Starting phenix.real_space_refine on Tue Mar 3 19:54:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgf_31967/03_2026/7vgf_31967.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgf_31967/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vgf_31967/03_2026/7vgf_31967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgf_31967/03_2026/7vgf_31967.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgf_31967/03_2026/7vgf_31967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgf_31967/03_2026/7vgf_31967.cif" } 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-5986/lib/python3.9/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: 2.05, per 1000 atoms: 0.25 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: 0.61 Conformation dependent library (CDL) restraints added in 322.5 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: 0.28 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: 1.48 Time building geometry restraints manager: 0.84 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: 4665 22.29 - 44.58: 279 44.58 - 66.87: 33 66.87 - 89.16: 12 89.16 - 111.45: 1 Dihedral angle restraints: 4990 sinusoidal: 1836 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 4987 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.280 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 14.500 111.448 2970 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 covalent geometry : bond 0.00439 ( 8422) covalent geometry : angle 0.69638 (11462) hydrogen bonds : bond 0.10683 ( 610) hydrogen bonds : angle 4.57150 ( 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 : 0.276 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: 0.0974 time to fit residues: 25.2927 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 : 0.300 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4084 r_free = 0.4084 target = 0.166621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142006 restraints weight = 11802.823| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.02 r_work: 0.3697 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8422 Z= 0.147 Angle : 0.536 5.134 11462 Z= 0.284 Chirality : 0.040 0.136 1374 Planarity : 0.004 0.031 1456 Dihedral : 7.891 96.076 1250 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.55 % Allowed : 9.31 % Favored : 89.14 % 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: 1.57 (0.66), residues: 50 loop : -0.98 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 658 TYR 0.011 0.001 TYR B 196 PHE 0.017 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 covalent geometry : bond 0.00316 ( 8422) covalent geometry : angle 0.53578 (11462) hydrogen bonds : bond 0.05394 ( 610) hydrogen bonds : angle 4.00900 ( 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 149 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8831 (tmmt) cc_final: 0.8271 (ttmm) REVERT: A 339 ASN cc_start: 0.7910 (m-40) cc_final: 0.7558 (m-40) REVERT: B 257 THR cc_start: 0.8672 (p) cc_final: 0.8470 (p) REVERT: B 260 ILE cc_start: 0.8288 (mm) cc_final: 0.8050 (tt) REVERT: B 324 LYS cc_start: 0.8705 (tmmt) cc_final: 0.8332 (ttmt) REVERT: B 327 ASN cc_start: 0.8810 (t0) cc_final: 0.8594 (t0) REVERT: B 530 TYR cc_start: 0.6324 (m-80) cc_final: 0.5899 (m-10) REVERT: B 633 ASP cc_start: 0.7908 (t0) cc_final: 0.7598 (m-30) outliers start: 13 outliers final: 10 residues processed: 140 average time/residue: 0.0811 time to fit residues: 16.4410 Evaluate side-chains 129 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 260 ILE Chi-restraints excluded: chain A residue 314 TRP 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 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: 5.9990 chunk 13 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 0.0270 overall best weight: 1.0240 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.164675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.140060 restraints weight = 11605.522| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.98 r_work: 0.3669 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8422 Z= 0.144 Angle : 0.501 5.464 11462 Z= 0.268 Chirality : 0.039 0.133 1374 Planarity : 0.003 0.026 1456 Dihedral : 7.037 82.970 1246 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.63 % Allowed : 11.34 % Favored : 86.04 % 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: 2.74 (0.26), residues: 1092 helix: 