Starting phenix.real_space_refine on Thu Jul 2 17:44:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wsr_32765/07_2026/7wsr_32765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsr_32765/07_2026/7wsr_32765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsr_32765/07_2026/7wsr_32765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsr_32765/07_2026/7wsr_32765.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wsr_32765/07_2026/7wsr_32765.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wsr_32765/07_2026/7wsr_32765.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wsr_32765/07_2026/7wsr_32765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsr_32765/07_2026/7wsr_32765.cif" } resolution = 2.9 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= -0.003 sd= 0.061 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 6268 2.51 5 N 1446 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9366 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4613 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 29, 'TRANS': 570} Chain breaks: 1 Chain: "B" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4613 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 29, 'TRANS': 570} Chain breaks: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.97, per 1000 atoms: 0.21 Number of scatterers: 9366 At special positions: 0 Unit cell: (101.905, 138.359, 82.0215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 1578 8.00 N 1446 7.00 C 6268 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: 0.84 Conformation dependent library (CDL) restraints added in 290.7 milliseconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 1 sheets defined 78.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 50 through 75 Processing helix chain 'A' and resid 81 through 104 removed outlier: 3.642A pdb=" N ALA A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 removed outlier: 3.541A pdb=" N TYR A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.651A pdb=" N LEU A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.576A pdb=" N GLY A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 191 removed outlier: 4.256A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 179 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.982A pdb=" N GLN A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 213 Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.564A pdb=" N TYR A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 265 Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.915A 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: 3.674A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 416 removed outlier: 3.927A 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: 3.731A pdb=" N VAL A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.553A pdb=" N LEU A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 470 through 501 removed outlier: 3.539A pdb=" N GLN A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 534 removed outlier: 3.562A pdb=" N ILE A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 545 through 560 removed outlier: 3.936A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 568 through 590 removed outlier: 3.639A pdb=" N ASP A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 removed outlier: 3.801A pdb=" N VAL A 606 " --> pdb=" O MET A 602 " (cutoff:3.500A) Proline residue: A 607 - end of helix removed outlier: 3.561A pdb=" N VAL A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 632 Processing helix chain 'A' and resid 632 through 664 removed outlier: 4.154A pdb=" N PHE A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Proline residue: A 641 - end of helix removed outlier: 3.508A pdb=" N THR A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 4.268A 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 75 Processing helix chain 'B' and resid 81 through 104 removed outlier: 3.642A pdb=" N ALA B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 132 removed outlier: 3.540A pdb=" N TYR B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA B 129 