.50e+03 pdb="HH12 ARG C 420 " -0.401 2.00e-02 2.50e+03 pdb="HH21 ARG C 420 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 420 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 534 " -0.402 9.50e-02 1.11e+02 2.37e-01 8.75e+02 pdb=" NE ARG B 534 " -0.193 2.00e-02 2.50e+03 pdb=" CZ ARG B 534 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG B 534 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 534 " 0.046 2.00e-02 2.50e+03 pdb="HH11 ARG B 534 " 0.404 2.00e-02 2.50e+03 pdb="HH12 ARG B 534 " -0.347 2.00e-02 2.50e+03 pdb="HH21 ARG B 534 " 0.130 2.00e-02 2.50e+03 pdb="HH22 ARG B 534 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 701 " 0.637 9.50e-02 1.11e+02 2.69e-01 6.63e+02 pdb=" NE ARG A 701 " 0.178 2.00e-02 2.50e+03 pdb=" CZ ARG A 701 " 0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG A 701 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 701 " -0.032 2.00e-02 2.50e+03 pdb="HH11 ARG A 701 " -0.336 2.00e-02 2.50e+03 pdb="HH12 ARG A 701 " 0.249 2.00e-02 2.50e+03 pdb="HH21 ARG A 701 " -0.183 2.00e-02 2.50e+03 pdb="HH22 ARG A 701 " 0.055 2.00e-02 2.50e+03 ... (remaining 2839 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1346 2.20 - 2.80: 40680 2.80 - 3.40: 57833 3.40 - 4.00: 73334 4.00 - 4.60: 110763 Nonbonded interactions: 283956 Sorted by model distance: nonbonded pdb=" OE1 GLN B 561 " pdb="HH21 ARG A 579 " model vdw 1.603 2.450 nonbonded pdb=" O ASN C 551 " pdb=" H TYR C 554 " model vdw 1.681 2.450 nonbonded pdb="HG23 THR B 468 " pdb=" H ASP B 471 " model vdw 1.719 2.270 nonbonded pdb=" HZ2 LYS A 603 " pdb=" OH TYR A 627 " model vdw 1.772 2.450 nonbonded pdb=" HZ2 LYS D 603 " pdb=" HE1 TYR D 627 " model vdw 1.776 2.100 ... (remaining 283951 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 387 through 463 or resid 467 through 712)) selection = (chain 'B' and resid 387 through 712) selection = (chain 'C' and (resid 387 through 463 or resid 467 through 712)) selection = (chain 'D' and resid 387 through 712) } 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: 5.260 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: 0.150 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.190 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 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 : 0.010 0.225 10324 Z= 0.687 Angle : 1.597 50.334 13938 Z= 1.045 Chirality : 0.079 0.613 1568 Planarity : 0.034 0.441 1678 Dihedral : 19.589 151.428 3832 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.93 % Allowed : 6.03 % Favored : 90.04 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 16.67 % 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: -0.89 (0.24), residues: 1178 helix: -0.12 (0.16), residues: 892 sheet: None (None), residues: 0 loop : -1.75 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 432 TYR 0.026 0.002 TYR D 653 PHE 0.028 0.002 PHE D 649 TRP 0.018 0.002 TRP A 426 HIS 0.008 0.002 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00982 / 0.69 (10324) covalent geometry : angle 1.59733 / 1.04 (13938) hydrogen bonds : bond 0.17612 / 11.23 ( 725) hydrogen bonds : angle 7.47266 / 5.38 ( 2139) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 343 time to evaluate : 0.513 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: B 535 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6205 (tptp) REVERT: B 628 ASN cc_start: 0.6546 (OUTLIER) cc_final: 0.6241 (t0) REVERT: A 570 GLU cc_start: 0.6613 (tp30) cc_final: 0.6380 (tp30) REVERT: D 682 MET cc_start: 0.7931 (mtp) cc_final: 0.7688 (mtt) REVERT: C 547 MET cc_start: 0.7854 (tpp) cc_final: 0.7459 (tpp) REVERT: C 689 ILE cc_start: 0.7684 (pt) cc_final: 0.7453 (pt) outliers start: 43 outliers final: 8 residues processed: 369 average time/residue: 0.1875 time to fit residues: 99.6702 Evaluate side-chains 282 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 272 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 598 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.186968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.169917 restraints weight = 41389.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.174842 restraints weight = 18014.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.177613 restraints weight = 9933.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.179817 restraints weight = 6635.