Starting phenix.real_space_refine on Fri Oct 10 23:22:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thi_41265/10_2025/8thi_41265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thi_41265/10_2025/8thi_41265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8thi_41265/10_2025/8thi_41265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thi_41265/10_2025/8thi_41265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8thi_41265/10_2025/8thi_41265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thi_41265/10_2025/8thi_41265.map" } resolution = 3.36 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= -0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 Na 2 4.78 5 C 6392 2.51 5 N 1464 2.21 5 O 1593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9519 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4739 Classifications: {'peptide': 613} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 586} Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4719 Classifications: {'peptide': 611} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 584} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' NA': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' NA': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Time building chain proxies: 2.66, per 1000 atoms: 0.28 Number of scatterers: 9519 At special positions: 0 Unit cell: (73.04, 88.312, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 2 15.00 Na 2 11.00 O 1593 8.00 N 1464 7.00 C 6392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.91 Conformation dependent library (CDL) restraints added in 311.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 39 through 63 removed outlier: 3.757A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.735A pdb=" N MET A 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 108 removed outlier: 4.445A pdb=" N PHE A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 126 through 149 removed outlier: 3.881A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 3.787A pdb=" N PHE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.733A pdb=" N PHE A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 178 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 179 " --> pdb=" O TRP A 176 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 180 " --> pdb=" O PHE A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 180' Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.222A pdb=" N PHE A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.763A pdb=" N ALA A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 4.471A pdb=" N VAL A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 260 removed outlier: 4.134A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 277 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.668A pdb=" N GLY A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 320 removed outlier: 3.592A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.897A pdb=" N LEU A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 356 through 387 removed outlier: 4.435A pdb=" N ILE A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 395 through 422 removed outlier: 5.324A pdb=" N TRP A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 426 through 445 Processing helix chain 'A' and resid 450 through 485 removed outlier: 3.969A pdb=" N VAL A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.839A pdb=" N VAL A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.786A pdb=" N PHE A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Proline residue: A 531 - end of helix Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.583A pdb=" N GLY A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 565 through 576 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 589 through 603 removed outlier: 4.493A pdb=" N VAL A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.599A pdb=" N VAL A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Proline residue: A 611 - end of helix Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 39 through 63 removed outlier: 3.799A pdb=" N TYR B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.048A pdb=" N MET B 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 109 removed outlier: 3.692A pdb=" N PHE