Starting phenix.real_space_refine on Wed Mar 4 00:27:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsr_32765/03_2026/7wsr_32765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsr_32765/03_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_32765/03_2026/7wsr_32765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsr_32765/03_2026/7wsr_32765.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsr_32765/03_2026/7wsr_32765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsr_32765/03_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-5986/lib/python3.9/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: 2.20, per 1000 atoms: 0.23 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: 0.74 Conformation dependent library (CDL) restraints added in 381.7 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: 0.26 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: 1.57 Time building geometry restraints manager: 0.96 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: 5427 16.38 - 32.77: 215 32.77 - 49.15: 70 49.15 - 65.54: 16 65.54 - 81.92: 2 Dihedral angle restraints: 5730 sinusoidal: 2324 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 5727 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.810 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.450 Find NCS groups from input model: 0.170 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:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 10.320 81.919 3572 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 covalent geometry : bond 0.00373 ( 9642) covalent geometry : angle 0.64569 (13122) SS BOND : bond 0.00185 ( 2) SS BOND : angle 2.08817 ( 4) hydrogen bonds : bond 0.21424 ( 640) hydrogen bonds : angle 6.89531 ( 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 : 0.314 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: 0.4566 time to fit residues: 96.5732 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 : 0.234 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.184451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149315 restraints weight = 10798.587| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.87 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: 0.8161 moved from start: 0.1803 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= 0.166 Angle : 0.583 6.457 13126 Z= 0.295 Chirality : 0.041 0.158 1486 Planarity : 0.004 0.033 1576 Dihedral : 7.577 53.574 1564 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.22 % Allowed : 10.08 % 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: 2.22 (0.25), residues: 1192 helix: 2.21 (0.18), residues: 844 sheet: None (None), residues: 0 loop : -0.38 (0.35), residues: 348 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 covalent geometry : bond 0.00375 ( 9642) covalent geometry : angle 0.58175 (13122) SS BOND : bond 0.00108 ( 2) SS BOND : angle 2.16558 ( 4) hydrogen bonds : bond 0.04908 ( 640) hydrogen bonds : angle 4.58254 ( 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 173 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.351 Fit side-chains REVERT: A 194 TYR cc_start: 0.8263 (m-10) cc_final: 0.8049 (m-10) REVERT: A 396 MET cc_start: 0.7381 (mpp) cc_final: 0.6030 (tmt) REVERT: A 440 TYR cc_start: 0.7964 (t80) cc_final: 0.7648 (t80) REVERT: A 453 TYR cc_start: 0.8440 (m-10) cc_final: 0.8148 (m-10) REVERT: A 506 LYS cc_start: 0.6557 (pttp) cc_final: 0.6260 (ptmt) REVERT: A 509 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.6151 (ttp) REVERT: A 620 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8340 (tp) REVERT: A 633 LYS cc_start: 0.8255 (tptm) cc_final: 0.7903 (tptt) REVERT: B 194 TYR cc_start: 0.8275 (m-10) cc_final: 0.8058 (m-10) REVERT: B 396 MET cc_start: 0.7389 (mpp) cc_final: 0.6033 (tmt) REVERT: B 440 TYR cc_start: 0.7970 (t80) cc_final: 0.7656 (t80) REVERT: B 453 TYR cc_start: 0.8437 (m-10) cc_final: 0.8158 (m-10) REVERT: B 506 LYS cc_start: 0.6556 (pttp) cc_final: 0.6260 (ptmt) REVERT: B 509 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.6181 (ttp) REVERT: B 620 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8335 (tp) REVERT: B 633 LYS cc_start: 0.8223 (tptm) cc_final: 0.7870 (tptt) outliers start: 31 outliers final: 7 residues processed: 159 average time/residue: 0.4949 time to fit residues: 85.0235 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 193 ASP 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: 0.2980 chunk 96 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 115 optimal weight: 0.0570 chunk 26 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4149 r_free = 0.4149 target = 0.187603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152182 