Starting phenix.real_space_refine on Thu Jul 2 10:58:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vgf_31967/07_2026/7vgf_31967.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgf_31967/07_2026/7vgf_31967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vgf_31967/07_2026/7vgf_31967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgf_31967/07_2026/7vgf_31967.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vgf_31967/07_2026/7vgf_31967.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vgf_31967/07_2026/7vgf_31967.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vgf_31967/07_2026/7vgf_31967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgf_31967/07_2026/7vgf_31967.map" } resolution = 3.3 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= -0.001 sd= 0.059 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 6 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 5284 2.51 5 N 1412 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8280 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4108 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 13, 'TRANS': 536} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4108 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 13, 'TRANS': 536} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.50, per 1000 atoms: 0.18 Number of scatterers: 8280 At special positions: 0 Unit cell: (110.526, 67.938, 133.848, 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 20 16.00 P 6 15.00 Mg 2 11.99 O 1556 8.00 N 1412 7.00 C 5284 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: 0.50 Conformation dependent library (CDL) restraints added in 307.6 milliseconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 69.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 133 through 171 removed outlier: 3.642A pdb=" N ARG A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 186 through 234 Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.745A pdb=" N HIS A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 289 removed outlier: 4.163A pdb=" N LYS A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 290 through 339 removed outlier: 3.814A pdb=" N ALA A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 318 " --> pdb=" O TRP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 349 through 402 removed outlier: 3.870A pdb=" N ALA A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 removed outlier: 3.686A pdb=" N VAL A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 432 removed outlier: 3.668A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.560A pdb=" N LEU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'A' and resid 574 through 585 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 610 through 626 removed outlier: 3.647A pdb=" N LYS A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 656 removed outlier: 3.788A pdb=" N LYS A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.647A pdb=" N VAL A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'B' and resid 133 through 171 removed outlier: 3.642A pdb=" N ARG B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Proline residue: B 158 - end of helix Processing helix chain 'B' and resid 186 through 234 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.746A pdb=" N HIS B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 289 removed outlier: 4.163A pdb=" N LYS B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 290 through 339 removed outlier: 3.814A pdb=" N ALA B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TRP B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 318 " --> pdb=" O TRP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 349 through 402 removed outlier: 3.870A pdb=" N ALA B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 422 removed outlier: 3.686A pdb=" N VAL B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 432 removed outlier: 3.668A pdb=" N GLY B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 450 Processing helix chain 'B' and resid 512 through 519 Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.559A pdb=" N LEU B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 574 