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.180958 restraints weight = 4681.886| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10324 Z= 0.175 Angle : 0.622 8.042 13938 Z= 0.334 Chirality : 0.037 0.250 1568 Planarity : 0.008 0.123 1678 Dihedral : 15.117 130.777 1530 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.65 % Allowed : 13.71 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.29 (0.25), residues: 1178 helix: 1.60 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.57 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 432 TYR 0.016 0.001 TYR B 584 PHE 0.021 0.001 PHE A 429 TRP 0.012 0.002 TRP A 426 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (10324) covalent geometry : angle 0.62166 / 0.33 (13938) hydrogen bonds : bond 0.05309 / 3.31 ( 725) hydrogen bonds : angle 4.52119 / 3.19 ( 2139) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 290 time to evaluate : 0.523 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: B 535 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6296 (tptp) REVERT: B 692 GLU cc_start: 0.7400 (pm20) cc_final: 0.7069 (pm20) REVERT: B 712 PHE cc_start: 0.5527 (t80) cc_final: 0.4027 (t80) REVERT: A 397 GLU cc_start: 0.8100 (tt0) cc_final: 0.7876 (tt0) REVERT: A 479 ILE cc_start: 0.7822 (mm) cc_final: 0.7560 (mm) REVERT: D 634 CYS cc_start: 0.8110 (t) cc_final: 0.7905 (t) REVERT: C 516 PHE cc_start: 0.7452 (m-80) cc_final: 0.7177 (m-80) REVERT: C 541 MET cc_start: 0.8105 (ptm) cc_final: 0.7502 (ttp) outliers start: 18 outliers final: 15 residues processed: 303 average time/residue: 0.1742 time to fit residues: 77.8938 Evaluate side-chains 282 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 266 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 661 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.186033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169352 restraints weight = 41319.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.173934 restraints weight = 18136.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.176727 restraints weight = 10260.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.178586 restraints weight = 6879.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.179726 restraints weight = 5099.631| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10324 Z= 0.148 Angle : 0.553 8.048 13938 Z= 0.302 Chirality : 0.034 0.137 1568 Planarity : 0.004 0.045 1678 Dihedral : 12.365 118.038 1526 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.83 % Allowed : 14.44 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.25), residues: 1178 helix: 1.94 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -1.31 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 534 TYR 0.011 0.001 TYR D 627 PHE 0.030 0.001 PHE A 429 TRP 0.011 0.001 TRP A 426 HIS 0.003 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (10324) covalent geometry : angle 0.55253 / 0.30 (13938) hydrogen bonds : bond 0.05009 / 3.11 ( 725) hydrogen bonds : angle 4.30313 / 3.03 ( 2139) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6349 (tptp) REVERT: B 712 PHE cc_start: 0.5566 (t80) cc_final: 0.4073 (t80) REVERT: A 547 MET cc_start: 0.8203 (tpp) cc_final: 0.7824 (tpp) REVERT: C 541 MET cc_start: 0.8054 (ptm) cc_final: 0.7782 (ttp) REVERT: C 552 MET cc_start: 0.7889 (tpp) cc_final: 0.7636 (tpp) outliers start: 20 outliers final: 16 residues processed: 277 average time/residue: 0.2066 time to fit residues: 83.4661 Evaluate side-chains 269 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 661 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.181649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.164781 restraints weight = 41540.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.169216 restraints weight = 18324.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.171962 restraints weight = 10474.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.173747 restraints weight = 7077.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.174842 restraints weight = 5324.079| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10324 Z= 0.187 Angle : 0.571 7.934 13938 Z= 0.315 Chirality : 0.035 0.180 1568 Planarity : 0.004 0.044 1678 Dihedral : 11.278 88.818 1526 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.65 % Allowed : 14.90 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.88 (0.25), residues: 1178 helix: 2.05 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 534 TYR 0.014 0.001 TYR C 565 PHE 0.025 0.002 PHE A 429 TRP 0.010 0.002 TRP D 697 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (10324) covalent geometry : angle 0.57053 / 0.31 (13938) hydrogen bonds : bond 0.05152 / 3.21 ( 725) hydrogen bonds : angle 4.31508 / 3.05 ( 2139) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 712 PHE cc_start: 0.5622 (t80) cc_final: 0.3395 (t80) REVERT: A 429 PHE cc_start: 0.6558 (p90) cc_final: 0.6336 (p90) REVERT: D 664 LEU cc_start: 0.8712 (mm) cc_final: 0.8351 (mt) REVERT: C 541 MET cc_start: 0.8070 (ptm) cc_final: 0.7554 (ttp) REVERT: C 552 MET cc_start: 0.7873 (tpp) cc_final: 0.7599 (tpp) outliers start: 29 outliers final: 26 residues processed: 284 average time/residue: 0.1972 time to fit residues: 80.3932 Evaluate side-chains 280 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 634 CYS Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 661 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 0.0770 chunk 86 optimal weight: 0.7980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 700 GLN D 423 GLN D 687 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.182755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.166002 restraints weight = 40971.