restraints weight = 11008.274| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.54 r_work: 0.3515 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9644 Z= 0.121 Angle : 0.524 7.690 13126 Z= 0.261 Chirality : 0.039 0.119 1486 Planarity : 0.004 0.035 1576 Dihedral : 7.252 52.395 1564 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.60 % Allowed : 12.58 % 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: 2.42 (0.25), residues: 1192 helix: 2.35 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -0.33 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 552 TYR 0.010 0.001 TYR A 126 PHE 0.019 0.001 PHE A 638 TRP 0.016 0.001 TRP B 654 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9642) covalent geometry : angle 0.52293 (13122) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.85512 ( 4) hydrogen bonds : bond 0.04294 ( 640) hydrogen bonds : angle 4.22068 ( 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 175 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.327 Fit side-chains REVERT: A 396 MET cc_start: 0.7348 (mpp) cc_final: 0.5979 (tmt) REVERT: A 453 TYR cc_start: 0.8406 (m-10) cc_final: 0.8149 (m-10) REVERT: A 506 LYS cc_start: 0.6393 (pttp) cc_final: 0.6060 (ptmt) REVERT: A 591 PRO cc_start: 0.6954 (Cg_exo) cc_final: 0.6649 (Cg_endo) REVERT: A 633 LYS cc_start: 0.8305 (tptm) cc_final: 0.8007 (tptt) REVERT: B 396 MET cc_start: 0.7338 (mpp) cc_final: 0.5982 (tmt) REVERT: B 453 TYR cc_start: 0.8412 (m-10) cc_final: 0.8153 (m-10) REVERT: B 506 LYS cc_start: 0.6430 (pttp) cc_final: 0.6092 (ptmt) REVERT: B 591 PRO cc_start: 0.6950 (Cg_exo) cc_final: 0.6641 (Cg_endo) REVERT: B 633 LYS cc_start: 0.8295 (tptm) cc_final: 0.8007 (tptt) outliers start: 25 outliers final: 10 residues processed: 162 average time/residue: 0.4853 time to fit residues: 84.7799 Evaluate side-chains 145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 109 optimal weight: 0.6980 chunk 96 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.185840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.150975 restraints weight = 10998.046| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.79 r_work: 0.3489 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9644 Z= 0.143 Angle : 0.546 7.753 13126 Z= 0.272 Chirality : 0.040 0.129 1486 Planarity : 0.004 0.037 1576 Dihedral : 7.188 49.693 1564 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.70 % Allowed : 12.99 % Favored : 84.30 % 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: 2.31 (0.25), residues: 1192 helix: 2.27 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.49 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.010 0.001 TYR A 244 PHE 0.019 0.002 PHE B 638 TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9642) covalent geometry : angle 0.54471 (13122) SS BOND : bond 0.00094 ( 2) SS BOND : angle 1.88383 ( 4) hydrogen bonds : bond 0.04258 ( 640) hydrogen bonds : angle 4.19767 ( 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 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.355 Fit side-chains REVERT: A 396 MET cc_start: 0.7365 (mpp) cc_final: 0.5998 (tmt) REVERT: A 453 TYR cc_start: 0.8381 (m-10) cc_final: 0.8152 (m-10) REVERT: A 506 LYS cc_start: 0.6377 (pttp) cc_final: 0.6074 (ptmt) REVERT: A 509 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5715 (ttt) REVERT: A 633 LYS cc_start: 0.8229 (tptm) cc_final: 0.7910 (tptt) REVERT: B 396 MET cc_start: 0.7363 (mpp) cc_final: 0.5999 (tmt) REVERT: B 453 TYR cc_start: 0.8382 (m-10) cc_final: 0.8153 (m-10) REVERT: B 506 LYS cc_start: 0.6373 (pttp) cc_final: 0.6071 (ptmt) REVERT: B 509 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.5709 (ttt) REVERT: B 633 LYS cc_start: 0.8244 (tptm) cc_final: 0.7926 (tptt) outliers start: 26 outliers final: 11 residues processed: 158 average time/residue: 0.4561 time to fit residues: 78.2333 Evaluate side-chains 143 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 197 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.185765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150905 restraints weight = 10977.886| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.85 r_work: 0.3473 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9644 Z= 0.147 Angle : 0.552 7.925 13126 Z= 0.276 Chirality : 0.040 0.126 1486 Planarity : 0.004 0.038 1576 Dihedral : 7.166 46.759 1564 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.70 % Allowed : 13.83 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.25), residues: 1192 helix: 2.23 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.53 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 221 TYR 0.011 0.001 TYR A 244 PHE 0.014 