B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.975A pdb=" N GLY B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 126 through 149 removed outlier: 3.809A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 173 removed outlier: 3.767A pdb=" N PHE B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 removed outlier: 3.725A pdb=" N VAL B 179 " --> pdb=" O TRP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 191 through 207 removed outlier: 3.596A pdb=" N GLY B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.251A pdb=" N PHE B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 240 removed outlier: 4.252A pdb=" N VAL B 238 " --> pdb=" O THR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 260 removed outlier: 4.074A pdb=" N PHE B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 277 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.820A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.986A pdb=" N LEU B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 356 through 387 removed outlier: 4.360A pdb=" N ILE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 395 through 423 removed outlier: 5.638A pdb=" N TRP B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 412 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix removed outlier: 3.745A pdb=" N GLY B 423 " --> pdb=" O GLY B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 445 Processing helix chain 'B' and resid 450 through 485 removed outlier: 4.054A pdb=" N VAL B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.533A pdb=" N ARG B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.768A pdb=" N ASP B 500 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 517 removed outlier: 3.630A pdb=" N VAL B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 540 Proline residue: B 531 - end of helix Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 543 through 558 removed outlier: 3.658A pdb=" N GLY B 558 " --> pdb=" O ASN B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 565 through 576 removed outlier: 3.520A pdb=" N PHE B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 589 through 603 removed outlier: 4.395A pdb=" N VAL B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 615 removed outlier: 4.450A pdb=" N ILE B 607 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) Proline residue: B 611 - end of helix 699 hydrogen bonds defined for protein. 2061 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: 1.24 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1427 1.32 - 1.44: 2580 1.44 - 1.56: 5611 1.56 - 1.69: 4 1.69 - 1.81: 122 Bond restraints: 9744 Sorted by residual: bond pdb=" N ILE A 4 " pdb=" CA ILE A 4 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.32e+01 bond pdb=" N THR A 280 " pdb=" CA THR A 280 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.19e+00 bond pdb=" N ASN A 5 " pdb=" CA ASN A 5 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.36e-02 5.41e+03 6.43e+00 bond pdb=" N LYS A 178 " pdb=" CA LYS A 178 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.31e-02 5.83e+03 6.36e+00 bond pdb=" N VAL B 498 " pdb=" CA VAL B 498 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.33e-02 5.65e+03 6.35e+00 ... (remaining 9739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 12758 1.14 - 2.28: 366 2.28 - 3.42: 79 3.42 - 4.56: 15 4.56 - 5.70: 20 Bond angle restraints: 13238 Sorted by residual: angle pdb=" N VAL A 498 " pdb=" CA VAL A 498 " pdb=" C VAL A 498 " ideal model delta sigma weight residual 113.10 110.06 3.04 9.70e-01 1.06e+00 9.81e+00 angle pdb=" C GLY A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta sigma weight residual 120.31 115.67 4.64 1.52e+00 4.33e-01 9.33e+00 angle pdb=" N ASN A 5 " pdb=" CA ASN A 5 " pdb=" C ASN A 5 " ideal model delta sigma weight residual 114.04 110.50 3.54 1.24e+00 6.50e-01 8.16e+00 angle pdb=" CA ASP B 500 " pdb=" C ASP B 500 " pdb=" O ASP B 500 " ideal model delta sigma weight residual 121.07 117.93 3.14 1.10e+00 8.26e-01 8.14e+00 angle pdb=" N LYS A 178 " pdb=" CA LYS A 178 " pdb=" C LYS A 178 " ideal model delta sigma weight residual 113.18 109.97 3.21 1.21e+00 6.83e-01 7.06e+00 ... (remaining 13233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 5031 16.30 - 32.61: 529 32.61 - 48.91: 