Starting phenix.real_space_refine on Fri Feb 14 00:03:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsr_32765/02_2025/7wsr_32765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsr_32765/02_2025/7wsr_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_32765/02_2025/7wsr_32765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsr_32765/02_2025/7wsr_32765.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsr_32765/02_2025/7wsr_32765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsr_32765/02_2025/7wsr_32765.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.62, per 1000 atoms: 0.71 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: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.79 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: 2.57 Time building geometry restraints manager: 2.81 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: 0.05 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: 3.810 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.810 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.100 ------------------------------------------------------------------------------- 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 9642 Z= 0.243 Angle : 0.646 12.024 13122 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (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 TRP 0.010 0.001 TRP B 167 HIS 0.001 0.001 HIS A 212 PHE 0.006 0.001 PHE B 110 TYR 0.007 0.001 TYR A 422 ARG 0.002 0.000 ARG A 225 *********************** 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 : 1.039 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: 0.6923 (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: 1.0325 time to fit residues: 219.7464 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 : 0.963 ------------------------------------------------------------------------------- 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 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 70 optimal weight: 0.0040 chunk 108 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.186074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.151537 restraints weight = 10894.498| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.82 r_work: 0.3490 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9642 Z= 0.216 Angle : 0.573 6.656 13122 Z= 0.290 Chirality : 0.040 0.156 1486 Planarity : 0.004 0.032 1576 Dihedral : 7.545 52.897 1564 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.12 % Allowed : 9.98 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.25), residues: 1192 helix: 2.26 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.40 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 PHE 0.019 0.002 PHE A 638 TYR 0.011 0.001 TYR B 126 ARG 0.001 0.000 ARG A 187 *********************** 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 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.027 Fit side-chains REVERT: A 194 TYR cc_start: 0.8228 (m-10) cc_final: 0.8009 (m-10) REVERT: A 396 MET cc_start: 0.7408 (mpp) cc_final: 0.6032 (tmt) REVERT: A 440 TYR cc_start: 0.7945 (t80) cc_final: 0.7617 (t80) REVERT: A 453 TYR cc_start: 0.8426 (m-10) cc_final: 0.8139 (m-10) REVERT: A 506 LYS cc_start: 0.6533 (pttp) cc_final: 0.6253 (ptmt) REVERT: A 509 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6145 (ttp) REVERT: A 620 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 633 LYS cc_start: 0.8230 (tptm) cc_final: 0.7918 (tptt) REVERT: B 194 TYR cc_start: 0.8239 (m-10) cc_final: 0.8015 (m-10) REVERT: B 396 MET cc_start: 0.7428 (mpp) cc_final: 0.6037 (tmt) REVERT: B 440 TYR cc_start: 0.7953 (t80) cc_final: 0.7630 (t80) REVERT: B 453 TYR cc_start: 0.8440 (m-10) cc_final: 0.8152 (m-10) REVERT: B 506 LYS cc_start: 0.6535 (pttp) cc_final: 0.6258 (ptmt) REVERT: B 509 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6184 (ttp) REVERT: B 620 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8306 (tp) REVERT: B 633 LYS cc_start: 0.8214 (tptm) cc_final: 0.7853 (tptt) outliers start: 30 outliers final: 4 residues processed: 160 average time/residue: 1.0874 time to fit residues: 187.6239 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 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 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 104 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 chunk 109 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.187763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153573 restraints weight = 11030.695| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.87 r_work: 0.3505 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9642 Z= 0.169 Angle : 0.524 7.734 13122 Z= 0.261 Chirality : 0.039 0.120 1486 Planarity : 0.004 0.033 1576 Dihedral : 7.202 51.448 1564 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.70 % Allowed : 12.