through 585 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 610 through 626 removed outlier: 3.648A pdb=" N LYS B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 656 removed outlier: 3.789A pdb=" N LYS B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.646A pdb=" N VAL B 670 " --> pdb=" O ARG B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 693 Processing sheet with id=AA1, first strand: chain 'A' and resid 488 through 491 removed outlier: 5.702A pdb=" N VAL A 477 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 477 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS A 526 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 548 through 551 removed outlier: 6.489A pdb=" N VAL A 501 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LYS A 500 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE A 677 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 502 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU A 679 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 504 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 686 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP A 680 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 561 Processing sheet with id=AA4, first strand: chain 'B' and resid 488 through 491 removed outlier: 5.703A pdb=" N VAL B 477 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 477 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS B 526 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 548 through 551 removed outlier: 6.489A pdb=" N VAL B 501 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS B 500 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE B 677 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 502 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU B 679 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 504 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 686 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 680 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 560 through 561 610 hydrogen bonds defined for protein. 1794 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: 0.99 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2690 1.34 - 1.46: 1056 1.46 - 1.57: 4627 1.57 - 1.69: 8 1.69 - 1.81: 41 Bond restraints: 8422 Sorted by residual: bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.609 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C4 ANP A 901 " pdb=" C5 ANP A 901 " ideal model delta sigma weight residual 1.387 1.471 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" N3B ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.669 1.750 -0.081 2.00e-02 2.50e+03 1.66e+01 ... (remaining 8417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 11358 3.29 - 6.59: 87 6.59 - 9.88: 15 9.88 - 13.17: 1 13.17 - 16.46: 1 Bond angle restraints: 11462 Sorted by residual: angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 110.49 16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" N GLU B 604 " pdb=" CA GLU B 604 " pdb=" C GLU B 604 " ideal model delta sigma weight residual 111.07 106.69 4.38 1.07e+00 8.73e-01 1.68e+01 angle pdb=" N GLU A 604 " pdb=" CA GLU A 604 " pdb=" C GLU A 604 " ideal model delta sigma weight residual 111.07 106.71 4.36 1.07e+00 8.73e-01 1.66e+01 angle pdb=" N VAL A 450 " pdb=" CA VAL A 450 " pdb=" C VAL A 450 " ideal model delta sigma weight residual 112.98 108.30 4.68 1.25e+00 6.40e-01 1.40e+01 angle pdb=" N VAL B 450 " pdb=" CA VAL B 450 " pdb=" C VAL B 450 " ideal model delta sigma weight residual 112.98 108.33 4.65 1.25e+00 6.40e-01 1.38e+01 ... (remaining 11457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.29: 4651 22.29 - 44.58: 250 44.58 - 66.87: 20 66.87 - 89.16: 12 89.16 - 111.45: 1 Dihedral angle restraints: 4934 sinusoidal: 1780 harmonic: 3154 Sorted by residual: dihedral pdb=" O1A ANP A 901 " pdb=" O3A ANP A 901 " pdb=" PA ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sinusoidal sigma weight residual 83.11 -165.44 -111.45 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" CA ARG A 520 " pdb=" C ARG A 520 " pdb=" N PHE A 521 " pdb=" CA PHE A 521 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ARG