120 48.91 - 65.21: 23 65.21 - 81.51: 5 Dihedral angle restraints: 5708 sinusoidal: 2193 harmonic: 3515 Sorted by residual: dihedral pdb=" CB MET B 556 " pdb=" CG MET B 556 " pdb=" SD MET B 556 " pdb=" CE MET B 556 " ideal model delta sinusoidal sigma weight residual 60.00 114.20 -54.20 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CB LYS B 236 " pdb=" CG LYS B 236 " pdb=" CD LYS B 236 " pdb=" CE LYS B 236 " ideal model delta sinusoidal sigma weight residual -60.00 -114.11 54.11 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CB MET A 556 " pdb=" CG MET A 556 " pdb=" SD MET A 556 " pdb=" CE MET A 556 " ideal model delta sinusoidal sigma weight residual 60.00 114.10 -54.10 3 1.50e+01 4.44e-03 9.26e+00 ... (remaining 5705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1255 0.046 - 0.091: 299 0.091 - 0.137: 45 0.137 - 0.183: 1 0.183 - 0.229: 3 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL B 498 " pdb=" CA VAL B 498 " pdb=" CG1 VAL B 498 " pdb=" CG2 VAL B 498 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL B 498 " pdb=" N VAL B 498 " pdb=" C VAL B 498 " pdb=" CB VAL B 498 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 1600 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 281 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C GLY A 281 " -0.037 2.00e-02 2.50e+03 pdb=" O GLY A 281 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY A 282 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 498 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL B 498 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 498 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 499 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 426 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 427 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.018 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1184 2.75 - 3.29: 9613 3.29 - 3.82: 15789 3.82 - 4.36: 17014 4.36 - 4.90: 31284 Nonbonded interactions: 74884 Sorted by model distance: nonbonded pdb=" O SER A 298 " pdb="NA NA A 702 " model vdw 2.209 2.470 nonbonded pdb=" O VAL B 179 " pdb=" OH TYR B 185 " model vdw 2.209 3.040 nonbonded pdb=" O GLY A 277 " pdb=" OG1 THR A 391 " model vdw 2.234 3.040 nonbonded pdb=" O THR B 450 " pdb=" OG SER B 453 " model vdw 2.281 3.040 nonbonded pdb=" O GLY A 337 " pdb="NA NA A 702 " model vdw 2.303 2.470 ... (remaining 74879 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 615 or (resid 701 and (name C1 or name C11 or na \ me C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C4 or n \ ame C5 or name C6 or name O11 or name O1P or name O2 or name O2P or name O3 or n \ ame O31 or name O3P or name O4P or name O5 or name O6 or name P )) or resid 702) \ ) 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: 10.060 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.350 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.003 0.045 9744 Z= 0.163 Angle : 0.510 5.699 13238 Z= 0.290 Chirality : 0.038 0.229 1603 Planarity : 0.003 0.033 1597 Dihedral : 13.987 81.514 3444 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.29 % Allowed : 3.05 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.97 (0.25), residues: 1220 helix: 2.44 (0.17), residues: 954 sheet: None (None), residues: 0 loop : 0.27 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.010 0.001 TYR A 3 PHE 0.014 0.001 PHE B 98 TRP 0.007 0.001 TRP A 200 HIS 0.002 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9744) covalent geometry : angle 0.50962 (13238) hydrogen bonds : bond 0.13600 ( 699) hydrogen bonds : angle 4.54355 ( 2061) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7850 (mtp) cc_final: 0.7553 (mtm) REVERT: A 178 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7069 (mmtt) REVERT: A 198 LEU cc_start: 0.8513 (tp) cc_final: 0.8178 (mp) REVERT: A 264 ILE cc_start: 0.8538 (mt) cc_final: 0.8323 (tp) REVERT: A 508 MET cc_start: 0.8623 (mmt) cc_final: 0.8415 (mmm) REVERT: A 566 MET cc_start: 0.8181 (mmm) cc_final: 0.7977 (mmt) REVERT: B 10 TRP cc_start: 0.8262 (m100) cc_final: 0.7987 (m100) REVERT: B 564 MET cc_start: 0.8459 (tpp) cc_final: 0.7890 (tpp) outliers start: 3 outliers final: 0 residues processed: 185 average time/residue: 0.0727 time to fit residues: 20.8257 