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.25), residues: 1192 helix: 2.39 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -0.34 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 654 HIS 0.002 0.001 HIS A 212 PHE 0.020 0.001 PHE A 638 TYR 0.011 0.001 TYR A 126 ARG 0.001 0.000 ARG B 552 *********************** 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 176 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.970 Fit side-chains REVERT: A 396 MET cc_start: 0.7369 (mpp) cc_final: 0.5966 (tmt) REVERT: A 453 TYR cc_start: 0.8384 (m-10) cc_final: 0.8157 (m-10) REVERT: A 506 LYS cc_start: 0.6395 (pttp) cc_final: 0.6038 (ptmt) REVERT: A 591 PRO cc_start: 0.6835 (Cg_exo) cc_final: 0.6508 (Cg_endo) REVERT: A 633 LYS cc_start: 0.8293 (tptm) cc_final: 0.7988 (tptt) REVERT: B 396 MET cc_start: 0.7368 (mpp) cc_final: 0.5969 (tmt) REVERT: B 453 TYR cc_start: 0.8382 (m-10) cc_final: 0.8151 (m-10) REVERT: B 506 LYS cc_start: 0.6427 (pttp) cc_final: 0.6067 (ptmt) REVERT: B 591 PRO cc_start: 0.6824 (Cg_exo) cc_final: 0.6494 (Cg_endo) REVERT: B 633 LYS cc_start: 0.8289 (tptm) cc_final: 0.7990 (tptt) outliers start: 26 outliers final: 12 residues processed: 162 average time/residue: 1.0599 time to fit residues: 185.8682 Evaluate side-chains 149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 634 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.186276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150696 restraints weight = 10955.305| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.71 r_work: 0.3485 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9642 Z= 0.205 Angle : 0.542 7.691 13122 Z= 0.269 Chirality : 0.040 0.128 1486 Planarity : 0.004 0.036 1576 Dihedral : 7.145 48.818 1564 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.70 % Allowed : 12.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.25), residues: 1192 helix: 2.30 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.47 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 PHE 0.017 0.002 PHE A 638 TYR 0.010 0.001 TYR B 244 ARG 0.001 0.000 ARG A 552 *********************** 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 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.878 Fit side-chains REVERT: A 396 MET cc_start: 0.7307 (mpp) cc_final: 0.5953 (tmt) REVERT: A 453 TYR cc_start: 0.8377 (m-10) cc_final: 0.8153 (m-10) REVERT: A 506 LYS cc_start: 0.6387 (pttp) cc_final: 0.6087 (ptmt) REVERT: A 509 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5779 (ttt) REVERT: A 633 LYS cc_start: 0.8228 (tptm) cc_final: 0.7918 (tptt) REVERT: B 396 MET cc_start: 0.7311 (mpp) cc_final: 0.5957 (tmt) REVERT: B 453 TYR cc_start: 0.8377 (m-10) cc_final: 0.8154 (m-10) REVERT: B 506 LYS cc_start: 0.6403 (pttp) cc_final: 0.6107 (ptmt) REVERT: B 509 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.5785 (ttt) REVERT: B 633 LYS cc_start: 0.8255 (tptm) cc_final: 0.7946 (tptt) outliers start: 26 outliers final: 13 residues processed: 162 average time/residue: 1.0298 time to fit residues: 181.1118 Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 197 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 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 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 116 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 79 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.185982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.150466 restraints weight = 10883.776| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.60 r_work: 0.3492 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9642 Z= 0.210 Angle : 0.552 7.969 13122 Z= 0.274 Chirality : 0.040 0.130 1486 Planarity : 0.004 0.037 1576 