0.001 PHE A 638 TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9642) covalent geometry : angle 0.55138 (13122) SS BOND : bond 0.00072 ( 2) SS BOND : angle 1.84363 ( 4) hydrogen bonds : bond 0.04233 ( 640) hydrogen bonds : angle 4.19325 ( 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 176 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.333 Fit side-chains REVERT: A 396 MET cc_start: 0.7308 (mpp) cc_final: 0.5932 (tmt) REVERT: A 453 TYR cc_start: 0.8365 (m-10) cc_final: 0.8128 (m-10) REVERT: A 506 LYS cc_start: 0.6401 (pttp) cc_final: 0.6071 (ptmt) REVERT: A 509 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.5741 (ttt) REVERT: A 633 LYS cc_start: 0.8239 (tptm) cc_final: 0.7906 (tptt) REVERT: B 396 MET cc_start: 0.7316 (mpp) cc_final: 0.5938 (tmt) REVERT: B 453 TYR cc_start: 0.8367 (m-10) cc_final: 0.8132 (m-10) REVERT: B 506 LYS cc_start: 0.6399 (pttp) cc_final: 0.6082 (ptmt) REVERT: B 509 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.5711 (ttt) REVERT: B 633 LYS cc_start: 0.8255 (tptm) cc_final: 0.7926 (tptt) outliers start: 26 outliers final: 12 residues processed: 166 average time/residue: 0.5474 time to fit residues: 97.3599 Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.0070 chunk 56 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151458 restraints weight = 10966.573| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.66 r_work: 0.3508 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9644 Z= 0.140 Angle : 0.549 8.881 13126 Z= 0.272 Chirality : 0.039 0.130 1486 Planarity : 0.004 0.037 1576 Dihedral : 7.075 45.770 1564 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.12 % Allowed : 12.89 % Favored : 83.99 % 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: 2.23 (0.25), residues: 1192 helix: 2.20 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.47 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.010 0.001 TYR A 244 PHE 0.020 0.001 PHE A 638 TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9642) covalent geometry : angle 0.54826 (13122) SS BOND : bond 0.00072 ( 2) SS BOND : angle 1.78575 ( 4) hydrogen bonds : bond 0.04103 ( 640) hydrogen bonds : angle 4.14872 ( 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 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.383 Fit side-chains REVERT: A 396 MET cc_start: 0.7192 (mpp) cc_final: 0.5924 (tmt) REVERT: A 440 TYR cc_start: 0.7894 (t80) cc_final: 0.7653 (t80) REVERT: A 453 TYR cc_start: 0.8308 (m-10) cc_final: 0.8100 (m-10) REVERT: A 502 GLN cc_start: 0.8490 (mp10) cc_final: 0.8289 (mp10) REVERT: A 509 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.5701 (ttt) REVERT: A 633 LYS cc_start: 0.8309 (tptm) cc_final: 0.7984 (tptt) REVERT: B 396 MET cc_start: 0.7205 (mpp) cc_final: 0.5927 (tmt) REVERT: B 440 TYR cc_start: 0.7910 (t80) cc_final: 0.7663 (t80) REVERT: B 453 TYR cc_start: 0.8309 (m-10) cc_final: 0.8104 (m-10) REVERT: B 509 MET cc_start: 0.6332 (OUTLIER) cc_final: 0.5657 (ttt) REVERT: B 633 LYS cc_start: 0.8300 (tptm) cc_final: 0.7970 (tptt) outliers start: 30 outliers final: 16 residues processed: 177 average time/residue: 0.4960 time to fit residues: 94.7084 Evaluate side-chains 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 155 ASN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 95 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4133 r_free = 0.4133 target = 0.187034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153481 restraints weight = 11038.405| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.71 r_work: 0.3519 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2769 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= 0.123 Angle : 0.553 8.764 13126 Z= 0.272 Chirality : 0.039 0.135 1486 Planarity : 0.004 0.036 1576 Dihedral : 6.893 45.280 1564 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.87 % Allowed : 15.28 % Favored : 82.85 % 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: 2.28 (0.25), residues: 1192 helix: 2.19 (0.18), residues: 872 sheet: None (None), residues: 0 loop : -0.40 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 221 TYR 0.009 0.001 TYR A 422 PHE 0.019 0.001 PHE B 638 TRP 0.016 0.001 TRP B 654 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9642) covalent geometry : angle 0.55237 (13122) SS BOND : bond 0.00092 ( 2) SS BOND : angle 1.66078 ( 4) hydrogen bonds : bond 0.03860 ( 640) hydrogen bonds : angle 4.09207 ( 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 169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.317 Fit side-chains REVERT: A 396 MET cc_start: 0.7255 (mpp) cc_final: 0.5949 (tmt) REVERT: A 440 TYR cc_start: 0.7847 (t80) cc_final: 0.7594 (t80) REVERT: A 509 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.5668 (ttt) REVERT: A 633 LYS cc_start: 0.8261 (tptm) cc_final: 0.7928 (tptt) REVERT: B 396 MET cc_start: 0.7257 (mpp) cc_final: 0.5946 (tmt) REVERT: B 440 TYR cc_start: 0.7862 (t80) cc_final: 0.7605 (t80) REVERT: B 508 MET cc_start: 0.7924 (tpt) cc_final: 0.7602 (tpt) REVERT: B 509 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.5628 (ttt) REVERT: B 633 LYS cc_start: 0.8276 (tptm) cc_final: 0.7945 (tptt) outliers start: 18 outliers final: 12 residues processed: 163 average time/residue: 0.5096 time to fit residues: 89.3728 Evaluate side-chains 155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 0.8980 chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 0.0770 chunk 33 optimal weight: 0.0470 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152341 restraints weight = 10901.261| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.61 r_work: 0.3536 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9644 Z= 0.134 Angle : 0.573 9.059 13126 Z= 0.280 Chirality : 0.040 0.132 1486 Planarity : 0.004 0.037 1576 Dihedral : 6.852 45.431 1564 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.60 % Allowed : 15.70 % Favored : 81.70 % 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: 2.23 (0.18), residues: 846 sheet: None (None), residues: 0 loop : -0.42 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 221 TYR 0.009 0.001 TYR B 244 PHE 0.017 0.001 PHE B 638 TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9642) covalent geometry : angle 0.57199 (13122) SS BOND : bond 0.00066 ( 2) SS BOND : angle 1.64772 ( 4) hydrogen bonds : bond 0.03997 ( 640) hydrogen bonds : angle 4.12284 ( 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 177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.330 Fit side-chains REVERT: A 309 LYS cc_start: 0.8251 (tppt) cc_final: 0.7750 (tptm) REVERT: A 396 MET cc_start: 0.7370 (mpp) cc_final: 0.5959 (tmt) REVERT: A 440 TYR cc_start: 0.7961 (t80) cc_final: 0.7660 (t80) REVERT: A 453 TYR cc_start: 0.8400 (m-10) cc_final: 0.8199 (m-80) REVERT: A 509 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.5849 (ttt) REVERT: A 633 LYS cc_start: 0.8269 (tptm) cc_final: 0.7912 (tptt) REVERT: B 309 LYS cc_start: 0.8245 (tppt) cc_final: 0.7742 (tptm) REVERT: B 396 MET cc_start: 0.7368 (mpp) cc_final: 0.5959 (tmt) REVERT: B 440 TYR cc_start: 0.7989 (t80) cc_final: 0.7671 (t80) REVERT: B 453 TYR cc_start: 0.8392 (m-10) cc_final: 0.8190 (m-80) REVERT: B 509 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.5894 (ttt) REVERT: B 633 LYS cc_start: 0.8292 (tptm) cc_final: 0.7937 (tptt) outliers start: 25 outliers final: 17 residues processed: 169 average time/residue: 0.4652 time to fit residues: 84.9083 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 : 0.286 ------------------------------------------------------------------------------- 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 193 ASP 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 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 193 ASP Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.184649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151401 restraints weight = 10917.360| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.72 r_work: 0.3486 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9644 Z= 0.157 Angle : 0.593 9.274 13126 Z= 0.293 Chirality : 0.041 0.156 1486 Planarity : 0.004 0.039 1576 Dihedral : 7.001 46.384 1564 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.49 % Allowed : 16.53 % Favored : 80.98 % 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: 2.07 (0.25), residues: 1192 helix: 2.09 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -0.52 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.011 0.001 TYR A 244 PHE 0.014 0.001 PHE B 638 TRP 0.013 0.001 TRP A 654 HIS 0.002 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9642) covalent geometry : angle 0.59241 (13122) SS BOND : bond 0.00028 ( 2) SS BOND : angle 1.72363 ( 4) hydrogen bonds : bond 0.04178 ( 640) hydrogen bonds : angle 4.20688 ( 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 167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.283 Fit side-chains REVERT: A 309 LYS cc_start: 0.8222 (tppt) cc_final: 0.7744 (tptm) REVERT: A 396 MET cc_start: 0.7238 (mpp) cc_final: 0.5944 (tmt) REVERT: A 440 TYR cc_start: 0.7909 (t80) cc_final: 0.7678 (t80) REVERT: A 453 TYR cc_start: 0.8328 (m-10) cc_final: 0.8067 (m-80) REVERT: A 509 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.5597 (ttt) REVERT: A 633 LYS cc_start: 0.8267 (tptm) cc_final: 0.7932 (tptt) REVERT: B 309 LYS