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 removed outlier: 3.651A pdb=" N LEU B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.575A pdb=" N GLY B 150 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 191 removed outlier: 4.256A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY B 179 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.980A pdb=" N GLN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 213 Processing helix chain 'B' and resid 219 through 243 removed outlier: 3.565A pdb=" N TYR B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 265 Processing helix chain 'B' and resid 272 through 281 removed outlier: 3.914A 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: 3.674A pdb=" N LYS B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 416 removed outlier: 3.927A 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: 3.732A pdb=" N VAL B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.553A pdb=" N LEU B 444 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 464 Processing helix chain 'B' and resid 470 through 501 removed outlier: 3.539A pdb=" N GLN B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 534 removed outlier: 3.563A pdb=" N ILE B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 545 through 560 removed outlier: 3.936A pdb=" N LEU B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 568 through 590 removed outlier: 3.639A pdb=" N ASP B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 removed outlier: 3.801A pdb=" N VAL B 606 " --> pdb=" O MET B 602 " (cutoff:3.500A) Proline residue: B 607 - end of helix removed outlier: 3.561A pdb=" N VAL B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 632 Processing helix chain 'B' and resid 632 through 664 removed outlier: 4.153A pdb=" N PHE B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Proline residue: B 641 - end of helix removed outlier: 3.508A pdb=" N THR B 655 " --> pdb=" O ASP B 651 " (cutoff:3.500A) removed outlier: 4.268A 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 675 640 hydrogen bonds defined for protein. 1896 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: 1.53 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2720 1.35 - 1.47: 2551 1.47 - 1.58: 4245 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 9642 Sorted by residual: bond pdb=" CAI Y01 A 802 " pdb=" CAK Y01 A 802 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CAI Y01 B 701 " pdb=" CAK Y01 B 701 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CAI Y01 B 702 " pdb=" CAK Y01 B 702 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CAI Y01 A 801 " pdb=" CAK Y01 A 801 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CAI Y01 B 701 " pdb=" CAZ Y01 B 701 " ideal model delta sigma weight residual 1.332 1.382 -0.050 2.00e-02 2.50e+03 6.28e+00 ... (remaining 9637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 12973 2.40 - 4.81: 115 4.81 - 7.21: 18 7.21 - 9.62: 8 9.62 - 12.02: 8 Bond angle restraints: 13122 Sorted by residual: angle pdb=" OAG Y01 A 802 " pdb=" CAY Y01 A 802 " pdb=" OAW Y01 A 802 " ideal model delta sigma weight residual 123.38 111.36 12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" OAG Y01 B 701 " pdb=" CAY Y01 B 701 " pdb=" OAW Y01 B 701 " ideal model delta sigma weight residual 123.38 111.37 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" OAG Y01 B 702 " pdb=" CAY Y01 B 702 " pdb=" OAW Y01 B 702 " ideal model delta sigma weight residual 123.38 111.51 11.87 3.00e+00 1.11e-01 1.56e+01 angle pdb=" OAG Y01 A 801 " pdb=" CAY Y01 A 801 " pdb=" OAW Y01 A 801 " ideal model delta sigma weight residual 123.38 111.53 11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CAM Y01 B 701 " pdb=" CAY Y01 B 701 " pdb=" OAW Y01 B 701 " ideal model delta sigma weight residual 111.19 123.01 -11.82 3.00e+00 1.11e-01 1.55e+01 ... (remaining 13117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 5227 16.38 - 32.77: 199 32.77 - 49.15: 58 49.15 - 65.54: 12 65.54 - 81.92: 2 Dihedral angle restraints: 5498 sinusoidal: 2092 harmonic: 3406 Sorted by residual: 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 -117.84 31.84 1 1.00e+01 1.00e-02 1.44e+01 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 -117.83 31.83 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CA MET A 322 " pdb=" CB MET A 322 " pdb=" CG MET A 322 " pdb=" SD MET A 322 " ideal model delta sinusoidal sigma weight residual -60.00 -115.05 55.05 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 5495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1157 0.044 - 0.088: 263 0.088 - 0.133: 54 0.133 - 0.177: 6 0.177 - 0.221: 6 Chirality restraints: 1486 Sorted by residual: 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 -2.67 0.22 2.00e-01 2.50e+01 1.22e+00 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 -2.66 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CBG Y01 A 802 " pdb=" CAQ Y01 A 802 " pdb=" CBD Y01 A 802 " pdb=" CBI Y01 A 802 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 1483 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 606 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO B 607 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 607 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 607 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 606 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 607 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 156 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO B 157 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " -0.015 5.00e-02 4.00e+02 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1980 2.78 - 3.31: 9367 3.31 - 3.84: 15499 3.84 - 4.37: 18913 4.37 - 4.90: 32771 Nonbonded interactions: 78530 Sorted by model distance: nonbonded pdb=" O VAL A 123 " pdb=" OG1 THR A 127 " model vdw 2.244 3.040 nonbonded pdb=" O VAL B 123 " pdb=" OG1 THR B 127 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP A 446 " pdb=" NE2 GLN A 493 " model vdw 2.246 3.120 nonbonded pdb=" OD1 ASP B 446 " pdb=" NE2 GLN B 493 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR A 328 " pdb=" O LYS A 567 " model vdw 2.311 3.040 ... (remaining 78525 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' selection = chain 'B' } 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: 5.000 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.410 Find NCS groups from input model: 0.090 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.004 0.087 9644 Z= 0.184 Angle : 0.647 12.024 13126 Z= 0.295 Chirality : 0.040 0.221 1486 Planarity : 0.003 0.029 1576 Dihedral : 9.919 81.919 3340 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.83 % Allowed : 2.49 % Favored : 96.67 % 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: 1.52 (0.24), residues: 1192 helix: 1.70 (0.17), residues: 850 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.007 0.001 TYR A 422 PHE 0.006 0.001 PHE B 110 TRP 0.010 0.001 TRP B 167 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 ( 9642) covalent geometry : angle 0.64569 / 0.30 (13122) SS BOND : bond 0.00185 / 0.09 ( 2) SS BOND : angle 2.08817 / 1.20 ( 4) hydrogen bonds : bond 0.21424 / 14.66 ( 640) hydrogen bonds : angle 6.89531 / 4.92 ( 1896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 0.316 Fit side-chains REVERT: A 111 THR cc_start: 0.8030 (p) cc_final: 0.7715 (t) REVERT: A 506 LYS cc_start: 0.7162 (pttp) cc_final: 0.6924 (ptmt) REVERT: A 633 LYS cc_start: 0.8486 (tptm) cc_final: 0.8200 (tptt) REVERT: B 111 THR cc_start: 0.8036 (p) cc_final: 0.7721 (t) REVERT: B 506 LYS cc_start: 0.7160 (pttp) cc_final: 0.6926 (ptmt) REVERT: B 633 LYS cc_start: 0.8486 (tptm) cc_final: 0.8200 (tptt) outliers start: 8 outliers final: 2 residues processed: 196 average time/residue: 0.4369 time to fit residues: 93.0713 Evaluate side-chains 138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 192 VAL 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: 0.6980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.184488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149306 restraints weight = 10795.393| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.86 r_work: 0.3496 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9644 Z= 