Evaluate side-chains 114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 overall best weight: 0.4670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 228 ASN A 486 GLN B 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.099349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077344 restraints weight = 23699.214| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.10 r_work: 0.3122 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9744 Z= 0.118 Angle : 0.555 11.335 13238 Z= 0.275 Chirality : 0.040 0.221 1603 Planarity : 0.004 0.034 1597 Dihedral : 5.878 64.989 1340 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.77 % Allowed : 8.55 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.92 (0.25), residues: 1220 helix: 2.37 (0.17), residues: 963 sheet: None (None), residues: 0 loop : 0.28 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.015 0.001 TYR A 349 PHE 0.019 0.001 PHE A 158 TRP 0.015 0.001 TRP A 10 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9744) covalent geometry : angle 0.55470 (13238) hydrogen bonds : bond 0.04276 ( 699) hydrogen bonds : angle 3.70808 ( 2061) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 10 TRP cc_start: 0.8756 (m100) cc_final: 0.8422 (m100) REVERT: A 264 ILE cc_start: 0.8616 (mt) cc_final: 0.8413 (tp) REVERT: A 508 MET cc_start: 0.8670 (mmt) cc_final: 0.8406 (mmm) REVERT: B 10 TRP cc_start: 0.8660 (m100) cc_final: 0.8445 (m100) REVERT: B 204 MET cc_start: 0.8474 (tpp) cc_final: 0.8164 (tpt) REVERT: B 316 MET cc_start: 0.6960 (mtp) cc_final: 0.6740 (mtp) REVERT: B 376 MET cc_start: 0.6762 (mmt) cc_final: 0.6517 (mmt) REVERT: B 378 MET cc_start: 0.8681 (tpp) cc_final: 0.8250 (tpp) REVERT: B 408 TRP cc_start: 0.8218 (m-90) cc_final: 0.7955 (m100) REVERT: B 564 MET cc_start: 0.8473 (tpp) cc_final: 0.7970 (tpp) outliers start: 18 outliers final: 7 residues processed: 133 average time/residue: 0.0741 time to fit residues: 15.5853 Evaluate side-chains 114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 0.0070 chunk 17 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.098011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075667 restraints weight = 23839.254| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.11 r_work: 0.3086 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9744 Z= 0.118 Angle : 0.532 8.487 13238 Z= 0.265 Chirality : 0.039 0.149 1603 Planarity : 0.004 0.033 1597 Dihedral : 5.920 65.972 1336 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.87 % Allowed : 9.63 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.01 (0.25), residues: 1220 helix: 2.43 (0.17), residues: 966 sheet: None (None), residues: 0 loop : 0.33 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.013 0.001 TYR A 349 PHE 0.019 0.001 PHE B 20 TRP 0.009 0.001 TRP A 10 HIS 0.003 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9744) covalent geometry : angle 0.53206 (13238) hydrogen bonds : bond 0.04104 ( 699) hydrogen bonds : angle 3.68325 ( 2061) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.383 Fit side-chains REVERT: A 10 TRP cc_start: 0.8787 (m100) cc_final: 0.8411 (m100) REVERT: A 508 MET cc_start: 0.8691 (mmt) cc_final: 0.8425 (mmm) REVERT: B 204 MET cc_start: 0.8499 (tpp) cc_final: 0.8252 (tpt) REVERT: B 378 MET cc_start: 0.8776 (tpp) cc_final: 0.8364 (tpp) REVERT: B 408 TRP cc_start: 0.8282 (m-90) cc_final: 0.8016 (m100) REVERT: B 564 MET cc_start: 0.8509 (tpp) cc_final: 0.8006 (tpp) outliers start: 19 outliers final: 13 residues processed: 124 average time/residue: 0.0718 time to fit residues: 14.2672 Evaluate side-chains 115 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.095550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.072745 restraints weight = 24204.078| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.10 r_work: 0.3029 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9744 Z= 0.148 Angle : 0.551 6.967 13238 Z= 0.278 Chirality : 0.040 0.150 1603 Planarity : 0.004 0.038 1597 Dihedral : 5.727 66.158 1336 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.96 % Allowed : 11.10 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.85 (0.25), residues: 1220 helix: 2.30 (0.17), residues: 968 sheet: None (None), residues: 0 loop : 0.32 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 