Dihedral : 7.119 45.759 1564 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.81 % Allowed : 14.24 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.25), residues: 1192 helix: 2.27 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 654 HIS 0.002 0.001 HIS A 344 PHE 0.018 0.001 PHE A 638 TYR 0.010 0.001 TYR B 146 ARG 0.001 0.000 ARG A 221 *********************** 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 178 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.949 Fit side-chains REVERT: A 396 MET cc_start: 0.7277 (mpp) cc_final: 0.5940 (tmt) REVERT: A 453 TYR cc_start: 0.8359 (m-10) cc_final: 0.8140 (m-10) REVERT: A 506 LYS cc_start: 0.6428 (pttp) cc_final: 0.6113 (ptmt) REVERT: A 509 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5767 (ttt) REVERT: A 633 LYS cc_start: 0.8253 (tptm) cc_final: 0.7930 (tptt) REVERT: B 396 MET cc_start: 0.7282 (mpp) cc_final: 0.5947 (tmt) REVERT: B 453 TYR cc_start: 0.8362 (m-10) cc_final: 0.8145 (m-10) REVERT: B 506 LYS cc_start: 0.6427 (pttp) cc_final: 0.6114 (ptmt) REVERT: B 509 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5759 (ttt) REVERT: B 633 LYS cc_start: 0.8269 (tptm) cc_final: 0.7954 (tptt) outliers start: 27 outliers final: 12 residues processed: 167 average time/residue: 1.1998 time to fit residues: 215.5929 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 : 1.045 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 117 optimal weight: 0.2980 chunk 99 optimal weight: 0.5980 chunk 80 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.186705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152371 restraints weight = 10824.789| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.60 r_work: 0.3531 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9642 Z= 0.183 Angle : 0.537 8.312 13122 Z= 0.266 Chirality : 0.039 0.131 1486 Planarity : 0.004 0.036 1576 Dihedral : 6.952 45.291 1564 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.91 % Allowed : 13.41 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.25), residues: 1192 helix: 2.26 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.43 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 654 HIS 0.001 0.001 HIS A 344 PHE 0.018 0.001 PHE B 638 TYR 0.009 0.001 TYR B 422 ARG 0.002 0.000 ARG B 221 *********************** 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 184 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.010 Fit side-chains REVERT: A 396 MET cc_start: 0.7240 (mpp) cc_final: 0.5949 (tmt) REVERT: A 440 TYR cc_start: 0.7869 (t80) cc_final: 0.7630 (t80) REVERT: A 453 TYR cc_start: 0.8290 (m-10) cc_final: 0.8070 (m-10) REVERT: A 509 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5671 (ttt) REVERT: A 633 LYS cc_start: 0.8255 (tptm) cc_final: 0.7948 (tptt) REVERT: B 396 MET cc_start: 0.7251 (mpp) cc_final: 0.5948 (tmt) REVERT: B 440 TYR cc_start: 0.7878 (t80) cc_final: 0.7642 (t80) REVERT: B 453 TYR cc_start: 0.8273 (m-10) cc_final: 0.8051 (m-10) REVERT: B 509 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.5672 (ttt) REVERT: B 633 LYS cc_start: 0.8286 (tptm) cc_final: 0.7970 (tptt) outliers start: 28 outliers final: 14 residues processed: 174 average time/residue: 1.0716 time to fit residues: 201.5607 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 : 0.968 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 115 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 83 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 ** 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 = 0.4116 r_free = 0.4116 target = 0.185432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152200 restraints weight = 10961.803| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.69 r_work: 0.3499 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9642 Z= 0.215 Angle : 0.566 8.527 13122 Z= 0.277 Chirality : 0.040 0.122 1486 Planarity : 0.004 0.037 1576 Dihedral : 6.951 45.777 1564 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.70 % Allowed : 14.