0.164 Angle : 0.585 6.294 13126 Z= 0.295 Chirality : 0.041 0.158 1486 Planarity : 0.004 0.032 1576 Dihedral : 6.040 54.216 1332 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.12 % Allowed : 10.19 % Favored : 86.69 % 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: 2.18 (0.25), residues: 1192 helix: 2.17 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -0.48 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 187 TYR 0.011 0.002 TYR B 126 PHE 0.018 0.002 PHE A 534 TRP 0.018 0.002 TRP B 654 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9642) covalent geometry : angle 0.58385 / 0.29 (13122) SS BOND : bond 0.00105 / 0.05 ( 2) SS BOND : angle 2.18558 / 1.18 ( 4) hydrogen bonds : bond 0.04875 / 3.26 ( 640) hydrogen bonds : angle 4.57390 / 3.28 ( 1896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.225 Fit side-chains REVERT: A 194 TYR cc_start: 0.8268 (m-10) cc_final: 0.8054 (m-10) REVERT: A 396 MET cc_start: 0.7366 (mpp) cc_final: 0.6007 (tmt) REVERT: A 440 TYR cc_start: 0.7964 (t80) cc_final: 0.7649 (t80) REVERT: A 453 TYR cc_start: 0.8440 (m-10) cc_final: 0.8152 (m-10) REVERT: A 506 LYS cc_start: 0.6555 (pttp) cc_final: 0.6282 (ptmt) REVERT: A 509 MET cc_start: 0.6529 (OUTLIER) cc_final: 0.6155 (ttp) REVERT: A 620 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8328 (tp) REVERT: A 633 LYS cc_start: 0.8251 (tptm) cc_final: 0.7902 (tptt) REVERT: B 194 TYR cc_start: 0.8280 (m-10) cc_final: 0.8063 (m-10) REVERT: B 396 MET cc_start: 0.7377 (mpp) cc_final: 0.6010 (tmt) REVERT: B 440 TYR cc_start: 0.7956 (t80) cc_final: 0.7645 (t80) REVERT: B 453 TYR cc_start: 0.8443 (m-10) cc_final: 0.8153 (m-10) REVERT: B 506 LYS cc_start: 0.6552 (pttp) cc_final: 0.6279 (ptmt) REVERT: B 509 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6181 (ttp) REVERT: B 620 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8326 (tp) REVERT: B 633 LYS cc_start: 0.8219 (tptm) cc_final: 0.7868 (tptt) outliers start: 30 outliers final: 6 residues processed: 158 average time/residue: 0.4644 time to fit residues: 79.1886 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 634 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 115 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.186247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151429 restraints weight = 10966.730| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.83 r_work: 0.3486 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9644 Z= 0.141 Angle : 0.545 7.816 13126 Z= 0.271 Chirality : 0.039 0.123 1486 Planarity : 0.004 0.036 1576 Dihedral : 5.811 55.290 1332 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.49 % Allowed : 12.68 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.29 (0.25), residues: 1192 helix: 2.25 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 552 TYR 0.010 0.001 TYR B 126 PHE 0.019 0.002 PHE A 638 TRP 0.016 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9642) covalent geometry : angle 0.54364 / 0.27 (13122) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 1.98153 / 1.08 ( 4) hydrogen bonds : bond 0.04473 / 2.99 ( 640) hydrogen bonds : angle 4.27317 / 3.07 ( 1896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.330 Fit side-chains REVERT: A 396 MET cc_start: 0.7364 (mpp) cc_final: 0.5960 (tmt) REVERT: A 453 TYR cc_start: 0.8413 (m-10) cc_final: 0.8146 (m-10) REVERT: A 506 LYS cc_start: 0.6318 (pttp) cc_final: 0.5978 (ptmt) REVERT: A 591 PRO cc_start: 0.6864 (Cg_exo) cc_final: 0.6521 (Cg_endo) REVERT: A 633 LYS cc_start: 0.8320 (tptm) cc_final: 0.7999 (tptt) REVERT: B 396 MET cc_start: 0.7377 (mpp) cc_final: 0.5971 (tmt) REVERT: B 453 TYR cc_start: 0.8420 (m-10) cc_final: 0.8198 (m-10) REVERT: B 506 LYS cc_start: 0.6349 (pttp) cc_final: 0.6004 (ptmt) REVERT: B 591 PRO cc_start: 0.6859 (Cg_exo) cc_final: 0.6514 (Cg_endo) REVERT: B 633 LYS cc_start: 0.8266 (tptm) cc_final: 0.7950 (tptt) outliers start: 24 outliers final: 11 residues processed: 159 average time/residue: 0.4450 time to fit residues: 76.6341 Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 602 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 