Starting phenix.real_space_refine on Tue Nov 18 00:45:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wst_32766/11_2025/7wst_32766.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wst_32766/11_2025/7wst_32766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wst_32766/11_2025/7wst_32766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wst_32766/11_2025/7wst_32766.map" model { file = "/net/cci-nas-00/data/ceres_data/7wst_32766/11_2025/7wst_32766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wst_32766/11_2025/7wst_32766.cif" } resolution = 2.7 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= -0.002 sd= 0.088 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: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 74 5.16 5 C 6314 2.51 5 N 1454 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9438 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4627 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 29, 'TRANS': 571} Chain breaks: 1 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {' FE': 1, '554': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 92 Unusual residues: {' FE': 1, '554': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B Time building chain proxies: 3.92, per 1000 atoms: 0.42 Number of scatterers: 9438 At special positions: 0 Unit cell: (120.132, 100.248, 82.0215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 74 16.00 O 1594 8.00 N 1454 7.00 C 6314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 250 " - pdb=" SG CYS B 671 " distance=2.03 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: 0.98 Conformation dependent library (CDL) restraints added in 381.0 milliseconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 1 sheets defined 78.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 50 through 73 Processing helix chain 'A' and resid 81 through 103 removed outlier: 3.502A pdb=" N LEU A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 removed outlier: 3.972A pdb=" N ILE A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 141 Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.712A pdb=" N GLY A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 192 removed outlier: 3.553A pdb=" N ALA A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY A 179 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.079A pdb=" N GLN A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 213 Processing helix chain 'A' and resid 219 through 243 removed outlier: 4.206A pdb=" N PHE A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 265 removed outlier: 3.553A pdb=" N GLN A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.803A pdb=" N ILE A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 359 removed outlier: 3.597A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 416 removed outlier: 3.798A pdb=" N TYR A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 420 through 446 removed outlier: 3.699A pdb=" N VAL A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 470 through 501 removed outlier: 3.574A pdb=" N SER A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 534 Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 545 through 560 removed outlier: 4.044A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 590 removed outlier: 3.569A pdb=" N MET A 590 " --> pdb=" O THR A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.632A pdb=" N LYS A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 612 through 632 Processing helix chain 'A' and resid 632 through 664 removed outlier: 4.038A pdb=" N PHE A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Proline residue: A 641 - end of helix removed outlier: 3.580A pdb=" N THR A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 656 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Proline residue: A 657 - end of helix Processing helix chain 'B' and resid 50 through 73 Processing helix chain 'B' and resid 81 through 103 removed outlier: 3.502A pdb=" N LEU B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 132 removed outlier: 3.971A pdb=" N ILE B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA B 129 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 141 Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.712A pdb=" N GLY B 150 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 192 removed outlier: 3.553A pdb=" N ALA B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY B 179 