80 TYR 0.009 0.001 TYR B 380 PHE 0.022 0.001 PHE A 251 TRP 0.009 0.001 TRP A 227 HIS 0.004 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9744) covalent geometry : angle 0.55053 (13238) hydrogen bonds : bond 0.04314 ( 699) hydrogen bonds : angle 3.82741 ( 2061) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.370 Fit side-chains REVERT: A 10 TRP cc_start: 0.8826 (m100) cc_final: 0.8405 (m100) REVERT: A 508 MET cc_start: 0.8759 (mmt) cc_final: 0.8484 (mmm) REVERT: B 10 TRP cc_start: 0.8711 (m100) cc_final: 0.7929 (m100) REVERT: B 204 MET cc_start: 0.8584 (tpp) cc_final: 0.8238 (tpp) REVERT: B 291 SER cc_start: 0.8606 (t) cc_final: 0.8385 (m) REVERT: B 378 MET cc_start: 0.8841 (tpp) cc_final: 0.8471 (tpp) REVERT: B 471 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8083 (mtm) REVERT: B 564 MET cc_start: 0.8520 (tpp) cc_final: 0.8023 (tpp) outliers start: 20 outliers final: 12 residues processed: 119 average time/residue: 0.0717 time to fit residues: 13.6184 Evaluate side-chains 112 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 79 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 612 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.096750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074091 restraints weight = 24098.636| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.11 r_work: 0.3052 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9744 Z= 0.117 Angle : 0.528 10.922 13238 Z= 0.262 Chirality : 0.038 0.162 1603 Planarity : 0.004 0.040 1597 Dihedral : 5.543 66.718 1336 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.87 % Allowed : 13.06 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.84 (0.25), residues: 1220 helix: 2.29 (0.17), residues: 966 sheet: None (None), residues: 0 loop : 0.32 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.007 0.001 TYR B 380 PHE 0.018 0.001 PHE B 167 TRP 0.022 0.001 TRP B 408 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9744) covalent geometry : angle 0.52757 (13238) hydrogen bonds : bond 0.03864 ( 699) hydrogen bonds : angle 3.73108 ( 2061) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.373 Fit side-chains REVERT: A 10 TRP cc_start: 0.8842 (m100) cc_final: 0.8390 (m100) REVERT: A 508 MET cc_start: 0.8766 (mmt) cc_final: 0.8478 (mmm) REVERT: B 10 TRP cc_start: 0.8667 (m100) cc_final: 0.7892 (m100) REVERT: B 378 MET cc_start: 0.8846 (tpp) cc_final: 0.8448 (tpp) REVERT: B 471 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8008 (mtm) REVERT: B 564 MET cc_start: 0.8498 (tpp) cc_final: 0.8202 (tpp) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.0724 time to fit residues: 12.9138 Evaluate side-chains 110 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.096143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073549 restraints weight = 24088.265| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.12 r_work: 0.3041 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9744 Z= 0.119 Angle : 0.520 9.354 13238 Z= 0.259 Chirality : 0.038 0.162 1603 Planarity : 0.004 0.047 1597 Dihedral : 5.310 63.986 1336 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.87 % Allowed : 13.26 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.86 (0.25), residues: 1220 helix: 2.31 (0.17), residues: 964 sheet: None (None), residues: 0 loop : 0.34 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 30 TYR 0.008 0.001 TYR B 380 PHE 0.019 0.001 PHE B 167 TRP 0.012 0.001 TRP B 408 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9744) covalent geometry : angle 0.51962 (13238) hydrogen bonds : bond 0.03846 ( 699) hydrogen bonds : angle 3.72523 ( 2061) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.407 Fit side-chains REVERT: A 10 TRP cc_start: 0.8840 (m100) cc_final: 0.8393 (m100) REVERT: A 508 MET cc_start: 0.8795 (mmt) cc_final: 0.8512 (mmm) REVERT: B 10 TRP cc_start: 0.8675 (m100) cc_final: 0.7959 (m100) REVERT: B 98 PHE cc_start: 0.9188 (t80) cc_final: 0.8686 (t80) REVERT: B 204 MET cc_start: 0.8300 (tpt) cc_final: 0.8099 (tpt) REVERT: B 378 MET cc_start: 0.8876 (tpp) cc_final: 0.8485 (tpp) REVERT: B 471 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8097 (mtm) REVERT: B 564 MET cc_start: 0.8498 (tpp) cc_final: 0.8212 (tpp) outliers start: 