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.170431 restraints weight = 17962.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.173167 restraints weight = 10238.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.174817 restraints weight = 6938.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.176006 restraints weight = 5305.052| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10324 Z= 0.154 Angle : 0.545 8.020 13938 Z= 0.299 Chirality : 0.034 0.162 1568 Planarity : 0.004 0.076 1678 Dihedral : 10.534 89.405 1518 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.56 % Allowed : 16.45 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.01 (0.25), residues: 1178 helix: 2.17 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.49 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 701 TYR 0.013 0.001 TYR A 671 PHE 0.015 0.001 PHE C 582 TRP 0.012 0.001 TRP D 697 HIS 0.001 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (10324) covalent geometry : angle 0.54500 / 0.30 (13938) hydrogen bonds : bond 0.05005 / 3.10 ( 725) hydrogen bonds : angle 4.20576 / 2.98 ( 2139) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.541 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: B 712 PHE cc_start: 0.5618 (t80) cc_final: 0.3339 (t80) REVERT: C 541 MET cc_start: 0.8087 (ptm) cc_final: 0.7603 (ttp) outliers start: 28 outliers final: 25 residues processed: 274 average time/residue: 0.1794 time to fit residues: 72.9842 Evaluate side-chains 282 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 661 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.4980 chunk 30 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 628 ASN B 700 GLN C 408 ASN C 410 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.175376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.158761 restraints weight = 41826.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.163103 restraints weight = 18367.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.165795 restraints weight = 10517.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.167531 restraints weight = 7161.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.168748 restraints weight = 5413.503| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10324 Z= 0.217 Angle : 0.596 8.006 13938 Z= 0.330 Chirality : 0.037 0.224 1568 Planarity : 0.004 0.046 1678 Dihedral : 10.619 92.632 1518 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.74 % Allowed : 16.73 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.66 (0.25), residues: 1178 helix: 1.92 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.65 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 701 TYR 0.017 0.002 TYR C 565 PHE 0.019 0.002 PHE C 448 TRP 0.010 0.002 TRP A 426 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (10324) covalent geometry : angle 0.59632 / 0.33 (13938) hydrogen bonds : bond 0.05466 / 3.39 ( 725) hydrogen bonds : angle 4.40917 / 3.13 ( 2139) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.540 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: B 675 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 712 PHE cc_start: 0.5675 (t80) cc_final: 0.3517 (t80) REVERT: D 519 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: D 653 TYR cc_start: 0.7078 (p90) cc_final: 0.6595 (p90) REVERT: C 541 MET cc_start: 0.8122 (ptm) cc_final: 0.7643 (ttp) outliers start: 30 outliers final: 25 residues processed: 292 average time/residue: 0.2037 time to fit residues: 86.7380 Evaluate side-chains 292 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 519 GLN Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 537 TYR Chi-restraints excluded: chain D residue 634 CYS Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 661 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 628 ASN B 700 GLN C 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.176540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.159811 restraints weight = 41692.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.164194 restraints weight = 18200.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.166896 restraints weight = 10368.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.168669 restraints weight = 7012.