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 4.079A pdb=" N GLN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 213 Processing helix chain 'B' and resid 219 through 243 removed outlier: 4.205A pdb=" N PHE B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 265 removed outlier: 3.553A pdb=" N GLN B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 removed outlier: 3.803A pdb=" N ILE B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 300 through 306 Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 359 removed outlier: 3.596A pdb=" N LYS B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 416 removed outlier: 3.797A pdb=" N TYR B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 420 through 446 removed outlier: 3.699A pdb=" N VAL B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'B' and resid 449 through 464 Processing helix chain 'B' and resid 470 through 501 removed outlier: 3.573A pdb=" N SER B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 534 Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 545 through 560 removed outlier: 4.044A pdb=" N LEU B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 590 removed outlier: 3.569A pdb=" N MET B 590 " --> pdb=" O THR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.633A pdb=" N LYS B 596 " --> pdb=" O HIS B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 609 Processing helix chain 'B' and resid 612 through 632 Processing helix chain 'B' and resid 632 through 664 removed outlier: 4.038A pdb=" N PHE B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Proline residue: B 641 - end of helix removed outlier: 3.581A pdb=" N THR B 655 " --> pdb=" O ASP B 651 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE B 656 " --> pdb=" O GLY B 652 " (cutoff:3.500A) Proline residue: B 657 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 675 634 hydrogen bonds defined for protein. 1884 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: 1.59 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2713 1.34 - 1.46: 1689 1.46 - 1.57: 5186 1.57 - 1.69: 2 1.69 - 1.81: 126 Bond restraints: 9716 Sorted by residual: bond pdb=" CAI Y01 A 801 " pdb=" CAK Y01 A 801 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" CAI Y01 B 702 " pdb=" CAK Y01 B 702 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CAI Y01 A 804 " pdb=" CAK Y01 A 804 " ideal model delta sigma weight residual 1.492 1.407 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CAI Y01 B 701 " pdb=" CAK Y01 B 701 " ideal model delta sigma weight residual 1.492 1.408 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1 554 B 704 " pdb=" C2 554 B 704 " ideal model delta sigma weight residual 1.528 1.460 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 9711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 12950 2.39 - 4.78: 208 4.78 - 7.17: 40 7.17 - 9.55: 12 9.55 - 11.94: 14 Bond angle restraints: 13224 Sorted by residual: angle pdb=" OAG Y01 A 801 " pdb=" CAY Y01 A 801 " pdb=" OAW Y01 A 801 " ideal model delta sigma weight residual 123.38 111.44 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" OAG Y01 B 702 " pdb=" CAY Y01 B 702 " pdb=" OAW Y01 B 702 " ideal model delta sigma weight residual 123.38 111.44 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" OAG Y01 A 804 " pdb=" CAY Y01 A 804 " pdb=" OAW Y01 A 804 " ideal model delta sigma weight residual 123.38 111.44 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" OAG Y01 B 701 " pdb=" CAY Y01 B 701 " pdb=" OAW Y01 B 701 " ideal model delta sigma weight residual 123.38 111.51 11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CAM Y01 A 804 " pdb=" CAY Y01 A 804 " pdb=" OAW Y01 A 804 " ideal model delta sigma weight residual 111.19 122.88 -11.69 3.00e+00 1.11e-01 1.52e+01 ... (remaining 13219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 5292 16.84 - 33.69: 394 33.69 - 50.53: 86 50.53 - 67.37: 22 67.37 - 84.22: 4 Dihedral angle restraints: 5798 sinusoidal: 2386 harmonic: 3412 Sorted by residual: dihedral pdb=" CB CYS B 250 " pdb=" SG CYS B 250 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -149.27 63.27 1 1.00e+01 1.00e-02 5.28e+01 dihedral pdb=" CB CYS A 250 " pdb=" SG CYS A 250 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -149.27 63.27 1 1.00e+01 1.00e-02 5.28e+01 dihedral pdb=" CA MET A 602 " pdb=" C MET A 602 " pdb=" N ALA A 603 " pdb=" CA ALA A 603 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 