Starting phenix.real_space_refine on Fri Aug 7 07:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t10_40951/08_2026/8t10_40951_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t10_40951/08_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_40951/08_2026/8t10_40951_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t10_40951/08_2026/8t10_40951_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t10_40951/08_2026/8t10_40951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t10_40951/08_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-2.2rc3-6140/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, 46 Unusual residues: {' NA': 1, '8IJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 26 Unusual residues: {' NA': 1, 'NKN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 3.87, per 1000 atoms: 0.19 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: 1.91 Conformation dependent library (CDL) restraints added in 529.0 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: 0.33 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: 3.79 Time building geometry restraints manager: 2.70 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: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.640 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- 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 : 0.558 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: 0.2124 time to fit residues: 113.4367 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 : 0.521 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.187270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.170413 restraints weight = 41478.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.175429 restraints weight = 18445.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.177916 restraints weight = 10134.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.180156 restraints weight = 6915.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.181111 restraints weight = 4877.015| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10324 Z= 0.179 Angle : 0.622 8.004 13938 Z= 0.334 Chirality : 0.037 0.250 1568 Planarity : 0.008 0.123 1678 Dihedral : 15.105 130.449 1530 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.74 % Allowed : 13.71 % Favored : 84.55 % 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: 1.28 (0.25), residues: 1178 helix: 1.60 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.59 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 432 TYR 0.015 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 0.00380 / 0.18 (10324) covalent geometry : angle 0.62171 / 0.33 (13938) hydrogen bonds : bond 0.05249 / 3.27 ( 725) hydrogen bonds : angle 4.52084 / 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 307 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 288 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 535 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6314 (tptp) REVERT: B 692 GLU cc_start: 0.7390 (pm20) cc_final: 0.7069 (pm20) REVERT: B 712 PHE cc_start: 0.5522 (t80) cc_final: 0.3999 (t80) REVERT: A 397 GLU cc_start: 0.8103 (tt0) cc_final: 0.7875 (tt0) REVERT: A 479 ILE cc_start: 0.7837 (mm) cc_final: 0.7577 (mm) REVERT: C 508 VAL cc_start: 0.7271 (OUTLIER) cc_final: 0.7048 (m) REVERT: C 516 PHE cc_start: 0.7433 (m-80) cc_final: 0.7153 (m-80) REVERT: C 541 MET cc_start: 0.8092 (ptm) cc_final: 0.7491 (ttp) outliers start: 19 outliers final: 15 residues processed: 302 average time/residue: 0.2002 time to fit residues: 89.5180 Evaluate side-chains 282 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 265 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 508 VAL 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: 0.9980 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.184696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.167970 restraints weight = 41341.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.172769 restraints weight = 18252.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.175927 restraints weight = 10147.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.177657 restraints weight = 6469.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.179123 restraints weight = 4797.307| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10324 Z= 0.173 Angle : 0.569 8.075 13938 Z= 0.313 Chirality : 0.035 0.147 1568 Planarity : 0.005 0.052 1678 Dihedral : 12.661 110.699 1526 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.29 % Allowed : 14.90 % Favored : 82.82 % 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: 1.62 (0.25), residues: 1178 helix: 1.84 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.46 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 534 TYR 0.012 0.001 TYR C 565 PHE 0.027 0.002 PHE A 429 TRP 0.012 0.002 TRP A 426 HIS 0.003 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (10324) covalent geometry : angle 0.56872 / 0.31 (13938) hydrogen bonds : bond 0.05204 / 3.23 ( 725) hydrogen bonds : angle 4.39111 / 3.09 ( 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 289 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 264 time to evaluate : 0.504 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: 0.6791 (OUTLIER) cc_final: 0.6380 (tptp) REVERT: B 712 PHE cc_start: 0.5545 (t80) cc_final: 0.4071 (t80) REVERT: A 523 MET cc_start: 0.7388 (ttm) cc_final: 0.6936 (ttm) REVERT: A 547 MET cc_start: 0.8053 (tpp) cc_final: 0.7797 (tpp) REVERT: C 541 MET cc_start: 0.8093 (ptm) cc_final: 0.7505 (ttp) REVERT: C 552 MET cc_start: 0.7875 (tpp) cc_final: 0.7628 (tpp) outliers start: 25 outliers final: 21 residues processed: 279 average time/residue: 0.2017 time to fit residues: 82.9256 Evaluate side-chains 278 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 B residue 708 THR 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 547 MET Chi-restraints excluded: chain D residue 634 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.181855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.164952 restraints weight = 41480.