2.98 (0.19), residues: 724 sheet: 1.57 (0.69), residues: 50 loop : -1.09 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 224 TYR 0.011 0.001 TYR B 196 PHE 0.018 0.002 PHE A 385 TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8422) covalent geometry : angle 0.50126 (11462) hydrogen bonds : bond 0.05464 ( 610) hydrogen bonds : angle 3.93537 ( 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 158 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.309 Fit side-chains REVERT: A 324 LYS cc_start: 0.8787 (tmmt) cc_final: 0.8356 (ttmm) REVERT: A 339 ASN cc_start: 0.7993 (m-40) cc_final: 0.7706 (m-40) REVERT: A 409 ASP cc_start: 0.8016 (t0) cc_final: 0.7714 (t0) REVERT: A 493 PHE cc_start: 0.6705 (m-10) cc_final: 0.6499 (m-10) REVERT: B 324 LYS cc_start: 0.8689 (tmmt) cc_final: 0.8170 (ttmm) REVERT: B 530 TYR cc_start: 0.6440 (m-80) cc_final: 0.6040 (m-10) outliers start: 22 outliers final: 19 residues processed: 143 average time/residue: 0.0774 time to fit residues: 16.1905 Evaluate side-chains 139 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 280 LEU Chi-restraints excluded: chain A residue 314 TRP 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 314 TRP Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 412 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS B 381 GLN B 559 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133329 restraints weight = 11930.158| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.04 r_work: 0.3580 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8422 Z= 0.204 Angle : 0.588 9.485 11462 Z= 0.314 Chirality : 0.042 0.172 1374 Planarity : 0.004 0.025 1456 Dihedral : 7.297 78.180 1246 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.34 % Allowed : 13.84 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.26), residues: 1092 helix: 2.64 (0.19), residues: 724 sheet: 1.47 (0.73), residues: 50 loop : -1.24 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 224 TYR 0.012 0.002 TYR B 481 PHE 0.020 0.002 PHE A 161 TRP 0.007 0.001 TRP A 314 HIS 0.008 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 8422) covalent geometry : angle 0.58808 (11462) hydrogen bonds : bond 0.06505 ( 610) hydrogen bonds : angle 4.19217 ( 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 163 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8868 (tmmt) cc_final: 0.8498 (ttmm) REVERT: A 339 ASN cc_start: 0.8362 (m-40) cc_final: 0.7986 (m110) REVERT: A 409 ASP cc_start: 0.8384 (t0) cc_final: 0.8154 (t0) REVERT: B 324 LYS cc_start: 0.8745 (tmmt) cc_final: 0.8492 (ttmt) REVERT: B 530 TYR cc_start: 0.6541 (m-80) cc_final: 0.6208 (m-10) REVERT: B 663 ILE cc_start: 0.8235 (mt) cc_final: 0.7967 (mt) outliers start: 28 outliers final: 20 residues processed: 144 average time/residue: 0.0655 time to fit residues: 14.2756 Evaluate side-chains 142 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 280 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 566 LEU 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 280 LEU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 465 ILE 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: 5.9990 chunk 42 optimal weight: 0.0040 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.163151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138360 restraints weight = 11797.153| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.00 r_work: 0.3627 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2509 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= 0.130 Angle : 0.515 8.309 11462 Z= 0.275 Chirality : 0.039 0.156 1374 Planarity : 0.003 0.023 1456 Dihedral : 7.070 75.212 1246 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.98 % Allowed : 16.23 % Favored : 80.79 % 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: 2.88 (0.19), residues: 724 sheet: 1.42 (0.72), residues: 50 loop : -1.04 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 520 TYR 0.019 0.001 TYR A 345 PHE 0.022 0.002 PHE B 418 TRP 0.008 0.002 TRP B 314 HIS 0.003 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8422) covalent geometry : angle 0.51461 (11462) hydrogen bonds : bond 0.05551 ( 610) hydrogen bonds : angle 3.97288 ( 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 162 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8820 (tmmt) cc_final: 0.8471 (ttmm) REVERT: A 339 ASN cc_start: 0.7954 (m-40) cc_final: 0.7584 (m110) REVERT: A 345 TYR cc_start: 0.8605 (m-80) cc_final: 0.8341 (m-80) REVERT: A 409 ASP cc_start: 0.8264 (t0) cc_final: 0.8008 (t0) REVERT: A 493 PHE cc_start: 0.6953 (m-10) cc_final: 0.6487 (m-10) REVERT: B 279 MET cc_start: 0.8461 (mmt) cc_final: 0.8227 (ttp) REVERT: B 324 LYS cc_start: 0.8704 (tmmt) cc_final: 0.8269 (ttmm) REVERT: B 427 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6686 (tt) REVERT: B 530 TYR cc_start: 0.6467 (m-80) cc_final: 0.6114 (m-10) REVERT: B 559 HIS cc_start: 0.8219 (t70) cc_final: 0.7984 (t-90) REVERT: B 663 ILE cc_start: 0.8082 (mt) cc_final: 0.7783 (mt) outliers start: 25 outliers final: 22 residues processed: 143 average time/residue: 0.0653 time to fit residues: 13.8681 Evaluate side-chains 149 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 279 MET 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 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 222 ILE 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 386 SER 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 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: 0.0570 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.163731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138867 restraints weight = 11678.321| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.00 r_work: 0.3622 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8422 Z= 0.127 Angle : 0.502 7.932 11462 Z= 0.266 Chirality : 0.039 0.200 1374 Planarity : 0.003 0.023 1456 Dihedral : 6.821 71.656 1246 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.94 % Allowed : 16.35 % Favored : 79.71 % 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: 2.95 (0.19), residues: 726 sheet: 1.40 (0.73), residues: 50 loop : -0.97 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 658 TYR 0.020 0.001 TYR A 345 PHE 0.014 0.001 PHE A 214 TRP 0.008 0.002 TRP A 314 HIS 0.003 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8422) covalent geometry : angle 0.50181 (11462) hydrogen bonds : bond 0.05343 ( 610) hydrogen bonds : angle 3.88653 ( 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 : 0.320 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8784 (tmmt) cc_final: 0.8432 (ttmm) REVERT: A 339 ASN cc_start: 0.7847 (m-40) cc_final: 0.7495 (m110) REVERT: A 345 TYR cc_start: 0.8700 (m-80) cc_final: 0.8295 (m-80) REVERT: A 409 ASP cc_start: 0.8252 (t0) cc_final: 0.7969 (t0) REVERT: A 427 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6815 (tp) REVERT: A 493 PHE cc_start: 0.6996 (m-10) cc_final: 0.6658 (m-10) REVERT: B 324 LYS cc_start: 0.8686 (tmmt) cc_final: 0.8272 (ttmm) REVERT: B 427 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6670 (tt) REVERT: B 530 TYR cc_start: 0.6465 (m-80) cc_final: 0.6102 (m-10) REVERT: B 559 HIS cc_start: 0.8170 (t70) cc_final: 0.7907 (t-90) REVERT: B 663 ILE cc_start: 0.8118 (mt) cc_final: 0.7795 (mt) outliers start: 33 outliers final: 29 residues processed: 146 average time/residue: 0.0636 time to fit residues: 14.1956 Evaluate side-chains 156 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 279 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 427 LEU 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 566 LEU 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 280 LEU Chi-restraints excluded: chain B residue 314 TRP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 SER 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 544 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 0.1980 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.164637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139780 restraints weight = 11858.064| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.06 r_work: 0.3638 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2603 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= 0.121 Angle : 0.497 7.540 11462 Z= 0.265 Chirality : 0.039 0.211 1374 Planarity : 0.003 0.023 1456 Dihedral : 6.615 68.054 1246 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 2.83 (0.26), residues: 1092 helix: 3.03 (0.19), residues: 724 sheet: 1.34 (0.73), residues: 50 loop : -0.95 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 520 TYR 0.017 0.001 TYR A 345 PHE 0.019 0.001 PHE B 418 TRP 0.008 0.002 TRP A 314 HIS 0.002 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8422) covalent