5795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1083 0.041 - 0.083: 311 0.083 - 0.124: 80 0.124 - 0.165: 12 0.165 - 0.207: 8 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CBF Y01 B 702 " pdb=" CAS Y01 B 702 " pdb=" CBD Y01 B 702 " pdb=" CBH Y01 B 702 " both_signs ideal model delta sigma weight residual False -2.45 -2.65 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CBF Y01 A 801 " pdb=" CAS Y01 A 801 " pdb=" CBD Y01 A 801 " pdb=" CBH Y01 A 801 " both_signs ideal model delta sigma weight residual False -2.45 -2.65 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C11 554 B 704 " pdb=" C10 554 B 704 " pdb=" C12 554 B 704 " pdb=" O8 554 B 704 " both_signs ideal model delta sigma weight residual False -2.32 -2.50 0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 1491 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 302 " -0.028 2.00e-02 2.50e+03 2.59e-02 1.67e+01 pdb=" CG TRP B 302 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP B 302 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP B 302 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 302 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 302 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 302 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 302 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 302 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 302 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 302 " 0.029 2.00e-02 2.50e+03 2.56e-02 1.63e+01 pdb=" CG TRP A 302 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 302 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 302 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 302 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 302 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 302 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 302 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 302 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 302 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 606 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO B 607 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 607 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 607 " 0.019 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 60 2.55 - 3.14: 7575 3.14 - 3.73: 14964 3.73 - 4.31: 21806 4.31 - 4.90: 35860 Nonbonded interactions: 80265 Sorted by model distance: nonbonded pdb="FE FE B 703 " pdb=" O4 554 B 704 " model vdw 1.968 2.260 nonbonded pdb="FE FE A 802 " pdb=" O4 554 A 803 " model vdw 1.968 2.260 nonbonded pdb="FE FE A 802 " pdb=" O6 554 A 803 " model vdw 1.982 2.260 nonbonded pdb="FE FE B 703 " pdb=" O6 554 B 704 " model vdw 1.983 2.260 nonbonded pdb="FE FE A 802 " pdb=" O1 554 A 803 " model vdw 2.001 2.260 ... (remaining 80260 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 45 through 801) selection = (chain 'B' and resid 45 through 701) } 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 individual isotropic 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: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.050 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.005 0.087 9718 Z= 0.214 Angle : 0.815 11.943 13228 Z= 0.377 Chirality : 0.043 0.207 1494 Planarity : 0.004 0.035 1586 Dihedral : 12.865 84.218 3636 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.24), residues: 1194 helix: 0.86 (0.17), residues: 822 sheet: None (None), residues: 0 loop : -1.02 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 552 TYR 0.017 0.002 TYR B 594 PHE 0.012 0.001 PHE B 534 TRP 0.068 0.002 TRP B 302 HIS 0.002 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9716) covalent geometry : angle 0.81490 (13224) SS BOND : bond 0.00095 ( 2) SS BOND : angle 1.61249 ( 4) hydrogen bonds : bond 0.22186 ( 634) hydrogen bonds : angle 7.50370 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 108 ARG cc_start: 0.6650 (mmm-85) cc_final: 0.6362 (mmt180) REVERT: A 195 LYS cc_start: 0.7764 (mttp) cc_final: 0.7336 (mmtt) REVERT: A 338 MET cc_start: 0.7785 (mmm) cc_final: 0.7583 (mmm) REVERT: A 593 LYS cc_start: 0.8455 (pptt) cc_final: 0.7956 (pttt) REVERT: A 665 LYS cc_start: 0.8377 (mtmt) cc_final: 0.7826 (mptp) REVERT: B 108 ARG cc_start: 0.6651 (mmm-85) cc_final: 0.6360 (mmt180) REVERT: B 195 LYS cc_start: 0.7764 (mttp) cc_final: 0.7337 (mmtt) REVERT: B 338 MET cc_start: 0.7787 (mmm) cc_final: 0.7583 (mmm) REVERT: B 593 LYS cc_start: 