Starting phenix.real_space_refine on Sun Jul 27 19:19:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wst_32766/07_2025/7wst_32766.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wst_32766/07_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_32766/07_2025/7wst_32766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wst_32766/07_2025/7wst_32766.map" model { file = "/net/cci-nas-00/data/ceres_data/7wst_32766/07_2025/7wst_32766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wst_32766/07_2025/7wst_32766.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.02, per 1000 atoms: 1.06 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: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.77 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: 3.07 Time building geometry restraints manager: 2.88 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 45 through 678 or resid 801)) selection = (chain 'B' and (resid 45 through 678 or resid 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: 2.520 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 31.020 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:16.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.880 ------------------------------------------------------------------------------- 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 : 6.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.068 0.002 TRP B 302 HIS 0.002 0.001 HIS A 284 PHE 0.012 0.001 PHE B 534 TYR 0.017 0.002 TYR B 594 ARG 0.003 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.22186 ( 634) hydrogen bonds : angle 7.50370 ( 1884) SS BOND : bond 0.00095 ( 2) SS BOND : angle 1.61249 ( 4) covalent geometry : bond 0.00453 ( 9716) covalent geometry : angle 0.81490 (13224) *********************** 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 : 0.912 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: 1.2855 time to fit residues: 221.8852 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 : 0.919 ------------------------------------------------------------------------------- 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 101 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.0010 chunk 108 optimal weight: 2.9990 overall best weight: 1.0090 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.152530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119636 restraints weight = 10089.534| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.61 r_work: 0.3195 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9718 Z= 0.187 Angle : 0.670 8.986 13228 Z= 0.335 Chirality : 0.044 0.177 1494 Planarity : 0.005 0.037 1586 Dihedral : 8.927 56.345 1626 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.01 % Allowed : 7.37 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1194 helix: 1.54 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 302 HIS 0.003 0.001 HIS A 284 PHE 0.020 0.002 PHE A 534 TYR 0.020 0.002 TYR B 126 ARG 0.004 0.001 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.05941 ( 634) hydrogen bonds : angle 4.72056 ( 1884) SS BOND : bond 0.00218 ( 2) SS BOND : angle 2.01399 ( 4) covalent geometry : bond 0.00442 ( 9716) covalent geometry : angle 0.66894 (13224) *********************** 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 184 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.009 Fit side-chains REVERT: A 98 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6500 (mtp180) REVERT: A 108 ARG cc_start: 0.6781 (mmm-85) cc_final: 0.6147 (mmt180) REVERT: A 165 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8258 (mm) REVERT: A 665 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8066 (mptp) REVERT: B 98 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6515 (mtp180) REVERT: B 108 ARG cc_start: 0.6786 (mmm-85) cc_final: 0.6144 (mmt180) REVERT: B 165 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8255 (mm) REVERT: B 356 MET cc_start: 0.7061 (tmm) cc_final: 0.6717 (ttp) REVERT: B 665 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8084 (mptp) outliers start: 29 outliers final: 5 residues processed: 171 average time/residue: 1.1654 time to fit residues: 213.8246 Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG 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 98 ARG 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 48 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 62 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.153877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119350 restraints weight = 10052.635| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.75 r_work: 0.3180 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9718 Z= 0.135 Angle : 0.576 6.635 13228 Z= 0.290 Chirality : 0.041 0.202 1494 Planarity : 0.004 0.039 1586 Dihedral : 8.301 54.258 1626 