B 520 " pdb=" C ARG B 520 " pdb=" N PHE B 521 " pdb=" CA PHE B 521 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1118 0.050 - 0.100: 225 0.100 - 0.151: 28 0.151 - 0.201: 2 0.201 - 0.251: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" C2' ANP A 901 " pdb=" C1' ANP A 901 " pdb=" C3' ANP A 901 " pdb=" O2' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.72 -2.55 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 1371 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 466 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 467 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 467 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 467 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 466 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 467 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 222 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE B 222 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE B 222 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG B 223 " -0.009 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 97 2.65 - 3.21: 8143 3.21 - 3.77: 12822 3.77 - 4.34: 16458 4.34 - 4.90: 27071 Nonbonded interactions: 64591 Sorted by model distance: nonbonded pdb=" OG SER B 512 " pdb="MG MG B 902 " model vdw 2.083 2.170 nonbonded pdb=" OG SER A 512 " pdb="MG MG A 902 " model vdw 2.084 2.170 nonbonded pdb=" O1G ANP B 901 " pdb="MG MG B 902 " model vdw 2.120 2.170 nonbonded pdb=" OG1 THR B 636 " pdb=" O2G ANP B 901 " model vdw 2.210 3.040 nonbonded pdb=" OG SER B 610 " pdb=" OE1 GLU B 613 " model vdw 2.259 3.040 ... (remaining 64586 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: 0.01 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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 0.144 8422 Z= 0.220 Angle : 0.696 16.463 11462 Z= 0.346 Chirality : 0.040 0.251 1374 Planarity : 0.003 0.043 1456 Dihedral : 13.760 111.448 2914 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.26), residues: 1092 helix: 2.84 (0.19), residues: 724 sheet: 1.10 (0.67), residues: 54 loop : -0.91 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 224 TYR 0.009 0.001 TYR A 196 PHE 0.020 0.002 PHE B 214 TRP 0.014 0.003 TRP B 314 HIS 0.002 0.000 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 ( 8422) covalent geometry : angle 0.69638 / 0.35 (11462) hydrogen bonds : bond 0.10683 / 7.14 ( 610) hydrogen bonds : angle 4.57150 / 3.46 ( 1794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8592 (tmmt) cc_final: 0.7919 (ttmm) REVERT: A 559 HIS cc_start: 0.7897 (t-90) cc_final: 0.7455 (t-90) REVERT: B 225 ILE cc_start: 0.8485 (mp) cc_final: 0.8270 (mp) REVERT: B 260 ILE cc_start: 0.7685 (mm) cc_final: 0.7458 (tt) REVERT: B 324 LYS cc_start: 0.8484 (tmmt) cc_final: 0.7915 (ttmt) REVERT: B 327 ASN cc_start: 0.8424 (t0) cc_final: 0.8142 (t0) REVERT: B 392 ILE cc_start: 0.8159 (tp) cc_final: 0.7817 (tt) REVERT: B 559 HIS cc_start: 0.7930 (t-90) cc_final: 0.7507 (t-90) REVERT: B 663 ILE cc_start: 0.7571 (mt) cc_final: 0.7331 (mt) outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.0720 time to fit residues: 19.0766 Evaluate side-chains 130 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 GLN B 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.166289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141614 restraints weight = 11792.479| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.01 r_work: 0.3691 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8422 Z= 0.150 Angle : 0.540 5.167 11462 Z= 0.287 Chirality : 0.040 0.139 1374 Planarity : 0.004 0.033 1456 Dihedral : 6.271 98.201 1194 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.67 % Allowed : 9.31 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.26), residues: 1092 helix: 2.96 (0.19), residues: 724 sheet: 1.60 (0.66), residues: 50 loop : -1.00 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 223 TYR 0.011 0.001 TYR B 196 PHE 0.018 0.002 PHE B 385 TRP 0.008 0.002 TRP A 314 HIS 0.004 0.001 HIS A 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8422) covalent geometry : angle 0.53993 / 0.29 (11462) hydrogen bonds : bond 