0.8456 (pptt) cc_final: 0.7987 (pttt) REVERT: B 665 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7833 (mptp) outliers start: 0 outliers final: 2 residues processed: 162 average time/residue: 0.6378 time to fit residues: 110.0145 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 148 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122742 restraints weight = 10190.020| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.63 r_work: 0.3255 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9718 Z= 0.146 Angle : 0.623 8.698 13228 Z= 0.313 Chirality : 0.042 0.143 1494 Planarity : 0.005 0.035 1586 Dihedral : 8.610 56.563 1626 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.80 % Allowed : 7.78 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.24), residues: 1194 helix: 1.64 (0.17), residues: 848 sheet: None (None), residues: 0 loop : -0.89 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 552 TYR 0.021 0.002 TYR B 126 PHE 0.017 0.002 PHE A 534 TRP 0.016 0.002 TRP B 302 HIS 0.002 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9716) covalent geometry : angle 0.62253 (13224) SS BOND : bond 0.00201 ( 2) SS BOND : angle 1.50113 ( 4) hydrogen bonds : bond 0.05229 ( 634) hydrogen bonds : angle 4.60695 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.396 Fit side-chains REVERT: A 108 ARG cc_start: 0.6678 (mmm-85) cc_final: 0.6092 (mmt180) REVERT: A 165 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8183 (mm) REVERT: A 195 LYS cc_start: 0.7909 (mttp) cc_final: 0.7306 (mmtt) REVERT: A 582 ILE cc_start: 0.8550 (mm) cc_final: 0.8349 (mt) REVERT: A 665 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8052 (mptp) REVERT: B 108 ARG cc_start: 0.6685 (mmm-85) cc_final: 0.6088 (mmt180) REVERT: B 165 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8163 (mm) REVERT: B 195 LYS cc_start: 0.7914 (mttp) cc_final: 0.7308 (mmtt) REVERT: B 356 MET cc_start: 0.7083 (tmm) cc_final: 0.6805 (ttp) REVERT: B 582 ILE cc_start: 0.8552 (mm) cc_final: 0.8351 (mt) REVERT: B 665 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8036 (mptp) outliers start: 27 outliers final: 5 residues processed: 176 average time/residue: 0.5781 time to fit residues: 109.1886 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 94 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN B 632 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116583 restraints weight = 10034.460| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.76 r_work: 0.3136 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9718 Z= 0.209 Angle : 0.657 5.819 13228 Z= 0.331 Chirality : 0.045 0.228 1494 Planarity : 0.005 0.044 1586 Dihedral : 8.855 55.187 1626 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.32 % Allowed : 9.65 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.39 (0.25), residues: 1194 helix: 1.62 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.84 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 552 TYR 0.017 0.002 TYR A 453 PHE 0.021 0.002 PHE A 534 TRP 0.014 0.002 TRP A 654 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9716) covalent geometry : angle 0.65601 (13224) SS BOND : bond 0.00203 ( 2) SS BOND : angle 2.22442 ( 4) hydrogen bonds : bond 0.05514 ( 634) hydrogen bonds : angle 4.49447 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.413 Fit side-chains REVERT: A 88 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8297 (mp) REVERT: A 98 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6483 (mtp180) REVERT: A 108 ARG cc_start: 0.6710 (mmm-85) cc_final: 0.6020 (mmt180) REVERT: A 195 LYS cc_start: 0.7928 (mttp) cc_final: 0.7460 (mmtm) REVERT: A 356 MET cc_start: 0.7152 (tmm) cc_final: 0.6873 (ttp) REVERT: A 433 MET cc_start: 0.8007 (tpt) cc_final: 0.7326 (ttm) REVERT: A 582 ILE cc_start: 0.8536 (mm) cc_final: 0.8328 (mt) REVERT: A 665 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8049 (mptp) REVERT: B 88 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8294 (mp) REVERT: B 98 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6498 (mtp180) REVERT: B 108 ARG cc_start: 0.6712 (mmm-85) cc_final: 0.6017 (mmt180) REVERT: B 195 LYS cc_start: 0.7912 (mttp) cc_final: 0.7445 (mmtm) REVERT: B 433 MET cc_start: 0.8015 (tpt) cc_final: 0.7376 (ttm) REVERT: B 582 ILE cc_start: 0.8541 (mm) cc_final: 0.8335 (mt) REVERT: B 665 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8058 (mptp) outliers start: 32 outliers