19 outliers final: 14 residues processed: 109 average time/residue: 0.0684 time to fit residues: 11.9256 Evaluate side-chains 112 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071040 restraints weight = 24333.950| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.11 r_work: 0.2992 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9744 Z= 0.161 Angle : 0.564 9.804 13238 Z= 0.282 Chirality : 0.039 0.179 1603 Planarity : 0.004 0.046 1597 Dihedral : 5.315 60.646 1336 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.16 % Allowed : 13.46 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.77 (0.25), residues: 1220 helix: 2.24 (0.17), residues: 964 sheet: None (None), residues: 0 loop : 0.33 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.011 0.001 TYR B 380 PHE 0.021 0.001 PHE B 167 TRP 0.021 0.001 TRP B 408 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9744) covalent geometry : angle 0.56358 (13238) hydrogen bonds : bond 0.04428 ( 699) hydrogen bonds : angle 3.87042 ( 2061) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.387 Fit side-chains REVERT: A 10 TRP cc_start: 0.8880 (m100) cc_final: 0.8353 (m100) REVERT: A 316 MET cc_start: 0.8069 (mtp) cc_final: 0.7842 (mtp) REVERT: A 508 MET cc_start: 0.8836 (mmt) cc_final: 0.8556 (mmm) REVERT: B 10 TRP cc_start: 0.8724 (m100) cc_final: 0.7989 (m100) REVERT: B 53 MET cc_start: 0.9459 (mmm) cc_final: 0.9237 (mmm) REVERT: B 98 PHE cc_start: 0.9191 (t80) cc_final: 0.8644 (t80) REVERT: B 204 MET cc_start: 0.8290 (tpt) cc_final: 0.8021 (tpt) REVERT: B 471 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8572 (mtm) REVERT: B 541 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8506 (p0) REVERT: B 564 MET cc_start: 0.8460 (tpp) cc_final: 0.8192 (tpp) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 0.0749 time to fit residues: 13.0484 Evaluate side-chains 112 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.095785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073233 restraints weight = 24251.967| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.14 r_work: 0.3025 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9744 Z= 0.118 Angle : 0.564 10.318 13238 Z= 0.276 Chirality : 0.039 0.219 1603 Planarity : 0.004 0.042 1597 Dihedral : 5.292 61.149 1336 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.67 % Allowed : 14.24 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.77 (0.25), residues: 1220 helix: 2.23 (0.17), residues: 965 sheet: None (None), residues: 0 loop : 0.37 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 181 TYR 0.009 0.001 TYR B 380 PHE 0.024 0.001 PHE B 167 TRP 0.016 0.001 TRP B 408 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9744) covalent geometry : angle 0.56427 (13238) hydrogen bonds : bond 0.03996 ( 699) hydrogen bonds : angle 3.76769 ( 2061) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.445 Fit side-chains REVERT: A 10 TRP cc_start: 0.8828 (m100) cc_final: 0.8373 (m100) REVERT: A 224 MET cc_start: 0.8946 (mtm) cc_final: 0.8686 (mtm) REVERT: A 508 MET cc_start: 0.8762 (mmt) cc_final: 0.8486 (mmm) REVERT: B 10 TRP cc_start: 0.8734 (m100) cc_final: 0.7984 (m100) REVERT: B 98 PHE cc_start: 0.9189 (t80) cc_final: 0.8617 (t80) REVERT: B 204 MET cc_start: 0.8252 (tpt) cc_final: 0.8024 (tpt) REVERT: B 378 MET cc_start: 0.8506 (tpp) cc_final: 0.8133 (tpp) REVERT: B 467 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7296 (p) REVERT: B 471 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8124 (mtm) REVERT: B 564 MET cc_start: 0.8475 (tpp) cc_final: 0.8204 (tpp) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.0703 time to fit residues: 12.3975 Evaluate side-chains 113 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 0.0770 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 22 optimal weight: 0.0040 chunk 115 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN B 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074571 restraints weight = 24205.131| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.16 r_work: 0.3057 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9744 Z= 0.106 Angle : 0.543 9.813 13238 Z= 0.264 Chirality : 0.038 0.206 1603 Planarity : 0.004 0.042 1597 Dihedral : 5.219 61.756 1336 