0.05362 / 3.68 ( 610) hydrogen bonds : angle 3.99380 / 2.96 ( 1794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8842 (tmmt) cc_final: 0.8301 (ttmm) REVERT: A 339 ASN cc_start: 0.7920 (m-40) cc_final: 0.7571 (m-40) REVERT: B 260 ILE cc_start: 0.8304 (mm) cc_final: 0.8049 (tt) REVERT: B 324 LYS cc_start: 0.8696 (tmmt) cc_final: 0.8343 (ttmt) REVERT: B 327 ASN cc_start: 0.8822 (t0) cc_final: 0.8607 (t0) REVERT: B 530 TYR cc_start: 0.6305 (m-80) cc_final: 0.5873 (m-10) REVERT: B 571 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.8003 (mm) REVERT: B 633 ASP cc_start: 0.7888 (t0) cc_final: 0.7615 (m-30) outliers start: 14 outliers final: 10 residues processed: 144 average time/residue: 0.0602 time to fit residues: 12.6387 Evaluate side-chains 132 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 HIS B 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.156938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132018 restraints weight = 11720.054| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.91 r_work: 0.3567 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8422 Z= 0.249 Angle : 0.640 7.333 11462 Z= 0.341 Chirality : 0.043 0.144 1374 Planarity : 0.004 0.030 1456 Dihedral : 5.840 89.593 1190 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.86 % Allowed : 13.13 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.25), residues: 1092 helix: 2.54 (0.19), residues: 720 sheet: 1.46 (0.71), residues: 50 loop : -1.35 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 658 TYR 0.015 0.002 TYR A 163 PHE 0.024 0.002 PHE A 385 TRP 0.006 0.001 TRP A 314 HIS 0.009 0.001 HIS B 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 ( 8422) covalent geometry : angle 0.63957 / 0.34 (11462) hydrogen bonds : bond 0.07149 / 4.88 ( 610) hydrogen bonds : angle 4.36775 / 3.23 ( 1794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.269 Fit side-chains REVERT: A 324 LYS cc_start: 0.8879 (tmmt) cc_final: 0.8487 (ttmm) REVERT: A 339 ASN cc_start: 0.8340 (m-40) cc_final: 0.7977 (m110) REVERT: A 493 PHE cc_start: 0.6909 (m-10) cc_final: 0.6632 (m-10) REVERT: B 224 ARG cc_start: 0.8407 (ttm110) cc_final: 0.8034 (mtm-85) REVERT: B 260 ILE cc_start: 0.8481 (mm) cc_final: 0.8246 (tp) REVERT: B 324 LYS cc_start: 0.8749 (tmmt) cc_final: 0.8432 (ttmt) REVERT: B 530 TYR cc_start: 0.6564 (m-80) cc_final: 0.6176 (m-10) REVERT: B 604 GLU cc_start: 0.7613 (pp20) cc_final: 0.7393 (tp30) outliers start: 24 outliers final: 19 residues processed: 143 average time/residue: 0.0555 time to fit residues: 11.8360 Evaluate side-chains 142 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 109 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 HIS ** B 559 HIS ** 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 = 0.4044 r_free = 0.4044 target = 0.163006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138137 restraints weight = 11818.628| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.02 r_work: 0.3612 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8422 Z= 0.128 Angle : 0.505 7.206 11462 Z= 0.269 Chirality : 0.039 0.140 1374 Planarity : 0.003 0.024 1456 Dihedral : 5.422 85.296 1190 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.27 % Allowed : 16.23 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.26), residues: 1092 helix: 2.90 (0.19), residues: 722 sheet: 1.53 (0.72), residues: 50 loop : -1.11 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 315 TYR 0.011 0.001 TYR A 196 PHE 0.015 0.001 PHE A 214 TRP 0.008 0.002 TRP B 314 HIS 0.008 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 8422) covalent geometry : angle 0.50502 / 0.27 (11462) hydrogen bonds : bond 0.05682 / 3.90 ( 610) hydrogen bonds : angle 4.01036 / 2.97 ( 1794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8834 (tmmt) cc_final: 0.8479 (ttmm) REVERT: A 339 ASN cc_start: 0.7972 (m-40) cc_final: 0.7640 (m110) REVERT: A 493 PHE cc_start: 0.6950 (m-10) cc_final: 0.6571 (m-10) REVERT: B 324 LYS cc_start: 0.8663 (tmmt) cc_final: 0.8197 (ttmm) REVERT: B 530 TYR cc_start: 0.6451 (m-80) cc_final: 0.6075 (m-10) REVERT: B 663 ILE cc_start: 0.8232 (mt) cc_final: 0.7860 (mt) outliers start: 19 outliers