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.169438 restraints weight = 18312.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.172189 restraints weight = 10441.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.173963 restraints weight = 7036.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.175005 restraints weight = 5281.788| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10324 Z= 0.177 Angle : 0.564 7.922 13938 Z= 0.311 Chirality : 0.035 0.178 1568 Planarity : 0.004 0.047 1678 Dihedral : 11.502 90.634 1526 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.65 % Allowed : 15.17 % Favored : 82.18 % 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: 1.78 (0.24), residues: 1178 helix: 1.98 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.52 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 534 TYR 0.013 0.001 TYR C 565 PHE 0.027 0.002 PHE A 429 TRP 0.011 0.001 TRP D 697 HIS 0.003 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (10324) covalent geometry : angle 0.56393 / 0.31 (13938) hydrogen bonds : bond 0.05181 / 3.22 ( 725) hydrogen bonds : angle 4.32218 / 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 293 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 0.557 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 684 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6514 (tm-30) REVERT: B 712 PHE cc_start: 0.5615 (t80) cc_final: 0.3375 (t80) REVERT: A 429 PHE cc_start: 0.6522 (p90) cc_final: 0.6273 (p90) REVERT: A 552 MET cc_start: 0.7941 (tpp) cc_final: 0.7552 (tpp) REVERT: C 541 MET cc_start: 0.8067 (ptm) cc_final: 0.7529 (ttp) outliers start: 29 outliers final: 25 residues processed: 281 average time/residue: 0.2129 time to fit residues: 87.1872 Evaluate side-chains 278 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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 525 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 634 CYS 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 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: 0.7980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.178658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.161938 restraints weight = 41402.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.166379 restraints weight = 18091.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169094 restraints weight = 10248.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.170835 restraints weight = 6888.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.171884 restraints weight = 5177.769| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10324 Z= 0.172 Angle : 0.561 8.012 13938 Z= 0.308 Chirality : 0.035 0.174 1568 Planarity : 0.004 0.081 1678 Dihedral : 10.765 90.040 1518 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.02 % Allowed : 16.27 % Favored : 80.71 % 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: 1.82 (0.25), residues: 1178 helix: 2.04 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.60 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 557 TYR 0.013 0.001 TYR C 565 PHE 0.016 0.002 PHE A 429 TRP 0.012 0.002 TRP D 697 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (10324) covalent geometry : angle 0.56085 / 0.31 (13938) hydrogen bonds : bond 0.05181 / 3.22 ( 725) hydrogen bonds : angle 4.29290 / 3.04 ( 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 299 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.560 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: 0.6843 (OUTLIER) cc_final: 0.6468 (tptp) REVERT: B 684 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6520 (tm-30) REVERT: B 712 PHE cc_start: 0.5661 (t80) cc_final: 0.3356 (t80) REVERT: A 429 PHE cc_start: 0.6630 (p90) cc_final: 0.6413 (p90) REVERT: A 552 MET cc_start: 0.7953 (tpp) cc_final: 0.7601 (tpp) REVERT: D 519 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: C 541 MET cc_start: 0.8090 (ptm) cc_final: 0.7590 (ttp) outliers start: 33 outliers final: 29 residues processed: 284 average time/residue: 0.1930 time to fit residues: 81.3060 Evaluate side-chains 292 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 535 LYS 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 A residue 402 SER Chi-restraints excluded: chain A residue 430 VAL 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 528 VAL 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 547 MET 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 D residue 708 THR 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: 0.9990 chunk 30 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 36 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5422 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.180200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.163481 restraints weight = 41218.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.167931 restraints weight = 17948.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.170681 restraints weight = 10161.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.172450 restraints weight = 6838.