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.67 % Allowed : 14.54 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.80 (0.25), residues: 1220 helix: 2.26 (0.17), residues: 963 sheet: None (None), residues: 0 loop : 0.33 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 181 TYR 0.008 0.001 TYR B 380 PHE 0.026 0.001 PHE B 167 TRP 0.025 0.001 TRP B 408 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9744) covalent geometry : angle 0.54344 (13238) hydrogen bonds : bond 0.03569 ( 699) hydrogen bonds : angle 3.69177 ( 2061) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.399 Fit side-chains REVERT: A 10 TRP cc_start: 0.8777 (m100) cc_final: 0.8365 (m100) REVERT: A 508 MET cc_start: 0.8726 (mmt) cc_final: 0.8460 (mmm) REVERT: B 10 TRP cc_start: 0.8672 (m100) cc_final: 0.8023 (m100) REVERT: B 98 PHE cc_start: 0.9123 (t80) cc_final: 0.8482 (t80) REVERT: B 378 MET cc_start: 0.8619 (tpp) cc_final: 0.8220 (tpp) REVERT: B 467 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7308 (p) REVERT: B 471 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8102 (mtm) REVERT: B 564 MET cc_start: 0.8492 (tpp) cc_final: 0.8178 (tpp) outliers start: 17 outliers final: 14 residues processed: 112 average time/residue: 0.0697 time to fit residues: 12.5457 Evaluate side-chains 114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 0.0470 chunk 74 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 121 optimal weight: 0.0370 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 84 optimal weight: 0.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.097585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075588 restraints weight = 24181.864| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.15 r_work: 0.3085 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9744 Z= 0.102 Angle : 0.550 10.539 13238 Z= 0.264 Chirality : 0.038 0.201 1603 Planarity : 0.004 0.047 1597 Dihedral : 5.203 62.451 1336 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.47 % Allowed : 14.73 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.79 (0.25), residues: 1220 helix: 2.25 (0.17), residues: 964 sheet: None (None), residues: 0 loop : 0.34 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 181 TYR 0.018 0.001 TYR A 321 PHE 0.026 0.001 PHE B 167 TRP 0.018 0.001 TRP B 408 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9744) covalent geometry : angle 0.55022 (13238) hydrogen bonds : bond 0.03377 ( 699) hydrogen bonds : angle 3.63440 ( 2061) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.368 Fit side-chains REVERT: A 10 TRP cc_start: 0.8761 (m100) cc_final: 0.8351 (m100) REVERT: A 508 MET cc_start: 0.8734 (mmt) cc_final: 0.8464 (mmm) REVERT: B 10 TRP cc_start: 0.8655 (m100) cc_final: 0.8023 (m100) REVERT: B 98 PHE cc_start: 0.9111 (t80) cc_final: 0.8466 (t80) REVERT: B 378 MET cc_start: 0.8612 (tpp) cc_final: 0.8212 (tpp) REVERT: B 467 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7302 (p) REVERT: B 471 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8092 (mtm) REVERT: B 564 MET cc_start: 0.8515 (tpp) cc_final: 0.8217 (tpp) outliers start: 15 outliers final: 12 residues processed: 114 average time/residue: 0.0704 time to fit residues: 12.9362 Evaluate side-chains 114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074577 restraints weight = 24304.017| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.16 r_work: 0.3061 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9744 Z= 0.115 Angle : 0.561 10.818 13238 Z= 0.269 Chirality : 0.039 0.222 1603 Planarity : 0.004 0.043 1597 Dihedral : 5.168 62.337 1336 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.57 % Allowed : 14.64 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.81 (0.25), residues: 1220 helix: 2.27 (0.17), residues: 964 sheet: None (None), residues: 0 loop : 0.31 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 30 TYR 0.014 0.001 TYR A 321 PHE 0.025 0.001 PHE B 167 TRP 0.021 0.001 TRP B 408 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9744) covalent geometry : angle 0.56085 (13238) hydrogen bonds : bond 0.03606 ( 699) hydrogen bonds : angle 3.67926 ( 2061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2183.29 seconds wall clock time: 38 minutes 18.61 seconds (2298.61 seconds total)