final: 15 residues processed: 147 average time/residue: 0.0600 time to fit residues: 13.0285 Evaluate side-chains 145 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 6.9990 chunk 42 optimal weight: 0.0270 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 559 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138811 restraints weight = 11796.369| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.01 r_work: 0.3631 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8422 Z= 0.125 Angle : 0.503 9.238 11462 Z= 0.265 Chirality : 0.039 0.189 1374 Planarity : 0.003 0.023 1456 Dihedral : 5.044 78.625 1190 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.58 % Allowed : 16.23 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.26), residues: 1092 helix: 2.99 (0.19), residues: 726 sheet: 1.49 (0.72), residues: 50 loop : -1.03 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 224 TYR 0.012 0.001 TYR A 196 PHE 0.021 0.001 PHE B 418 TRP 0.008 0.002 TRP B 314 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 8422) covalent geometry : angle 0.50266 / 0.27 (11462) hydrogen bonds : bond 0.05376 / 3.69 ( 610) hydrogen bonds : angle 3.91218 / 2.88 ( 1794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.289 Fit side-chains REVERT: A 324 LYS cc_start: 0.8805 (tmmt) cc_final: 0.8443 (ttmm) REVERT: A 339 ASN cc_start: 0.7943 (m-40) cc_final: 0.7589 (m110) REVERT: A 345 TYR cc_start: 0.8938 (m-80) cc_final: 0.8706 (m-80) REVERT: A 427 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6835 (tp) REVERT: A 493 PHE cc_start: 0.7005 (m-10) cc_final: 0.6669 (m-10) REVERT: B 224 ARG cc_start: 0.8371 (ttm110) cc_final: 0.7820 (mtm-85) REVERT: B 324 LYS cc_start: 0.8662 (tmmt) cc_final: 0.8204 (ttmm) REVERT: B 427 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6649 (tt) REVERT: B 530 TYR cc_start: 0.6430 (m-80) cc_final: 0.6068 (m-10) REVERT: B 663 ILE cc_start: 0.8125 (mt) cc_final: 0.7810 (mt) outliers start: 30 outliers final: 23 residues processed: 146 average time/residue: 0.0594 time to fit residues: 12.8211 Evaluate side-chains 152 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137428 restraints weight = 11669.343| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.99 r_work: 0.3615 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8422 Z= 0.140 Angle : 0.518 9.012 11462 Z= 0.275 Chirality : 0.040 0.201 1374 Planarity : 0.003 0.022 1456 Dihedral : 4.835 73.802 1190 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.94 % Allowed : 16.59 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.26), residues: 1092 helix: 2.97 (0.19), residues: 724 sheet: 1.50 (0.73), residues: 50 loop : -1.09 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 223 TYR 0.011 0.001 TYR A 196 PHE 0.016 0.001 PHE B 418 TRP 0.008 0.002 TRP B 314 HIS 0.004 0.001 HIS B 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8422) covalent geometry : angle 0.51788 / 0.27 (11462) hydrogen bonds : bond 0.05554 / 3.80 ( 610) hydrogen bonds : angle 3.94718 / 2.91 ( 1794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.274 Fit side-chains REVERT: A 324 LYS cc_start: 0.8806 (tmmt) cc_final: 0.8480 (ttmm) REVERT: A 339 ASN cc_start: 0.8008 (m-40) cc_final: 0.7647 (m110) REVERT: A 345 TYR cc_start: 0.8943 (m-10) cc_final: 0.8722 (m-80) REVERT: A 427 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6894 (tp) REVERT: A 493 PHE cc_start: 0.7044 (m-10) cc_final: 0.6682 (m-10) REVERT: B 260 ILE cc_start: 0.8390 (mm) cc_final: 0.8143 (tp) REVERT: B 324 LYS cc_start: 0.8700 (tmmt) cc_final: 0.8268 (ttmm) REVERT: B 427 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6888 (tt) REVERT: B 530 TYR cc_start: 0.6465 (m-80) cc_final: 0.6086 (m-10) REVERT: B 663 ILE cc_start: 0.8111 (mt) cc_final: 0.7794 (mt) outliers start: 33 outliers final: 26 residues processed: 147 average time/residue: 0.0535 time to fit residues: 12.1125 Evaluate side-chains 158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 0.0670 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.164487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139762 restraints weight = 11745.808| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.99 