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.169782 restraints weight = 5293.801| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10324 Z= 0.158 Angle : 0.552 8.111 13938 Z= 0.305 Chirality : 0.034 0.135 1568 Planarity : 0.004 0.062 1678 Dihedral : 10.270 91.472 1512 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.93 % Allowed : 17.28 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.25), residues: 1178 helix: 2.05 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.54 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 534 TYR 0.012 0.001 TYR D 627 PHE 0.017 0.001 PHE C 582 TRP 0.012 0.002 TRP C 697 HIS 0.001 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (10324) covalent geometry : angle 0.55217 / 0.30 (13938) hydrogen bonds : bond 0.05169 / 3.20 ( 725) hydrogen bonds : angle 4.28604 / 3.03 ( 2139) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.475 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: B 675 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 712 PHE cc_start: 0.5663 (t80) cc_final: 0.3487 (t80) REVERT: D 519 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: D 653 TYR cc_start: 0.7063 (p90) cc_final: 0.6612 (p90) REVERT: C 541 MET cc_start: 0.8029 (ptm) cc_final: 0.7543 (ttp) outliers start: 32 outliers final: 25 residues processed: 287 average time/residue: 0.1774 time to fit residues: 75.1777 Evaluate side-chains 294 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain D residue 519 GLN Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 537 TYR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 661 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 0.0010 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.177016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.160246 restraints weight = 41467.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.164630 restraints weight = 18168.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.167286 restraints weight = 10410.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.169032 restraints weight = 7093.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.170133 restraints weight = 5391.642| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10324 Z= 0.153 Angle : 0.542 8.163 13938 Z= 0.298 Chirality : 0.034 0.129 1568 Planarity : 0.004 0.055 1678 Dihedral : 9.980 87.849 1512 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.83 % Allowed : 17.55 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.01 (0.25), residues: 1178 helix: 2.17 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.52 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 534 TYR 0.011 0.001 TYR C 565 PHE 0.016 0.001 PHE C 582 TRP 0.011 0.002 TRP C 697 HIS 0.001 0.000 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (10324) covalent geometry : angle 0.54192 / 0.30 (13938) hydrogen bonds : bond 0.05036 / 3.12 ( 725) hydrogen bonds : angle 4.21817 / 2.98 ( 2139) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 271 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 675 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (mp) REVERT: B 712 PHE cc_start: 0.5667 (t80) cc_final: 0.3454 (t80) REVERT: D 519 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: D 522 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7289 (m-10) REVERT: C 541 MET cc_start: 0.8036 (ptm) cc_final: 0.7563 (ttp) outliers start: 31 outliers final: 24 residues processed: 289 average time/residue: 0.1860 time to fit residues: 79.9199 Evaluate side-chains 286 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain D residue 519 GLN Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 537 TYR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 661 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.180100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.163827 restraints weight = 41074.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.168065 restraints weight = 18324.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.170696 restraints weight = 10571.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.172384 restraints weight = 7221.