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.173409 restraints weight = 5130.965| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3624 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= 0.136 Angle : 0.524 8.066 13938 Z= 0.287 Chirality : 0.033 0.158 1568 Planarity : 0.003 0.044 1678 Dihedral : 10.369 86.571 1518 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.56 % Allowed : 17.00 % Favored : 80.44 % 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: 2.11 (0.25), residues: 1178 helix: 2.25 (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 0.003 0.000 ARG C 575 TYR 0.013 0.001 TYR C 653 PHE 0.017 0.001 PHE A 429 TRP 0.011 0.001 TRP D 697 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (10324) covalent geometry : angle 0.52403 / 0.29 (13938) hydrogen bonds : bond 0.04912 / 3.04 ( 725) hydrogen bonds : angle 4.15451 / 2.94 ( 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 295 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 0.511 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 684 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6545 (tm-30) REVERT: B 712 PHE cc_start: 0.5622 (t80) cc_final: 0.3408 (t80) REVERT: D 653 TYR cc_start: 0.6979 (p90) cc_final: 0.6552 (p90) REVERT: C 541 MET cc_start: 0.8062 (ptm) cc_final: 0.7576 (ttp) outliers start: 28 outliers final: 25 residues processed: 282 average time/residue: 0.1774 time to fit residues: 74.4556 Evaluate side-chains 286 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 422 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 chunk 79 optimal weight: 0.8980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 628 ASN B 700 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.178663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.161833 restraints weight = 41538.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.166282 restraints weight = 18318.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.169005 restraints weight = 10456.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.170738 restraints weight = 7088.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.171863 restraints weight = 5368.945| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10324 Z= 0.160 Angle : 0.544 8.100 13938 Z= 0.299 Chirality : 0.034 0.193 1568 Planarity : 0.004 0.049 1678 Dihedral : 10.069 90.118 1518 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.74 % Allowed : 17.64 % 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: 2.04 (0.25), residues: 1178 helix: 2.20 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 284 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 0.032 0.001 PHE A 429 TRP 0.011 0.002 TRP A 426 HIS 0.004 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (10324) covalent geometry : angle 0.54366 / 0.30 (13938) hydrogen bonds : bond 0.04982 / 3.09 ( 725) hydrogen bonds : angle 4.19950 / 2.98 ( 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 302 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 272 time to evaluate : 0.444 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: B 684 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6508 (tm-30) REVERT: B 712 PHE cc_start: 0.5614 (t80) cc_final: 0.3428 (t80) REVERT: D 519 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: C 448 PHE cc_start: 0.7391 (t80) cc_final: 0.7051 (t80) REVERT: C 541 MET cc_start: 0.8042 (ptm) cc_final: 0.7598 (ttp) outliers start: 30 outliers final: 23 residues processed: 288 average time/residue: 0.1805 time to fit residues: 77.8684 Evaluate side-chains 291 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 628 ASN Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 675 LEU 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 D residue 427 ASP 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 634 CYS 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 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: 2.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.177546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.160768 restraints weight = 41357.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.165208 restraints weight = 18080.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.167925 restraints weight = 10241.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.169702 restraints weight = 6906.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.170694 restraints weight = 5212.725| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3925 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= 0.156 Angle : 0.543 8.095 13938 Z= 0.299 Chirality : 0.034 0.133 1568 Planarity : 0.004 0.046 1678 Dihedral : 9.845 95.764 1512 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.74 % Allowed : 18.01 % Favored : 79.25 % 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: 2.13 (0.25), residues: 1178 helix: 2.28 (0.17), residues: 892 sheet: None (None), residues: 0 loop : -1.52 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 409 TYR 0.014 0.001 TYR D 627 PHE 0.031 0.001 PHE A 429 TRP 0.010 0.001 TRP C 697 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (10324) covalent geometry : angle 0.54284 / 0.30 (13938) hydrogen bonds : bond 0.04973 / 3.08 ( 725) hydrogen bonds : angle 4.18948 / 2.97 ( 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 299 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.445 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: B 675 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8421 (mp) REVERT: B 684 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6591 (tm-30) REVERT: B 712 PHE cc_start: 0.5639 (t80) cc_final: 0.3442 (t80) REVERT: D 519 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: C 448 PHE cc_start: 0.7400 (t80) cc_final: 0.7078 (t80) REVERT: C 541 MET cc_start: 0.8080 (ptm) cc_final: 0.7608 (ttp) outliers start: 30 outliers final: 24 residues processed: 286 average time/residue: 0.1918 time to fit residues: 81.2903 Evaluate side-chains 294 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 552 MET 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 D residue 427 ASP 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 414 LEU 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: 0.9980 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 700 GLN C 408 ASN C 410 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.175874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.159317 restraints weight = 41497.