r_work: 0.3636 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8422 Z= 0.120 Angle : 0.490 8.444 11462 Z= 0.259 Chirality : 0.039 0.216 1374 Planarity : 0.003 0.022 1456 Dihedral : 4.612 67.182 1190 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.70 % Allowed : 17.30 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.26), residues: 1092 helix: 3.07 (0.19), residues: 726 sheet: 1.44 (0.73), residues: 50 loop : -1.03 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 223 TYR 0.012 0.001 TYR A 196 PHE 0.014 0.001 PHE A 214 TRP 0.009 0.002 TRP B 314 HIS 0.002 0.001 HIS B 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 8422) covalent geometry : angle 0.48961 / 0.26 (11462) hydrogen bonds : bond 0.05097 / 3.49 ( 610) hydrogen bonds : angle 3.81799 / 2.80 ( 1794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.179 Fit side-chains REVERT: A 324 LYS cc_start: 0.8797 (tmmt) cc_final: 0.8448 (ttmm) REVERT: A 339 ASN cc_start: 0.7837 (m-40) cc_final: 0.7506 (m110) REVERT: A 427 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6786 (tp) REVERT: A 493 PHE cc_start: 0.7048 (m-10) cc_final: 0.6796 (m-10) REVERT: B 324 LYS cc_start: 0.8632 (tmmt) cc_final: 0.8189 (ttmm) REVERT: B 392 ILE cc_start: 0.8652 (tp) cc_final: 0.8328 (tt) REVERT: B 427 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6567 (tt) REVERT: B 530 TYR cc_start: 0.6413 (m-80) cc_final: 0.6079 (m-10) REVERT: B 663 ILE cc_start: 0.8132 (mt) cc_final: 0.7799 (mt) outliers start: 31 outliers final: 26 residues processed: 152 average time/residue: 0.0572 time to fit residues: 12.8908 Evaluate side-chains 157 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.161983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137071 restraints weight = 11738.736| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.99 r_work: 0.3600 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8422 Z= 0.146 Angle : 0.528 8.376 11462 Z= 0.280 Chirality : 0.041 0.211 1374 Planarity : 0.003 0.021 1456 Dihedral : 4.578 62.518 1190 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.82 % Allowed : 18.02 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.26), residues: 1092 helix: 3.05 (0.19), residues: 724 sheet: 1.46 (0.74), residues: 50 loop : -1.08 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 223 TYR 0.017 0.001 TYR A 345 PHE 0.036 0.002 PHE A 262 TRP 0.008 0.002 TRP A 314 HIS 0.004 0.001 HIS B 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 8422) covalent geometry : angle 0.52827 / 0.28 (11462) hydrogen bonds : bond 0.05533 / 3.78 ( 610) hydrogen bonds : angle 3.89986 / 2.85 ( 1794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.178 Fit side-chains REVERT: A 324 LYS cc_start: 0.8790 (tmmt) cc_final: 0.8459 (ttmm) REVERT: A 339 ASN cc_start: 0.7978 (m-40) cc_final: 0.7631 (m110) REVERT: A 345 TYR cc_start: 0.8586 (m-80) cc_final: 0.8249 (m-80) REVERT: A 427 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6850 (tp) REVERT: A 493 PHE cc_start: 0.7116 (m-10) cc_final: 0.6809 (m-10) REVERT: B 324 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8247 (ttmm) REVERT: B 427 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6843 (tt) REVERT: B 530 TYR cc_start: 0.6475 (m-80) cc_final: 0.6115 (m-10) REVERT: B 663 ILE cc_start: 0.8145 (mt) cc_final: 0.7835 (mt) outliers start: 32 outliers final: 25 residues processed: 147 average time/residue: 0.0524 time to fit residues: 11.9169 Evaluate side-chains 161 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 631 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.163354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138560 restraints weight = 11774.366| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.96 r_work: 0.3618 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8422 Z= 0.132 Angle : 0.523 8.122 11462 Z= 0.274 Chirality : 0.040 0.217 1374 Planarity : 0.003 0.022 1456 Dihedral : 4.528 58.378 1190 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.94 % Allowed : 18.02 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.26), residues: 1092 helix: 3.08 (0.19), residues: 724 sheet: 1.44 (0.75), residues: 