final: 12 residues processed: 156 average time/residue: 0.5978 time to fit residues: 99.9376 Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 354 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 119 optimal weight: 0.0670 chunk 8 optimal weight: 0.0980 chunk 43 optimal weight: 0.4980 chunk 5 optimal weight: 0.0020 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 overall best weight: 0.2526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 632 ASN B 115 ASN B 632 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.156106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122589 restraints weight = 10050.378| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.66 r_work: 0.3241 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9718 Z= 0.111 Angle : 0.533 6.499 13228 Z= 0.268 Chirality : 0.039 0.169 1494 Planarity : 0.004 0.037 1586 Dihedral : 7.917 55.945 1626 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.90 % Allowed : 12.03 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.25), residues: 1194 helix: 1.92 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -0.71 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 552 TYR 0.018 0.001 TYR A 126 PHE 0.012 0.001 PHE A 579 TRP 0.015 0.001 TRP B 395 HIS 0.001 0.000 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9716) covalent geometry : angle 0.53293 (13224) SS BOND : bond 0.00136 ( 2) SS BOND : angle 1.40853 ( 4) hydrogen bonds : bond 0.04070 ( 634) hydrogen bonds : angle 4.09675 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.351 Fit side-chains REVERT: A 98 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6462 (mtp180) REVERT: A 108 ARG cc_start: 0.6608 (mmm-85) cc_final: 0.5948 (mmt180) REVERT: A 148 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 195 LYS cc_start: 0.7912 (mttp) cc_final: 0.7449 (mmtm) REVERT: A 396 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5489 (mmp) REVERT: A 433 MET cc_start: 0.7846 (tpt) cc_final: 0.7299 (ttm) REVERT: A 582 ILE cc_start: 0.8626 (mm) cc_final: 0.8418 (mt) REVERT: A 665 LYS cc_start: 0.8694 (mtmt) cc_final: 0.7995 (mptp) REVERT: B 98 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6460 (mtp180) REVERT: B 108 ARG cc_start: 0.6619 (mmm-85) cc_final: 0.5954 (mmt180) REVERT: B 148 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7877 (tt) REVERT: B 195 LYS cc_start: 0.7900 (mttp) cc_final: 0.7436 (mmtm) REVERT: B 396 MET cc_start: 0.5771 (OUTLIER) cc_final: 0.5484 (mmp) REVERT: B 433 MET cc_start: 0.7848 (tpt) cc_final: 0.7311 (ttm) REVERT: B 582 ILE cc_start: 0.8634 (mm) cc_final: 0.8430 (mt) REVERT: B 665 LYS cc_start: 0.8703 (mtmt) cc_final: 0.7990 (mptp) outliers start: 28 outliers final: 4 residues processed: 159 average time/residue: 0.5410 time to fit residues: 92.4504 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 396 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 90 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.152644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118781 restraints weight = 10038.866| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.75 r_work: 0.3166 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9718 Z= 0.147 Angle : 0.583 7.459 13228 Z= 0.292 Chirality : 0.041 0.227 1494 Planarity : 0.004 0.042 1586 Dihedral : 8.146 58.282 1626 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.11 % Allowed : 12.76 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.25), residues: 1194 helix: 1.99 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.76 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.015 0.002 TYR A 453 PHE 0.015 0.002 PHE B 534 TRP 0.012 0.001 TRP A 654 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9716) covalent geometry : angle 0.58225 (13224) SS BOND : bond 0.00177 ( 2) SS BOND : angle 1.81926 ( 4) hydrogen bonds : bond 0.04557 ( 634) hydrogen bonds : angle 4.12145 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.366 Fit side-chains REVERT: A 88 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8236 (mp) REVERT: A 108 ARG cc_start: 0.6623 (mmm-85) cc_final: 0.5918 (mmt180) REVERT: A 148 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 195 LYS cc_start: 0.7934 (mttp) cc_final: 0.7261 (mmtt) REVERT: A 433 MET cc_start: 0.7906 (tpt) cc_final: 0.7521 (ttm) REVERT: A 582 ILE cc_start: 0.8604 (mm) cc_final: 0.8387 (mt) REVERT: A 665 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8026 (mptp) REVERT: B 88 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 108 ARG cc_start: 0.6620 (mmm-85) cc_final: 0.5916 (mmt180) REVERT: B 148 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7860 (tt) REVERT: B 195 LYS cc_start: 0.7904 (mttp) cc_final: 0.7252 (mmtt) REVERT: B 433 MET cc_start: 0.7920 (tpt) cc_final: 0.7353 (ttm) REVERT: B 582 ILE cc_start: 0.8590 (mm) cc_final: 0.8378 (mt) REVERT: B 665 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8024 (mptp) outliers start: 30 outliers final: 10 residues processed: 146 average time/residue: 0.5927 time to fit residues: 92.8216 Evaluate side-chains 141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 354 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119388 restraints weight = 10015.271| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.66 r_work: 0.3197 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9718 Z= 0.138 Angle : 0.576 7.957 13228 Z= 0.287 Chirality : 0.041 0.255 1494 Planarity : 0.004 0.042 1586 Dihedral : 8.001 59.916 1626 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.80 % Allowed : 14.42 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.25), residues: 1194 helix: 2.03 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.79 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 552 TYR 0.015 0.002 TYR B 126 PHE 0.015 0.002 PHE B 534 TRP 0.013 0.001 TRP B 654 HIS 0.002 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9716) covalent geometry : angle 0.57510 (13224) SS BOND : bond 0.00175 ( 2) SS BOND : angle 1.70970 ( 4) hydrogen bonds : bond 0.04385 ( 634) hydrogen bonds : angle 4.07995 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.379 Fit side-chains REVERT: A 88 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8240 (mp) REVERT: A 98 ARG cc_start: 0.6769 (mtp180) cc_final: 0.6002 (mtt-85) REVERT: A 108 ARG cc_start: 0.6616 (mmm-85) cc_final: 0.5906 (mmt180) REVERT: A 148 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7829 (tt) REVERT: A 195 LYS cc_start: 0.7901 (mttp) cc_final: 0.7186 (mmtt) REVERT: A 433 MET cc_start: 0.7859 (tpt) cc_final: 0.7472 (ttm) REVERT: A 582 ILE cc_start: 0.8572 (mm) cc_final: 0.8361 (mt) REVERT: A 665 LYS cc_start: 0.8693 (mtmt) cc_final: 0.7993 (mptp) REVERT: B 88 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8238 (mp) REVERT: B 98 ARG cc_start: 0.6766 (mtp180) cc_final: 0.6002 (mtt-85) REVERT: B 108 ARG cc_start: 0.6614 (mmm-85) cc_final: 0.5902 (mmt180) REVERT: B 148 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7850 (tt) REVERT: B 195 LYS cc_start: 0.7887 (mttp) cc_final: 0.7195 (mmtt) REVERT: B 433 MET cc_start: 0.7880 (tpt) cc_final: 0.7505 (ttm) REVERT: B 582 ILE cc_start: 0.8584 (mm) cc_final: 0.8380 (mt) REVERT: B 665 LYS cc_start: 0.8702 (mtmt) cc_final: 0.7984 (mptp) outliers start: 27 outliers final: 12 residues processed: 156 average time/residue: 0.5853 time to fit residues: 97.9643 Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 354 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 80 optimal weight: 0.0000 chunk 94 optimal weight: 0.6980 chunk 11 optimal weight: 0.0170 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.154689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121112 restraints weight = 10100.519| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.67 r_work: 0.3201 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9718 Z= 0.120 Angle : 0.559 8.884 13228 Z= 0.277 Chirality : 0.040 0.277 1494 Planarity : 0.004 0.041 1586 Dihedral : 7.681 58.480 1626 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.28 % Allowed : 15.25 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.25), residues: 1194 helix: 2.12 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.74 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 552 TYR 0.015 0.001 TYR A 126 PHE 0.013 0.001 PHE A 576 TRP 0.013 0.001 TRP A 654 HIS 0.002 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9716) covalent geometry : angle 0.55846 (13224) SS BOND : bond 0.00159 ( 2) SS BOND : angle 1.53749 ( 4) hydrogen bonds : bond 0.04078 ( 634) hydrogen bonds : angle 3.99203 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.422 Fit side-chains REVERT: A 88 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8252 (mp) REVERT: A 98 ARG cc_start: 0.6792 (mtp180) cc_final: 0.6019 (mtt-85) REVERT: A 108 ARG cc_start: 0.6623 (mmm-85) cc_final: 0.5911 (mmt180) REVERT: A 148 