155 ASN B 115 ASN B 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.185201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.150066 restraints weight = 10982.285| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.83 r_work: 0.3473 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9644 Z= 0.152 Angle : 0.548 7.599 13126 Z= 0.276 Chirality : 0.040 0.133 1486 Planarity : 0.004 0.038 1576 Dihedral : 5.754 55.947 1332 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.70 % Allowed : 13.41 % Favored : 83.89 % 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: 2.19 (0.25), residues: 1192 helix: 2.18 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.54 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 552 TYR 0.011 0.001 TYR A 244 PHE 0.018 0.002 PHE B 638 TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9642) covalent geometry : angle 0.54661 / 0.28 (13122) SS BOND : bond 0.00091 / 0.05 ( 2) SS BOND : angle 1.98417 / 1.07 ( 4) hydrogen bonds : bond 0.04337 / 2.90 ( 640) hydrogen bonds : angle 4.24438 / 3.06 ( 1896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.263 Fit side-chains REVERT: A 396 MET cc_start: 0.7331 (mpp) cc_final: 0.5962 (tmt) REVERT: A 453 TYR cc_start: 0.8402 (m-10) cc_final: 0.8163 (m-10) REVERT: A 506 LYS cc_start: 0.6343 (pttp) cc_final: 0.6035 (ptmt) REVERT: A 509 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.5678 (ttt) REVERT: A 633 LYS cc_start: 0.8248 (tptm) cc_final: 0.7913 (tptt) REVERT: B 396 MET cc_start: 0.7347 (mpp) cc_final: 0.5973 (tmt) REVERT: B 453 TYR cc_start: 0.8401 (m-10) cc_final: 0.8166 (m-10) REVERT: B 506 LYS cc_start: 0.6351 (pttp) cc_final: 0.6037 (ptmt) REVERT: B 509 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5700 (ttt) REVERT: B 633 LYS cc_start: 0.8272 (tptm) cc_final: 0.7939 (tptt) outliers start: 26 outliers final: 12 residues processed: 167 average time/residue: 0.4715 time to fit residues: 85.2998 Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 634 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 483 GLN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.184585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151339 restraints weight = 10914.082| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.81 r_work: 0.3483 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9644 Z= 0.154 Angle : 0.561 7.747 13126 Z= 0.279 Chirality : 0.040 0.129 1486 Planarity : 0.004 0.039 1576 Dihedral : 5.735 56.643 1332 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.22 % Allowed : 13.51 % Favored : 83.26 % 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: 2.16 (0.25), residues: 1192 helix: 2.15 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.53 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.011 0.001 TYR B 244 PHE 0.017 0.002 PHE A 638 TRP 0.015 0.001 TRP A 654 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9642) covalent geometry : angle 0.55982 / 0.28 (13122) SS BOND : bond 0.00059 / 0.03 ( 2) SS BOND : angle 1.91255 / 1.03 ( 4) hydrogen bonds : bond 0.04253 / 2.84 ( 640) hydrogen bonds : angle 4.22279 / 3.04 ( 1896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.377 Fit side-chains REVERT: A 396 MET cc_start: 0.7198 (mpp) cc_final: 0.5926 (tmt) REVERT: A 440 TYR cc_start: 0.7903 (t80) cc_final: 0.7632 (t80) REVERT: A 453 TYR cc_start: 0.8368 (m-10) cc_final: 0.8147 (m-10) REVERT: A 506 LYS cc_start: 0.6417 (pttp) cc_final: 0.6116 (mtpt) REVERT: A 509 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.5741 (ttt) REVERT: A 633 LYS cc_start: 0.8285 (tptm) cc_final: 0.7947 (tptt) REVERT: B 396 MET cc_start: 0.7204 (mpp) cc_final: 0.5928 (tmt) REVERT: B 440 TYR cc_start: 0.7913 (t80) cc_final: 0.7642 (t80) REVERT: B 453 TYR cc_start: 0.8363 (m-10) cc_final: 0.8140 (m-10) REVERT: B 506 LYS cc_start: 0.6411 (pttp) cc_final: 0.6111 (mtpt) REVERT: B 509 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.5735 (ttt) REVERT: B 633 LYS cc_start: 0.8281 (tptm) cc_final: 0.7949 (tptt) outliers start: 31 outliers final: 17 residues processed: 173 average time/residue: 0.5464 time to fit