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.18 % Allowed : 11.10 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1194 helix: 1.79 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -0.74 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 654 HIS 0.002 0.001 HIS B 284 PHE 0.016 0.002 PHE A 534 TYR 0.019 0.002 TYR B 126 ARG 0.003 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 634) hydrogen bonds : angle 4.29106 ( 1884) SS BOND : bond 0.00162 ( 2) SS BOND : angle 1.65984 ( 4) covalent geometry : bond 0.00305 ( 9716) covalent geometry : angle 0.57516 (13224) *********************** 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 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.918 Fit side-chains REVERT: A 88 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 108 ARG cc_start: 0.6627 (mmm-85) cc_final: 0.5971 (mmt180) REVERT: A 195 LYS cc_start: 0.8162 (mttp) cc_final: 0.7928 (mmtm) REVERT: A 433 MET cc_start: 0.8190 (tmm) cc_final: 0.7576 (ttm) REVERT: A 593 LYS cc_start: 0.8557 (pptt) cc_final: 0.8094 (pmtt) REVERT: A 665 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8024 (mptp) REVERT: B 88 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8262 (mp) REVERT: B 108 ARG cc_start: 0.6626 (mmm-85) cc_final: 0.5965 (mmt180) REVERT: B 195 LYS cc_start: 0.8166 (mttp) cc_final: 0.7933 (mmtm) REVERT: B 433 MET cc_start: 0.8202 (tmm) cc_final: 0.7590 (ttm) REVERT: B 665 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8016 (mptp) outliers start: 21 outliers final: 9 residues processed: 152 average time/residue: 1.1243 time to fit residues: 183.5647 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.0010 chunk 95 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.151282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117299 restraints weight = 9962.214| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.76 r_work: 0.3149 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9718 Z= 0.164 Angle : 0.612 6.395 13228 Z= 0.308 Chirality : 0.043 0.220 1494 Planarity : 0.005 0.043 1586 Dihedral : 8.440 57.422 1626 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.94 % Allowed : 10.27 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1194 helix: 1.83 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.77 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 654 HIS 0.003 0.001 HIS A 284 PHE 0.017 0.002 PHE B 534 TYR 0.016 0.002 TYR A 453 ARG 0.004 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 634) hydrogen bonds : angle 4.23365 ( 1884) SS BOND : bond 0.00223 ( 2) SS BOND : angle 1.95747 ( 4) covalent geometry : bond 0.00392 ( 9716) covalent geometry : angle 0.61143 (13224) *********************** 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 171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.921 Fit side-chains REVERT: A 88 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8281 (mp) REVERT: A 98 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6434 (mtp180) REVERT: A 108 ARG cc_start: 0.6653 (mmm-85) cc_final: 0.5961 (mmt180) REVERT: A 148 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 433 MET cc_start: 0.8173 (tmm) cc_final: 0.7637 (ttm) REVERT: A 593 LYS cc_start: 0.8641 (pptt) cc_final: 0.8099 (pmtt) REVERT: A 665 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8035 (mptp) REVERT: B 88 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8282 (mp) REVERT: B 98 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6442 (mtp180) REVERT: B 108 ARG cc_start: 0.6663 (mmm-85) cc_final: 0.5967 (mmt180) REVERT: B 148 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7841 (tt) REVERT: B 433 MET cc_start: 0.8189 (tmm) cc_final: 0.7651 (ttm) REVERT: B 665 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8027 (mptp) outliers start: 38 outliers final: 14 residues processed: 161 average time/residue: 1.1453 time to fit residues: 198.2776 Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 224 ILE 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 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 224 ILE Chi-restraints excluded: chain B residue 354 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 0.4980 chunk 103 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.153171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119430 restraints weight = 9975.475| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.72 r_work: 0.3183 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9718 Z= 0.132 Angle : 0.573 7.143 13228 Z= 0.286 Chirality : 0.041 0.225 1494 Planarity : 0.004 0.041 1586 Dihedral : 8.097 59.216 1626 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.63 % Allowed : 12.55 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1194 helix: 1.97 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.77 