50 loop : -1.02 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 223 TYR 0.016 0.001 TYR A 345 PHE 0.013 0.001 PHE A 214 TRP 0.010 0.002 TRP A 314 HIS 0.003 0.001 HIS B 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8422) covalent geometry : angle 0.52252 / 0.27 (11462) hydrogen bonds : bond 0.05337 / 3.65 ( 610) hydrogen bonds : angle 3.84846 / 2.82 ( 1794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8434 (ttmm) REVERT: A 339 ASN cc_start: 0.7797 (m-40) cc_final: 0.7493 (m110) REVERT: A 345 TYR cc_start: 0.8573 (m-80) cc_final: 0.8331 (m-80) REVERT: A 427 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6837 (tp) REVERT: A 493 PHE cc_start: 0.7073 (m-10) cc_final: 0.6795 (m-10) REVERT: B 324 LYS cc_start: 0.8666 (tmmt) cc_final: 0.8253 (ttmm) REVERT: B 427 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6872 (tt) REVERT: B 530 TYR cc_start: 0.6472 (m-80) cc_final: 0.6129 (m-10) REVERT: B 663 ILE cc_start: 0.8135 (mt) cc_final: 0.7816 (mt) outliers start: 33 outliers final: 27 residues processed: 147 average time/residue: 0.0610 time to fit residues: 13.5156 Evaluate side-chains 159 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.160939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136275 restraints weight = 11759.966| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.96 r_work: 0.3601 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8422 Z= 0.143 Angle : 0.533 8.227 11462 Z= 0.281 Chirality : 0.041 0.216 1374 Planarity : 0.003 0.023 1456 Dihedral : 4.525 52.771 1190 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.70 % Allowed : 18.26 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.26), residues: 1092 helix: 3.04 (0.19), residues: 724 sheet: 1.47 (0.76), residues: 50 loop : -1.06 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 223 TYR 0.019 0.001 TYR A 345 PHE 0.026 0.002 PHE A 262 TRP 0.009 0.002 TRP A 314 HIS 0.004 0.001 HIS B 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8422) covalent geometry : angle 0.53250 / 0.28 (11462) hydrogen bonds : bond 0.05548 / 3.79 ( 610) hydrogen bonds : angle 3.88017 / 2.85 ( 1794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8775 (tmmt) cc_final: 0.8466 (ttmm) REVERT: A 339 ASN cc_start: 0.7869 (m-40) cc_final: 0.7552 (m110) REVERT: A 345 TYR cc_start: 0.8623 (m-80) cc_final: 0.8345 (m-80) REVERT: A 427 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6884 (tp) REVERT: A 493 PHE cc_start: 0.7074 (m-10) cc_final: 0.6792 (m-10) REVERT: B 324 LYS cc_start: 0.8668 (tmmt) cc_final: 0.8232 (ttmm) REVERT: B 427 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6910 (tt) REVERT: B 530 TYR cc_start: 0.6518 (m-80) cc_final: 0.6170 (m-10) REVERT: B 663 ILE cc_start: 0.8146 (mt) cc_final: 0.7832 (mt) outliers start: 31 outliers final: 28 residues processed: 142 average time/residue: 0.0561 time to fit residues: 11.8711 Evaluate side-chains 158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 599 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.0270 chunk 61 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.165620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141013 restraints weight = 11673.467| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.00 r_work: 0.3654 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8422 Z= 0.117 Angle : 0.518 9.322 11462 Z= 0.270 Chirality : 0.040 0.237 1374 Planarity : 0.003 0.022 1456 Dihedral : 4.453 48.393 1190 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.34 % Allowed : 18.85 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.26), residues: 1092 helix: 3.08 (0.19), residues: 728 sheet: 1.40 (0.74), residues: 50 loop : -0.92 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 520 TYR 0.015 0.001 TYR A 345 PHE 0.033 0.001 PHE A 262 TRP 0.009 0.002 TRP A 314 HIS 0.002 0.001 HIS B 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 ( 8422) covalent geometry : angle 0.51794 / 0.27 (11462) hydrogen bonds : bond 0.04855 / 3.31 ( 610) hydrogen bonds : angle 3.75426 / 2.76 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.52 seconds wall clock time: 29 minutes 39.47 seconds (1779.47 seconds total)