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.25), residues: 1192 helix: 2.15 (0.18), residues: 872 sheet: None (None), residues: 0 loop : -0.40 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 PHE 0.018 0.001 PHE B 638 TYR 0.010 0.001 TYR A 244 ARG 0.004 0.000 ARG A 221 *********************** 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 175 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.943 Fit side-chains REVERT: A 396 MET cc_start: 0.7254 (mpp) cc_final: 0.5966 (tmt) REVERT: A 440 TYR cc_start: 0.7925 (t80) cc_final: 0.7672 (t80) REVERT: A 453 TYR cc_start: 0.8337 (m-10) cc_final: 0.8099 (m-10) REVERT: A 508 MET cc_start: 0.8007 (tpt) cc_final: 0.7627 (tpt) REVERT: A 509 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.5714 (ttt) REVERT: A 633 LYS cc_start: 0.8257 (tptm) cc_final: 0.7944 (tptt) REVERT: B 396 MET cc_start: 0.7265 (mpp) cc_final: 0.5965 (tmt) REVERT: B 440 TYR cc_start: 0.7930 (t80) cc_final: 0.7675 (t80) REVERT: B 453 TYR cc_start: 0.8334 (m-10) cc_final: 0.8097 (m-10) REVERT: B 508 MET cc_start: 0.8012 (tpt) cc_final: 0.7623 (tpt) REVERT: B 509 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5712 (ttt) REVERT: B 633 LYS cc_start: 0.8287 (tptm) cc_final: 0.7963 (tptt) outliers start: 26 outliers final: 16 residues processed: 165 average time/residue: 1.1054 time to fit residues: 196.3585 Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 29 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** 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 = 0.4112 r_free = 0.4112 target = 0.184725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151092 restraints weight = 11056.343| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.73 r_work: 0.3489 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9642 Z= 0.232 Angle : 0.595 8.748 13122 Z= 0.290 Chirality : 0.040 0.137 1486 Planarity : 0.004 0.038 1576 Dihedral : 7.013 46.397 1564 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.70 % Allowed : 16.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.25), residues: 1192 helix: 2.08 (0.18), residues: 866 sheet: None (None), residues: 0 loop : -0.38 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 654 HIS 0.002 0.001 HIS B 212 PHE 0.021 0.002 PHE A 110 TYR 0.011 0.001 TYR A 244 ARG 0.003 0.000 ARG A 221 *********************** 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 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.111 Fit side-chains REVERT: A 309 LYS cc_start: 0.8329 (tppt) cc_final: 0.7873 (tptm) REVERT: A 396 MET cc_start: 0.7230 (mpp) cc_final: 0.5947 (tmt) REVERT: A 440 TYR cc_start: 0.7967 (t80) cc_final: 0.7706 (t80) REVERT: A 453 TYR cc_start: 0.8374 (m-10) cc_final: 0.8123 (m-10) REVERT: A 509 MET cc_start: 0.6417 (OUTLIER) cc_final: 0.5706 (ttt) REVERT: A 633 LYS cc_start: 0.8247 (tptm) cc_final: 0.7933 (tptt) REVERT: B 309 LYS cc_start: 0.8236 (tppt) cc_final: 0.7779 (tptm) REVERT: B 396 MET cc_start: 0.7216 (mpp) cc_final: 0.5945 (tmt) REVERT: B 440 TYR cc_start: 0.7973 (t80) cc_final: 0.7710 (t80) REVERT: B 453 TYR cc_start: 0.8374 (m-10) cc_final: 0.8123 (m-10) REVERT: B 508 MET cc_start: 0.8028 (tpt) cc_final: 0.7628 (tpt) REVERT: B 509 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.5663 (ttt) REVERT: B 633 LYS cc_start: 0.8291 (tptm) cc_final: 0.7958 (tptt) outliers start: 26 outliers final: 20 residues processed: 160 average time/residue: 1.2010 time to fit residues: 206.5657 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 : 1.073 ------------------------------------------------------------------------------- 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 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 A residue 529 LEU 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 Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.184785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150907 restraints weight = 10946.124| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.58 r_work: 0.3503 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9642 Z= 0.226 Angle : 0.585 8.778 13122 Z= 0.288 Chirality : 0.040 0.152 1486 Planarity : 0.004 0.038 1576 Dihedral : 7.036 49.081 1564 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.81 % Allowed : 16.