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 654 HIS 0.002 0.001 HIS B 284 PHE 0.014 0.001 PHE A 534 TYR 0.017 0.002 TYR B 126 ARG 0.002 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 634) hydrogen bonds : angle 4.09643 ( 1884) SS BOND : bond 0.00161 ( 2) SS BOND : angle 1.72669 ( 4) covalent geometry : bond 0.00302 ( 9716) covalent geometry : angle 0.57187 (13224) *********************** 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 168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.838 Fit side-chains REVERT: A 88 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 108 ARG cc_start: 0.6619 (mmm-85) cc_final: 0.5916 (mmt180) REVERT: A 148 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7835 (tt) REVERT: A 195 LYS cc_start: 0.8108 (mttp) cc_final: 0.7354 (mmtt) REVERT: A 433 MET cc_start: 0.8102 (tmm) cc_final: 0.7670 (ttm) REVERT: A 593 LYS cc_start: 0.8621 (pptt) cc_final: 0.8082 (pmtt) REVERT: A 665 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8032 (mptp) REVERT: B 88 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8260 (mp) REVERT: B 108 ARG cc_start: 0.6629 (mmm-85) cc_final: 0.5917 (mmt180) REVERT: B 148 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7850 (tt) REVERT: B 195 LYS cc_start: 0.8109 (mttp) cc_final: 0.7353 (mmtt) REVERT: B 433 MET cc_start: 0.8107 (tmm) cc_final: 0.7679 (ttm) REVERT: B 665 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8036 (mptp) outliers start: 35 outliers final: 9 residues processed: 153 average time/residue: 1.1611 time to fit residues: 190.6114 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 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 = 0.3721 r_free = 0.3721 target = 0.152434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118705 restraints weight = 9994.021| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.74 r_work: 0.3163 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9718 Z= 0.141 Angle : 0.590 7.221 13228 Z= 0.292 Chirality : 0.041 0.258 1494 Planarity : 0.004 0.042 1586 Dihedral : 8.089 59.832 1626 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.11 % Allowed : 14.00 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.25), residues: 1194 helix: 2.00 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 654 HIS 0.002 0.001 HIS B 284 PHE 0.014 0.002 PHE A 534 TYR 0.016 0.002 TYR B 126 ARG 0.003 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 634) hydrogen bonds : angle 4.09243 ( 1884) SS BOND : bond 0.00170 ( 2) SS BOND : angle 1.81507 ( 4) covalent geometry : bond 0.00329 ( 9716) covalent geometry : angle 0.58931 (13224) *********************** 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 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.927 Fit side-chains REVERT: A 88 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 98 ARG cc_start: 0.6785 (mtp180) cc_final: 0.6027 (mtt-85) REVERT: A 108 ARG cc_start: 0.6641 (mmm-85) cc_final: 0.5926 (mmt180) REVERT: A 148 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7819 (tt) REVERT: A 340 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: A 433 MET cc_start: 0.8016 (tmm) cc_final: 0.7633 (ttm) REVERT: A 665 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8042 (mptp) REVERT: B 88 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8299 (mp) REVERT: B 98 ARG cc_start: 0.6827 (mtp180) cc_final: 0.6100 (mtt-85) REVERT: B 108 ARG cc_start: 0.6649 (mmm-85) cc_final: 0.5929 (mmt180) REVERT: B 148 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7830 (tt) REVERT: B 340 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: B 433 MET cc_start: 0.8019 (tmm) cc_final: 0.7640 (ttm) REVERT: B 665 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8039 (mptp) outliers start: 30 outliers final: 14 residues processed: 148 average time/residue: 1.2964 time to fit residues: 205.6933 Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 340 ASP 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 274 THR Chi-restraints excluded: chain B residue 340 ASP 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 30 optimal weight: 0.6980 chunk 111 optimal weight: 0.0870 chunk 83 optimal weight: 0.0000 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.119985 restraints weight = 10063.539| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.74 r_work: 0.3193 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9718 Z= 0.127 Angle : 0.573 7.674 13228 Z= 0.283 Chirality : 0.041 0.259 1494 Planarity : 0.004 0.041 1586 Dihedral : 7.797 58.128 1626 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.70 % Allowed : 14.