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.163674 restraints weight = 18241.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.166381 restraints weight = 10397.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.168131 restraints weight = 7040.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.169309 restraints weight = 5294.490| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4107 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= 0.175 Angle : 0.567 8.153 13938 Z= 0.312 Chirality : 0.035 0.205 1568 Planarity : 0.004 0.051 1678 Dihedral : 9.836 102.433 1512 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.68 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: 1.98 (0.25), residues: 1178 helix: 2.18 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.56 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 534 TYR 0.014 0.001 TYR C 565 PHE 0.024 0.002 PHE A 429 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 0.00375 / 0.18 (10324) covalent geometry : angle 0.56660 / 0.31 (13938) hydrogen bonds : bond 0.05131 / 3.18 ( 725) hydrogen bonds : angle 4.26539 / 3.02 ( 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 299 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 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: symmetry clash revert: symmetry clash REVERT: B 675 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 684 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6538 (tm-30) REVERT: B 712 PHE cc_start: 0.5667 (t80) cc_final: 0.3449 (t80) REVERT: D 519 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: C 541 MET cc_start: 0.8057 (ptm) cc_final: 0.7611 (ttp) outliers start: 27 outliers final: 24 residues processed: 286 average time/residue: 0.1822 time to fit residues: 77.0728 Evaluate side-chains 294 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 510 SER Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 552 MET 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 D residue 427 ASP 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 701 ARG Chi-restraints excluded: chain C residue 414 LEU 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: 0.8980 chunk 93 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.175543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.159212 restraints weight = 41689.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.163575 restraints weight = 18207.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.166232 restraints weight = 10320.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.167966 restraints weight = 6969.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.169087 restraints weight = 5239.445| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4254 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= 0.174 Angle : 0.565 8.112 13938 Z= 0.313 Chirality : 0.035 0.159 1568 Planarity : 0.004 0.053 1678 Dihedral : 9.750 101.686 1510 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.65 % Allowed : 18.92 % Favored : 78.43 % 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: 1.91 (0.25), residues: 1178 helix: 2.14 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.64 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 579 TYR 0.013 0.001 TYR C 565 PHE 0.018 0.002 PHE A 429 TRP 0.012 0.002 TRP D 549 HIS 0.003 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (10324) covalent geometry : angle 0.56519 / 0.31 (13938) hydrogen bonds : bond 0.05189 / 3.21 ( 725) hydrogen bonds : angle 4.25246 / 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 306 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 0.529 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: B 601 ASP cc_start: 0.6937 (t0) cc_final: 0.6485 (m-30) REVERT: B 675 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 684 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6562 (tm-30) REVERT: B 712 PHE cc_start: 0.5671 (t80) cc_final: 0.3605 (t80) REVERT: D 519 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: C 541 MET cc_start: 0.8061 (ptm) cc_final: 0.7608 (ttp) outliers start: 29 outliers final: 24 residues processed: 292 average time/residue: 0.1888 time to fit residues: 81.2475 Evaluate side-chains 295 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 510 SER 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 D residue 427 ASP 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 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: 0.6980 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: 0.6980 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.175517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159375 restraints weight = 41624.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.163695 restraints weight = 18230.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.166328 restraints weight = 10349.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.167830 restraints weight = 6991.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.169084 restraints weight = 5410.471| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10324 Z= 0.161 Angle : 0.562 8.133 13938 Z= 0.308 Chirality : 0.035 0.167 1568 Planarity : 0.004 0.068 1678 Dihedral : 9.553 98.297 1510 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.74 % Allowed : 18.92 % Favored : 78.34 % 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: 1.98 (0.25), residues: 1178 helix: 2.20 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.63 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 432 TYR 0.014 0.001 TYR D 555 PHE 0.021 0.001 PHE A 429 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 0.00344 / 0.16 (10324) covalent geometry : angle 0.56204 / 0.31 (13938) hydrogen bonds : bond 0.05109 / 3.17 ( 725) hydrogen bonds : angle 4.21985 / 2.99 ( 2139) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3361.52 seconds wall clock time: 58 minutes 3.33 seconds (3483.33 seconds total)