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.25), residues: 1192 helix: 2.12 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -0.52 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 PHE 0.014 0.001 PHE B 638 TYR 0.010 0.001 TYR A 244 ARG 0.003 0.000 ARG B 221 *********************** 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 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.920 Fit side-chains REVERT: A 309 LYS cc_start: 0.8281 (tppt) cc_final: 0.7815 (tptm) REVERT: A 396 MET cc_start: 0.7197 (mpp) cc_final: 0.5928 (tmt) REVERT: A 453 TYR cc_start: 0.8352 (m-10) cc_final: 0.8104 (m-10) REVERT: A 509 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.5643 (ttt) REVERT: A 633 LYS cc_start: 0.8262 (tptm) cc_final: 0.7945 (tptt) REVERT: B 309 LYS cc_start: 0.8208 (tppt) cc_final: 0.7739 (tptm) REVERT: B 396 MET cc_start: 0.7191 (mpp) cc_final: 0.5929 (tmt) REVERT: B 440 TYR cc_start: 0.7927 (t80) cc_final: 0.7715 (t80) REVERT: B 453 TYR cc_start: 0.8343 (m-10) cc_final: 0.8093 (m-10) REVERT: B 509 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5662 (ttt) REVERT: B 633 LYS cc_start: 0.8304 (tptm) cc_final: 0.7961 (tptt) outliers start: 27 outliers final: 18 residues processed: 163 average time/residue: 1.1108 time to fit residues: 195.6400 Evaluate side-chains 154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 108 optimal weight: 0.0770 chunk 83 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4124 r_free = 0.4124 target = 0.185723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151271 restraints weight = 11057.428| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.64 r_work: 0.3521 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9642 Z= 0.205 Angle : 0.595 9.704 13122 Z= 0.289 Chirality : 0.040 0.124 1486 Planarity : 0.004 0.038 1576 Dihedral : 7.013 56.526 1564 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.49 % Allowed : 17.15 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.25), residues: 1192 helix: 2.12 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -0.52 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 654 HIS 0.002 0.001 HIS B 212 PHE 0.012 0.001 PHE B 576 TYR 0.009 0.001 TYR B 244 ARG 0.004 0.000 ARG B 221 ********************** 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: 24 poor density : 138 time to evaluate : 0.943 Fit side-chains REVERT: A 309 LYS cc_start: 0.8234 (tppt) cc_final: 0.7799 (tptm) REVERT: A 396 MET cc_start: 0.7203 (mpp) cc_final: 0.5940 (tmt) REVERT: A 453 TYR cc_start: 0.8324 (m-10) cc_final: 0.8102 (m-10) REVERT: A 509 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5567 (ttt) REVERT: A 633 LYS cc_start: 0.8256 (tptm) cc_final: 0.7945 (tptt) REVERT: B 309 LYS cc_start: 0.8237 (tppt) cc_final: 0.7789 (tptm) REVERT: B 396 MET cc_start: 0.7201 (mpp) cc_final: 0.5938 (tmt) REVERT: B 453 TYR cc_start: 0.8318 (m-10) cc_final: 0.8090 (m-10) REVERT: B 509 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5623 (ttt) REVERT: B 633 LYS cc_start: 0.8291 (tptm) cc_final: 0.7961 (tptt) outliers start: 24 outliers final: 17 residues processed: 153 average time/residue: 1.1029 time to fit residues: 181.8059 Evaluate side-chains 155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 A residue 594 TYR Chi-restraints excluded: chain B residue 84 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 5 optimal weight: 0.0470 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 63 optimal weight: 0.0070 chunk 110 optimal weight: 0.8980 chunk 86 optimal weight: 0.0070 chunk 90 optimal weight: 1.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- 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** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.188594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.155372 restraints weight = 10974.098| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.56 r_work: 0.3559 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9642 Z= 0.164 Angle : 0.578 10.832 13122 Z= 0.279 Chirality : 0.039 0.129 1486 Planarity : 0.004 0.036 1576 Dihedral : 6.685 52.601 1564 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.56 % Allowed : 18.30 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.25), residues: 1192 helix: 2.27 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.39 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 PHE 0.019 0.001 PHE A 110 TYR 0.009 0.001 TYR A 422 ARG 0.003 0.000 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6434.22 seconds wall clock time: 114 minutes 31.71 seconds (6871.71 seconds total)