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1194 helix: 2.08 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.79 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 654 HIS 0.002 0.001 HIS B 284 PHE 0.014 0.001 PHE B 534 TYR 0.016 0.001 TYR B 126 ARG 0.002 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 634) hydrogen bonds : angle 4.02254 ( 1884) SS BOND : bond 0.00163 ( 2) SS BOND : angle 1.67015 ( 4) covalent geometry : bond 0.00291 ( 9716) covalent geometry : angle 0.57188 (13224) *********************** 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 167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.926 Fit side-chains REVERT: A 88 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8279 (mp) REVERT: A 98 ARG cc_start: 0.6778 (mtp180) cc_final: 0.6016 (mtt-85) REVERT: A 108 ARG cc_start: 0.6623 (mmm-85) cc_final: 0.5917 (mmt180) REVERT: A 148 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 195 LYS cc_start: 0.8089 (mttp) cc_final: 0.7365 (mmtt) REVERT: A 433 MET cc_start: 0.7984 (tmm) cc_final: 0.7551 (ttm) REVERT: A 665 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8019 (mptp) REVERT: B 88 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 98 ARG cc_start: 0.6784 (mtp180) cc_final: 0.6021 (mtt-85) REVERT: B 108 ARG cc_start: 0.6622 (mmm-85) cc_final: 0.5915 (mmt180) REVERT: B 148 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7848 (tt) REVERT: B 195 LYS cc_start: 0.8101 (mttp) cc_final: 0.7377 (mmtt) REVERT: B 433 MET cc_start: 0.7986 (tmm) cc_final: 0.7552 (ttm) REVERT: B 665 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8018 (mptp) outliers start: 26 outliers final: 13 residues processed: 161 average time/residue: 1.1298 time to fit residues: 195.6887 Evaluate side-chains 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 274 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.153273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119666 restraints weight = 10144.475| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.75 r_work: 0.3172 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9718 Z= 0.134 Angle : 0.593 9.563 13228 Z= 0.291 Chirality : 0.041 0.316 1494 Planarity : 0.004 0.042 1586 Dihedral : 7.674 55.376 1626 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.90 % Allowed : 14.94 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.25), residues: 1194 helix: 2.09 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 654 HIS 0.002 0.001 HIS B 284 PHE 0.014 0.001 PHE B 534 TYR 0.016 0.002 TYR A 126 ARG 0.002 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 634) hydrogen bonds : angle 4.01552 ( 1884) SS BOND : bond 0.00172 ( 2) SS BOND : angle 1.73760 ( 4) covalent geometry : bond 0.00309 ( 9716) covalent geometry : angle 0.59202 (13224) *********************** 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 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.943 Fit side-chains REVERT: A 88 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 98 ARG cc_start: 0.6795 (mtp180) cc_final: 0.6016 (mtt-85) REVERT: A 108 ARG cc_start: 0.6672 (mmm-85) cc_final: 0.5915 (mmt180) REVERT: A 195 LYS cc_start: 0.8087 (mttp) cc_final: 0.7365 (mmtt) REVERT: A 340 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: A 433 MET cc_start: 0.7938 (tmm) cc_final: 0.7626 (ttm) REVERT: A 665 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8023 (mptp) REVERT: B 88 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 98 ARG cc_start: 0.6789 (mtp180) cc_final: 0.6001 (mtt-85) REVERT: B 108 ARG cc_start: 0.6663 (mmm-85) cc_final: 0.5901 (mmt180) REVERT: B 195 LYS cc_start: 0.8083 (mttp) cc_final: 0.7385 (mmtt) REVERT: B 340 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: B 433 MET cc_start: 0.7946 (tmm) cc_final: 0.7634 (ttm) REVERT: B 665 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8032 (mptp) outliers start: 28 outliers final: 15 residues processed: 153 average time/residue: 1.2315 time to fit residues: 201.5605 Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 340 ASP 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 340 ASP 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 97 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 86 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.153739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120344 restraints weight = 10019.560| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.74 r_work: 0.3196 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2280 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= 0.130 Angle : 0.595 10.384 13228 Z= 0.290 Chirality : 0.042 0.346 1494 Planarity : 0.004 0.042 1586 Dihedral : 7.468 51.882 1626 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.80 % Allowed : 15.46 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.25), residues: 1194 helix: 2.11 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 654 HIS 0.002 0.001 HIS B 284 PHE 0.014 0.001 PHE B 576 TYR 0.016 0.001 TYR A 126 ARG 0.002 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 