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.173320 restraints weight = 5475.221| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10324 Z= 0.161 Angle : 0.555 8.192 13938 Z= 0.306 Chirality : 0.035 0.146 1568 Planarity : 0.004 0.055 1678 Dihedral : 9.662 88.531 1512 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.74 % Allowed : 18.10 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.97 (0.25), residues: 1178 helix: 2.19 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.62 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 534 TYR 0.012 0.001 TYR C 565 PHE 0.017 0.001 PHE C 582 TRP 0.010 0.002 TRP C 697 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (10324) covalent geometry : angle 0.55524 / 0.31 (13938) hydrogen bonds : bond 0.05070 / 3.14 ( 725) hydrogen bonds : angle 4.25975 / 3.01 ( 2139) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 0.608 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: B 601 ASP cc_start: 0.6832 (t0) cc_final: 0.6207 (m-30) REVERT: B 675 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8501 (mp) REVERT: B 712 PHE cc_start: 0.5653 (t80) cc_final: 0.3445 (t80) REVERT: D 519 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: D 522 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: C 448 PHE cc_start: 0.7308 (t80) cc_final: 0.7052 (t80) REVERT: C 541 MET cc_start: 0.8039 (ptm) cc_final: 0.7576 (ttp) outliers start: 30 outliers final: 25 residues processed: 286 average time/residue: 0.1917 time to fit residues: 81.2138 Evaluate side-chains 296 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 519 GLN Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 537 TYR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 634 CYS Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 661 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.175446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.159058 restraints weight = 41734.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.163387 restraints weight = 18311.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.166012 restraints weight = 10464.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.167724 restraints weight = 7111.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.168649 restraints weight = 5384.792| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10324 Z= 0.169 Angle : 0.561 8.173 13938 Z= 0.310 Chirality : 0.035 0.150 1568 Planarity : 0.004 0.057 1678 Dihedral : 9.435 91.338 1510 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.47 % Allowed : 18.65 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.25), residues: 1178 helix: 2.16 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.62 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 557 TYR 0.012 0.001 TYR C 565 PHE 0.016 0.001 PHE C 582 TRP 0.011 0.002 TRP D 549 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (10324) covalent geometry : angle 0.56114 / 0.31 (13938) hydrogen bonds : bond 0.05140 / 3.18 ( 725) hydrogen bonds : angle 4.25461 / 3.01 ( 2139) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.540 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: B 675 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8494 (mp) REVERT: B 712 PHE cc_start: 0.5592 (t80) cc_final: 0.3518 (t80) REVERT: D 519 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7022 (tt0) REVERT: D 522 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7361 (m-10) REVERT: C 541 MET cc_start: 0.8056 (ptm) cc_final: 0.7611 (ttp) outliers start: 27 outliers final: 24 residues processed: 292 average time/residue: 0.1862 time to fit residues: 80.7707 Evaluate side-chains 300 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 273 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 519 GLN Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 537 TYR Chi-restraints excluded: chain D residue 701 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 557 ARG Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 653 TYR Chi-restraints excluded: chain C residue 661 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 4 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.176579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.160314 restraints weight = 41584.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.164674 restraints weight = 18203.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.167342 restraints weight = 10306.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169041 restraints weight = 6951.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.170066 restraints weight = 5239.238| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10324 Z= 0.138 Angle : 0.542 8.165 13938 Z= 0.297 Chirality : 0.034 0.140 1568 Planarity : 0.004 0.071 1678 Dihedral : 9.167 87.800 1510 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.29 % Allowed : 18.92 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.18 (0.25), residues: 1178 helix: 2.34 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.54 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 432 TYR 0.015 0.001 TYR B 435 PHE 0.017 0.001 PHE C 582 TRP 0.011 0.002 TRP C 697 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (10324) covalent geometry : angle 0.54197 / 0.30 (13938) hydrogen bonds : bond 0.04920 / 3.05 ( 725) hydrogen bonds : angle 4.15073 / 2.94 ( 2139) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3372.46 seconds wall clock time: 58 minutes 16.26 seconds (3496.26 seconds total)