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7839 (tt) REVERT: A 195 LYS cc_start: 0.7940 (mttp) cc_final: 0.7233 (mmtt) REVERT: A 433 MET cc_start: 0.7844 (tpt) cc_final: 0.7178 (ttm) REVERT: A 582 ILE cc_start: 0.8646 (mm) cc_final: 0.8432 (mt) REVERT: A 593 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8148 (pmtt) REVERT: A 665 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8018 (mptp) REVERT: B 88 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8249 (mp) REVERT: B 98 ARG cc_start: 0.6789 (mtp180) cc_final: 0.6008 (mtt-85) REVERT: B 108 ARG cc_start: 0.6615 (mmm-85) cc_final: 0.5907 (mmt180) REVERT: B 148 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7857 (tt) REVERT: B 195 LYS cc_start: 0.7933 (mttp) cc_final: 0.7226 (mmtt) REVERT: B 433 MET cc_start: 0.7856 (tpt) cc_final: 0.7220 (ttm) REVERT: B 582 ILE cc_start: 0.8651 (mm) cc_final: 0.8443 (mt) REVERT: B 665 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8017 (mptp) outliers start: 22 outliers final: 10 residues processed: 154 average time/residue: 0.5884 time to fit residues: 96.9810 Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 354 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 91 optimal weight: 10.0000 chunk 39 optimal weight: 0.0980 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119361 restraints weight = 10036.227| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.67 r_work: 0.3176 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9718 Z= 0.141 Angle : 0.591 9.904 13228 Z= 0.293 Chirality : 0.042 0.335 1494 Planarity : 0.004 0.043 1586 Dihedral : 7.718 56.159 1626 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.39 % Allowed : 15.98 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.25), residues: 1194 helix: 2.08 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.77 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 552 TYR 0.014 0.002 TYR A 126 PHE 0.015 0.002 PHE B 534 TRP 0.011 0.001 TRP A 654 HIS 0.002 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9716) covalent geometry : angle 0.59073 (13224) SS BOND : bond 0.00185 ( 2) SS BOND : angle 1.75937 ( 4) hydrogen bonds : bond 0.04382 ( 634) hydrogen bonds : angle 4.04183 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.351 Fit side-chains REVERT: A 88 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 98 ARG cc_start: 0.6837 (mtp180) cc_final: 0.6018 (mtt-85) REVERT: A 108 ARG cc_start: 0.6675 (mmm-85) cc_final: 0.5917 (mmt180) REVERT: A 195 LYS cc_start: 0.7968 (mttp) cc_final: 0.7280 (mmtt) REVERT: A 433 MET cc_start: 0.7899 (tpt) cc_final: 0.7492 (ttm) REVERT: A 582 ILE cc_start: 0.8601 (mm) cc_final: 0.8392 (mt) REVERT: A 593 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8157 (pmtt) REVERT: A 665 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8026 (mptp) REVERT: B 88 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8267 (mp) REVERT: B 98 ARG cc_start: 0.6830 (mtp180) cc_final: 0.6011 (mtt-85) REVERT: B 108 ARG cc_start: 0.6668 (mmm-85) cc_final: 0.5908 (mmt180) REVERT: B 195 LYS cc_start: 0.7965 (mttp) cc_final: 0.7281 (mmtt) REVERT: B 433 MET cc_start: 0.7916 (tpt) cc_final: 0.7366 (ttm) REVERT: B 582 ILE cc_start: 0.8615 (mm) cc_final: 0.8414 (mt) REVERT: B 665 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8023 (mptp) outliers start: 23 outliers final: 12 residues processed: 151 average time/residue: 0.6035 time to fit residues: 97.1611 Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 354 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 106 optimal weight: 0.0030 chunk 46 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120799 restraints weight = 10002.228| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.72 r_work: 0.3205 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9718 Z= 0.127 Angle : 0.577 9.542 13228 Z= 0.285 Chirality : 0.041 0.322 1494 Planarity : 0.004 0.042 1586 Dihedral : 7.471 53.526 1626 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.07 % Allowed : 16.70 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1194 helix: 2.15 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 552 TYR 0.016 0.001 TYR A 126 PHE 0.014 0.001 PHE B 534 TRP 0.013 0.001 TRP A 654 HIS 0.002 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9716) covalent geometry : angle 0.57628 (13224) SS BOND : bond 0.00178 ( 2) SS BOND : angle 1.63516 ( 4) hydrogen bonds : bond 0.04175 ( 634) hydrogen bonds : angle 3.98971 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.324 Fit side-chains REVERT: A 88 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8247 (mp) REVERT: A 108 ARG cc_start: 0.6677 (mmm-85) cc_final: 0.5918 (mmt180) REVERT: A 148 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7799 (tt) REVERT: A 195 LYS cc_start: 0.7967 (mttp) cc_final: 0.7270 (mmtt) REVERT: A 433 MET cc_start: 0.7860 (tpt) cc_final: 0.7260 (ttm) REVERT: A 582 ILE cc_start: 0.8596 (mm) cc_final: 0.8390 (mt) REVERT: A 593 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8152 (pmtt) REVERT: A 665 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8026 (mptp) REVERT: B 88 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 108 ARG cc_start: 0.6672 (mmm-85) cc_final: 0.5911 (mmt180) REVERT: B 148 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 195 LYS cc_start: 0.7962 (mttp) cc_final: 0.7265 (mmtt) REVERT: B 433 MET cc_start: 0.7880 (tpt) cc_final: 0.7299 (ttm) REVERT: B 665 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8016 (mptp) outliers start: 20 outliers final: 10 residues processed: 148 average time/residue: 0.6155 time to fit residues: 97.3179 Evaluate side-chains 141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 354 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 115 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121263 restraints weight = 10044.767| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.75 r_work: 0.3208 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9718 Z= 0.124 Angle : 0.569 9.259 13228 Z= 0.282 Chirality : 0.041 0.304 1494 Planarity : 0.004 0.042 1586 Dihedral : 7.186 51.344 1626 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.76 % Allowed : 16.70 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.08 (0.25), residues: 1194 helix: 2.18 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 552 TYR 0.016 0.001 TYR A 126 PHE 0.013 0.001 PHE A 534 TRP 0.013 0.001 TRP A 654 HIS 0.002 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9716) covalent geometry : angle 0.56799 (13224) SS BOND : bond 0.00171 ( 2) SS BOND : angle 1.67920 ( 4) hydrogen bonds : bond 0.04116 ( 634) hydrogen bonds : angle 3.96927 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.365 Fit side-chains REVERT: A 88 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 108 ARG cc_start: 0.6683 (mmm-85) cc_final: 0.6334 (mmt180) REVERT: A 148 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7785 (tt) REVERT: A 195 LYS cc_start: 0.7970 (mttp) cc_final: 0.7255 (mmtt) REVERT: A 433 MET cc_start: 0.7831 (tpt) cc_final: 0.7205 (ttm) REVERT: A 582 ILE cc_start: 0.8606 (mm) cc_final: 0.8395 (mt) REVERT: A 593 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8137 (pmtt) REVERT: A 665 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8006 (mptp) REVERT: B 88 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8276 (mp) REVERT: B 108 ARG cc_start: 0.6670 (mmm-85) cc_final: 0.6339 (mmt180) REVERT: B 148 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7803 (tt) REVERT: B 195 LYS cc_start: 0.7963 (mttp) cc_final: 0.7255 (mmtt) REVERT: B 433 MET cc_start: 0.7855 (tpt) cc_final: 0.7273 (ttm) REVERT: B 665 LYS cc_start: 0.8703 (mtmt) cc_final: 0.7992 (mptp) outliers start: 17 outliers final: 10 residues processed: 140 average time/residue: 0.5988 time to fit residues: 89.8204 Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 354 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118251 restraints weight = 9936.037| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.72 r_work: 0.3165 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9718 Z= 0.164 Angle : 0.627 9.993 13228 Z= 0.310 Chirality : 0.044 0.374 1494 Planarity : 0.005 0.045 1586 Dihedral : 7.476 52.116 1626 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 16.70 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.92 (0.25), residues: 1194 helix: 2.05 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 552 TYR 0.015 0.002 TYR A 547 PHE 0.019 0.002 PHE B 534 TRP 0.010 0.001 TRP B 654 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9716) covalent geometry : angle 0.62671 (13224) SS BOND : bond 0.00219 ( 2) SS BOND : angle 1.87051 ( 4) hydrogen bonds : bond 0.04680 ( 634) hydrogen bonds : angle 4.12576 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3512.52 seconds wall clock time: 60 minutes 37.63 seconds (3637.63 seconds total)