cc_start: 0.8206 (tppt) cc_final: 0.7727 (tptm) REVERT: B 396 MET cc_start: 0.7238 (mpp) cc_final: 0.5941 (tmt) REVERT: B 440 TYR cc_start: 0.7922 (t80) cc_final: 0.7671 (t80) REVERT: B 453 TYR cc_start: 0.8318 (m-10) cc_final: 0.8057 (m-80) REVERT: B 509 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.5609 (ttt) REVERT: B 633 LYS cc_start: 0.8297 (tptm) cc_final: 0.7943 (tptt) outliers start: 24 outliers final: 14 residues processed: 158 average time/residue: 0.4773 time to fit residues: 81.4323 Evaluate side-chains 156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER 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 193 ASP 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 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 193 ASP Chi-restraints excluded: chain B residue 213 THR 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 98 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** 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 = 0.4108 r_free = 0.4108 target = 0.184259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150175 restraints weight = 10982.523| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.60 r_work: 0.3498 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9644 Z= 0.158 Angle : 0.599 9.695 13126 Z= 0.294 Chirality : 0.041 0.126 1486 Planarity : 0.004 0.039 1576 Dihedral : 7.126 55.321 1564 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.08 % Allowed : 17.36 % Favored : 80.56 % 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: 2.03 (0.25), residues: 1192 helix: 2.06 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -0.55 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.011 0.001 TYR B 244 PHE 0.013 0.001 PHE A 576 TRP 0.013 0.001 TRP A 654 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9642) covalent geometry : angle 0.59794 (13122) SS BOND : bond 0.00041 ( 2) SS BOND : angle 1.73555 ( 4) hydrogen bonds : bond 0.04193 ( 640) hydrogen bonds : angle 4.24392 ( 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: 20 poor density : 142 time to evaluate : 0.233 Fit side-chains REVERT: A 309 LYS cc_start: 0.8199 (tppt) cc_final: 0.7724 (tptm) REVERT: A 396 MET cc_start: 0.7248 (mpp) cc_final: 0.5946 (tmt) REVERT: A 440 TYR cc_start: 0.7910 (t80) cc_final: 0.7674 (t80) REVERT: A 453 TYR cc_start: 0.8301 (m-10) cc_final: 0.8064 (m-80) REVERT: A 509 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.5641 (ttt) REVERT: A 633 LYS cc_start: 0.8284 (tptm) cc_final: 0.7956 (tptt) REVERT: B 309 LYS cc_start: 0.8194 (tppt) cc_final: 0.7720 (tptm) REVERT: B 396 MET cc_start: 0.7238 (mpp) cc_final: 0.5941 (tmt) REVERT: B 440 TYR cc_start: 0.7923 (t80) cc_final: 0.7669 (t80) REVERT: B 453 TYR cc_start: 0.8289 (m-10) cc_final: 0.8054 (m-80) REVERT: B 509 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5621 (ttt) REVERT: B 633 LYS cc_start: 0.8306 (tptm) cc_final: 0.7959 (tptt) outliers start: 20 outliers final: 14 residues processed: 155 average time/residue: 0.4691 time to fit residues: 78.3348 Evaluate side-chains 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER 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 193 ASP 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 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 193 ASP Chi-restraints excluded: chain B residue 213 THR 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: 0.6980 chunk 95 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 31 optimal weight: 0.0170 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.185972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151502 restraints weight = 10902.827| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.56 r_work: 0.3530 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3003 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= 0.137 Angle : 0.595 10.886 13126 Z= 0.290 Chirality : 0.040 0.129 1486 Planarity : 0.004 0.038 1576 Dihedral : 6.961 54.824 1564 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.87 % Allowed : 17.88 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.25), residues: 1192 helix: 2.08 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.49 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 225 TYR 0.009 0.001 TYR B 244 PHE 0.012 0.001 PHE B 576 TRP 0.015 0.001 TRP A 654 HIS 0.003 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9642) covalent geometry : angle 0.59419 (13122) SS BOND : bond 0.00064 ( 2) SS BOND : angle 1.67910 ( 4) hydrogen bonds : bond 0.03993 ( 640) hydrogen bonds : angle 4.18759 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3120.83 seconds wall clock time: 54 minutes 2.58 seconds (3242.58 seconds total)