residues: 101.6808 Evaluate side-chains 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 99 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 602 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 74 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 483 GLN B 155 ASN B 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.185128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152129 restraints weight = 10974.355| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.84 r_work: 0.3495 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9644 Z= 0.135 Angle : 0.551 8.552 13126 Z= 0.273 Chirality : 0.039 0.132 1486 Planarity : 0.004 0.038 1576 Dihedral : 5.632 56.194 1332 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.64 % Allowed : 13.62 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.24 (0.25), residues: 1192 helix: 2.20 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 221 TYR 0.010 0.001 TYR B 597 PHE 0.019 0.001 PHE A 638 TRP 0.015 0.001 TRP A 654 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9642) covalent geometry : angle 0.55013 / 0.27 (13122) SS BOND : bond 0.00100 / 0.05 ( 2) SS BOND : angle 1.79670 / 0.98 ( 4) hydrogen bonds : bond 0.04054 / 2.70 ( 640) hydrogen bonds : angle 4.16009 / 3.01 ( 1896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.383 Fit side-chains REVERT: A 396 MET cc_start: 0.7204 (mpp) cc_final: 0.5931 (tmt) REVERT: A 440 TYR cc_start: 0.7920 (t80) cc_final: 0.7636 (t80) REVERT: A 453 TYR cc_start: 0.8306 (m-10) cc_final: 0.8090 (m-10) REVERT: A 506 LYS cc_start: 0.6396 (pttp) cc_final: 0.6094 (mtpt) REVERT: A 633 LYS cc_start: 0.8288 (tptm) cc_final: 0.7959 (tptt) REVERT: B 396 MET cc_start: 0.7206 (mpp) cc_final: 0.5932 (tmt) REVERT: B 440 TYR cc_start: 0.7925 (t80) cc_final: 0.7640 (t80) REVERT: B 453 TYR cc_start: 0.8308 (m-10) cc_final: 0.8092 (m-10) REVERT: B 506 LYS cc_start: 0.6391 (pttp) cc_final: 0.6085 (mtpt) REVERT: B 633 LYS cc_start: 0.8297 (tptm) cc_final: 0.7964 (tptt) outliers start: 35 outliers final: 15 residues processed: 174 average time/residue: 0.5063 time to fit residues: 95.0636 Evaluate side-chains 158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 99 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 498 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 0.0970 chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 91 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 483 GLN B 155 ASN B 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.185539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151789 restraints weight = 11036.838| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.68 r_work: 0.3513 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9644 Z= 0.129 Angle : 0.558 8.606 13126 Z= 0.274 Chirality : 0.039 0.138 1486 Planarity : 0.004 0.038 1576 Dihedral : 5.555 55.124 1332 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.01 % Allowed : 14.66 % Favored : 82.33 % 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: 2.24 (0.25), residues: 1192 helix: 2.19 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.43 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.009 0.001 TYR B 422 PHE 0.019 0.001 PHE B 638 TRP 0.015 0.001 TRP A 654 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9642) covalent geometry : angle 0.55756 / 0.27 (13122) SS BOND : bond 0.00075 / 0.04 ( 2) SS BOND : angle 1.74669 / 0.95 ( 4) hydrogen bonds : bond 0.03971 / 2.64 ( 640) hydrogen bonds : angle 4.12732 / 2.98 ( 1896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.345 Fit side-chains REVERT: A 396 MET cc_start: 0.7231 (mpp) cc_final: 0.5929 (tmt) REVERT: A 440 TYR cc_start: 0.7843 (t80) cc_final: 0.7559 (t80) REVERT: A 506 LYS cc_start: 0.6324 (pttp) cc_final: 0.5968 (mtpt) REVERT: A 509 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5767 (ttt) REVERT: A 633 LYS cc_start: 0.8263 (tptm) cc_final: 0.7933 (tptt) REVERT: B 396 MET cc_start: 0.7267 (mpp) cc_final: 0.5961 (tmt) REVERT: B 440 TYR cc_start: 0.7843 (t80) cc_final: 0.7559 (t80) REVERT: B 506 LYS cc_start: 0.6389 (pttp) cc_final: 0.6046 (mtpt) REVERT: B 509 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5771 (ttt) REVERT: B 633 LYS cc_start: 0.8294 (tptm) cc_final: 0.7951 (tptt) outliers start: 29 outliers final: 12 residues processed: 157 average time/residue: 0.5298 time to fit residues: 89.6014 Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 0.0870 chunk 108 optimal weight: 0.0050 chunk 33 optimal weight: 0.9980 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN B 155 ASN B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.186106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152643 restraints weight = 10914.897| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.74 r_work: 0.3509 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9644 Z= 0.128 Angle : 0.563 8.821 13126 Z= 0.276 Chirality : 0.039 0.130 1486 Planarity : 0.004 0.038 1576 Dihedral : 5.486 53.494 1332 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.39 % Allowed : 15.70 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.22 (0.25), residues: 1192 helix: 2.18 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.45 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.009 0.001 TYR A 422 PHE 0.018 0.001 PHE B 638 TRP 0.015 0.001 TRP A 654 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9642) covalent geometry : angle 0.56226 / 0.28 (13122) SS BOND : bond 0.00078 / 0.04 ( 2) SS BOND : angle 1.71597 / 0.93 ( 4) hydrogen bonds : bond 0.03912 / 2.61 ( 640) hydrogen bonds : angle 4.11925 / 2.98 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.519 Fit side-chains REVERT: A 396 MET cc_start: 0.7269 (mpp) cc_final: 0.5976 (tmt) REVERT: A 440 TYR cc_start: 0.7825 (t80) cc_final: 0.7565 (t80) REVERT: A 453 TYR cc_start: 0.8305 (m-10) cc_final: 0.8102 (m-80) REVERT: A 506 LYS cc_start: 0.6373 (pttp) cc_final: 0.6035 (mtpt) REVERT: A 633 LYS cc_start: 0.8244 (tptm) cc_final: 0.7925 (tptt) REVERT: B 396 MET cc_start: 0.7252 (mpp) cc_final: 0.5972 (tmt) REVERT: B 440 TYR cc_start: 0.7829 (t80) cc_final: 0.7570 (t80) REVERT: B 453 TYR cc_start: 0.8295 (m-10) cc_final: 0.8090 (m-80) REVERT: B 508 MET cc_start: 0.8011 (tpt) cc_final: 0.7475 (tpt) REVERT: B 509 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5763 (ttt) REVERT: B 633 LYS cc_start: 0.8284 (tptm) cc_final: 0.7949 (tptt) outliers start: 23 outliers final: 18 residues processed: 154 average time/residue: 0.4980 time to fit residues: 82.9744 Evaluate side-chains 150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 602 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 0.5980 chunk 93 optimal weight: 0.1980 chunk 114 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.185384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151170 restraints weight = 10902.505| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.58 r_work: 0.3511 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9644 Z= 0.140 Angle : 0.585 9.127 13126 Z= 0.286 Chirality : 0.040 0.122 1486 Planarity : 0.004 0.039 1576 Dihedral : 5.527 52.579 1332 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.49 % Allowed : 16.11 % Favored : 81.39 % 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: 2.17 (0.25), residues: 1192 helix: 2.18 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -0.57 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.010 0.001 TYR B 244 PHE 0.022 0.001 PHE B 110 TRP 0.014 0.001 TRP A 654 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9642) covalent geometry : angle 0.58429 / 0.29 (13122) SS BOND : bond 0.00049 / 0.02 ( 2) SS BOND : angle 1.74674 / 0.94 ( 4) hydrogen bonds : bond 0.04044 / 2.70 ( 640) hydrogen bonds : angle 4.17037 / 3.01 ( 1896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.345 Fit side-chains REVERT: A 396 MET cc_start: 0.7247 (mpp) cc_final: 0.5960 (tmt) REVERT: A 440 TYR cc_start: 0.7824 (t80) cc_final: 0.7541 (t80) REVERT: A 453 TYR cc_start: 0.8287 (m-10) cc_final: 0.8060 (m-80) REVERT: A 506 LYS cc_start: 0.6364 (pttp) cc_final: 0.6064 (mtpt) REVERT: A 509 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.5773 (ttt) REVERT: A 633 LYS cc_start: 0.8249 (tptm) cc_final: 