634) hydrogen bonds : angle 3.99332 ( 1884) SS BOND : bond 0.00170 ( 2) SS BOND : angle 1.68344 ( 4) covalent geometry : bond 0.00299 ( 9716) covalent geometry : angle 0.59468 (13224) *********************** 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 161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.011 Fit side-chains REVERT: A 88 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8272 (mp) REVERT: A 98 ARG cc_start: 0.6814 (mtp180) cc_final: 0.5986 (mtt-85) REVERT: A 108 ARG cc_start: 0.6700 (mmm-85) cc_final: 0.5921 (mtt-85) REVERT: A 195 LYS cc_start: 0.8084 (mttp) cc_final: 0.7387 (mmtt) REVERT: A 340 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: A 433 MET cc_start: 0.7951 (tmm) cc_final: 0.7514 (ttm) REVERT: B 88 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8281 (mp) REVERT: B 98 ARG cc_start: 0.6810 (mtp180) cc_final: 0.5972 (mtt-85) REVERT: B 108 ARG cc_start: 0.6687 (mmm-85) cc_final: 0.5901 (mtt-85) REVERT: B 195 LYS cc_start: 0.8079 (mttp) cc_final: 0.7382 (mmtt) REVERT: B 340 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: B 433 MET cc_start: 0.7962 (tmm) cc_final: 0.7529 (ttm) outliers start: 27 outliers final: 15 residues processed: 153 average time/residue: 1.2164 time to fit residues: 199.1326 Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 340 ASP 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 340 ASP 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 111 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 80 optimal weight: 0.0270 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.153207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119737 restraints weight = 10104.693| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.75 r_work: 0.3202 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9718 Z= 0.135 Angle : 0.603 9.698 13228 Z= 0.294 Chirality : 0.042 0.332 1494 Planarity : 0.004 0.042 1586 Dihedral : 7.309 51.670 1626 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.18 % Allowed : 16.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.25), residues: 1194 helix: 2.09 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 654 HIS 0.002 0.001 HIS B 284 PHE 0.015 0.002 PHE B 534 TYR 0.016 0.002 TYR A 126 ARG 0.002 0.000 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 634) hydrogen bonds : angle 4.01508 ( 1884) SS BOND : bond 0.00178 ( 2) SS BOND : angle 1.72676 ( 4) covalent geometry : bond 0.00312 ( 9716) covalent geometry : angle 0.60259 (13224) ********************** 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 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.875 Fit side-chains REVERT: A 88 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8273 (mp) REVERT: A 108 ARG cc_start: 0.6686 (mmm-85) cc_final: 0.6350 (mmt180) REVERT: A 195 LYS cc_start: 0.8071 (mttp) cc_final: 0.7391 (mmtt) REVERT: A 340 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7757 (m-30) REVERT: A 433 MET cc_start: 0.7901 (tmm) cc_final: 0.7440 (ttm) REVERT: B 88 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8288 (mp) REVERT: B 108 ARG cc_start: 0.6672 (mmm-85) cc_final: 0.6336 (mmt180) REVERT: B 195 LYS cc_start: 0.8067 (mttp) cc_final: 0.7385 (mmtt) REVERT: B 340 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7764 (m-30) REVERT: B 433 MET cc_start: 0.7910 (tmm) cc_final: 0.7596 (ttm) outliers start: 21 outliers final: 15 residues processed: 145 average time/residue: 1.3119 time to fit residues: 202.8544 Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 340 ASP 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 340 ASP 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 74 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.149337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115652 restraints weight = 10051.238| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.73 r_work: 0.3106 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9718 Z= 0.216 Angle : 0.701 10.607 13228 Z= 0.343 Chirality : 0.047 0.444 1494 Planarity : 0.005 0.046 1586 Dihedral : 8.026 53.389 1626 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.97 % Allowed : 17.12 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1194 helix: 1.87 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -0.89 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 654 HIS 0.004 0.001 HIS A 284 PHE 0.021 0.002 PHE A 534 TYR 0.018 0.002 TYR A 547 ARG 0.005 0.001 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.05221 ( 634) hydrogen bonds : angle 4.27664 ( 1884) SS BOND : bond 0.00289 ( 2) SS BOND : angle 2.05063 ( 4) covalent geometry : bond 0.00532 ( 9716) covalent geometry : angle 0.70033 (13224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7481.48 seconds wall clock time: 128 minutes 9.68 seconds (7689.68 seconds total)