0.7922 (tptt) REVERT: B 396 MET cc_start: 0.7227 (mpp) cc_final: 0.5955 (tmt) REVERT: B 440 TYR cc_start: 0.7828 (t80) cc_final: 0.7549 (t80) REVERT: B 453 TYR cc_start: 0.8278 (m-10) cc_final: 0.8050 (m-80) REVERT: B 508 MET cc_start: 0.8013 (tpt) cc_final: 0.7478 (tpt) REVERT: B 509 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.5694 (ttt) REVERT: B 633 LYS cc_start: 0.8280 (tptm) cc_final: 0.7936 (tptt) outliers start: 24 outliers final: 18 residues processed: 152 average time/residue: 0.4908 time to fit residues: 80.6505 Evaluate side-chains 151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 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 99 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 602 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 33 optimal weight: 0.0070 chunk 10 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.186693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152556 restraints weight = 10979.926| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.66 r_work: 0.3540 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9644 Z= 0.126 Angle : 0.572 9.724 13126 Z= 0.281 Chirality : 0.039 0.143 1486 Planarity : 0.004 0.037 1576 Dihedral : 5.417 51.176 1332 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.29 % Allowed : 16.94 % Favored : 80.77 % 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: 2.22 (0.25), residues: 1192 helix: 2.22 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -0.54 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 225 TYR 0.009 0.001 TYR B 422 PHE 0.013 0.001 PHE B 171 TRP 0.016 0.001 TRP B 654 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9642) covalent geometry : angle 0.57104 / 0.28 (13122) SS BOND : bond 0.00079 / 0.04 ( 2) SS BOND : angle 1.71833 / 0.94 ( 4) hydrogen bonds : bond 0.03830 / 2.56 ( 640) hydrogen bonds : angle 4.12292 / 2.99 ( 1896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.303 Fit side-chains REVERT: A 396 MET cc_start: 0.7224 (mpp) cc_final: 0.5959 (tmt) REVERT: A 440 TYR cc_start: 0.7775 (t80) cc_final: 0.7548 (t80) REVERT: A 453 TYR cc_start: 0.8241 (m-10) cc_final: 0.8003 (m-80) REVERT: A 506 LYS cc_start: 0.6398 (pttp) cc_final: 0.6086 (mtpt) REVERT: A 509 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.5720 (ttt) REVERT: A 633 LYS cc_start: 0.8301 (tptm) cc_final: 0.7971 (tptt) REVERT: B 396 MET cc_start: 0.7205 (mpp) cc_final: 0.5963 (tmt) REVERT: B 440 TYR cc_start: 0.7778 (t80) cc_final: 0.7553 (t80) REVERT: B 453 TYR cc_start: 0.8233 (m-10) cc_final: 0.7994 (m-80) REVERT: B 509 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.5681 (ttt) REVERT: B 633 LYS cc_start: 0.8273 (tptm) cc_final: 0.7932 (tptt) outliers start: 22 outliers final: 9 residues processed: 152 average time/residue: 0.4917 time to fit residues: 80.7550 Evaluate side-chains 147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 74 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.184872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150641 restraints weight = 10887.573| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.58 r_work: 0.3505 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9644 Z= 0.151 Angle : 0.595 10.759 13126 Z= 0.290 Chirality : 0.041 0.223 1486 Planarity : 0.004 0.039 1576 Dihedral : 5.500 50.096 1332 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.29 % Allowed : 17.26 % Favored : 80.46 % 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: 2.06 (0.25), residues: 1192 helix: 2.10 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.60 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 225 TYR 0.010 0.001 TYR B 244 PHE 0.013 0.001 PHE B 576 TRP 0.013 0.001 TRP A 654 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 9642) covalent geometry : angle 0.59441 / 0.29 (13122) SS BOND : bond 0.00028 / 0.01 ( 2) SS BOND : angle 1.74028 / 0.93 ( 4) hydrogen bonds : bond 0.04112 / 2.74 ( 640) hydrogen bonds : angle 4.21039 / 3.03 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3088.20 seconds wall clock time: 53 minutes 33.83 seconds (3213.83 seconds total)