geometry : angle 0.49741 (11462) hydrogen bonds : bond 0.05079 ( 610) hydrogen bonds : angle 3.81299 ( 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 167 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8800 (tmmt) cc_final: 0.8416 (ttmm) REVERT: A 339 ASN cc_start: 0.7849 (m-40) cc_final: 0.7499 (m110) REVERT: A 345 TYR cc_start: 0.8771 (m-80) cc_final: 0.8438 (m-80) REVERT: A 409 ASP cc_start: 0.8222 (t0) cc_final: 0.7909 (t0) REVERT: A 427 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6648 (tp) REVERT: A 493 PHE cc_start: 0.7089 (m-10) cc_final: 0.6731 (m-10) REVERT: B 324 LYS cc_start: 0.8676 (tmmt) cc_final: 0.8198 (ttmm) REVERT: B 392 ILE cc_start: 0.8637 (tp) cc_final: 0.8317 (tt) REVERT: B 427 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6653 (tt) REVERT: B 530 TYR cc_start: 0.6452 (m-80) cc_final: 0.6095 (m-10) REVERT: B 663 ILE cc_start: 0.8111 (mt) cc_final: 0.7794 (mt) outliers start: 31 outliers final: 26 residues processed: 146 average time/residue: 0.0722 time to fit residues: 15.8159 Evaluate side-chains 154 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 279 MET 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 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 314 TRP Chi-restraints excluded: chain B residue 386 SER 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: 2.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 559 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136209 restraints weight = 11752.993| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.00 r_work: 0.3592 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2813 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= 0.155 Angle : 0.540 7.487 11462 Z= 0.286 Chirality : 0.041 0.206 1374 Planarity : 0.003 0.024 1456 Dihedral : 6.742 64.864 1246 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.42 % Allowed : 17.06 % Favored : 78.52 % 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: 2.71 (0.26), residues: 1092 helix: 2.94 (0.19), residues: 724 sheet: 1.35 (0.74), residues: 50 loop : -1.01 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 223 TYR 0.019 0.001 TYR A 345 PHE 0.016 0.002 PHE B 418 TRP 0.009 0.002 TRP A 314 HIS 0.005 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8422) covalent geometry : angle 0.54005 (11462) hydrogen bonds : bond 0.05683 ( 610) hydrogen bonds : angle 3.92167 ( 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 168 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.8127 (tpp) cc_final: 0.7864 (mmm) REVERT: A 324 LYS cc_start: 0.8807 (tmmt) cc_final: 0.8465 (ttmm) REVERT: A 339 ASN cc_start: 0.8020 (m-40) cc_final: 0.7656 (m110) REVERT: A 345 TYR cc_start: 0.8898 (m-80) cc_final: 0.8631 (m-80) REVERT: A 427 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6838 (tp) REVERT: A 493 PHE cc_start: 0.7115 (m-10) cc_final: 0.6716 (m-10) REVERT: B 324 LYS cc_start: 0.8703 (tmmt) cc_final: 0.8265 (ttmm) REVERT: B 427 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6866 (tt) REVERT: B 530 TYR cc_start: 0.6520 (m-80) cc_final: 0.6180 (m-10) REVERT: B 663 ILE cc_start: 0.8156 (mt) cc_final: 0.7836 (mt) outliers start: 37 outliers final: 31 residues processed: 143 average time/residue: 0.0674 time to fit residues: 14.7160 Evaluate side-chains 164 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 222 ILE Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 279 MET 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 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 222 ILE 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 386 SER 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 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: 0.0020 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.163568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138729 restraints weight = 11729.293| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.03 r_work: 0.3627 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2784 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= 0.125 Angle : 0.520 7.167 11462 Z= 0.274 Chirality : 0.040 0.222 1374 Planarity : 0.003 0.023 1456 Dihedral : 6.655 61.836 1246 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.94 % Allowed : 17.18 % Favored : 78.88 % 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: 2.79 (0.26), residues: 1092 helix: 2.99 (0.19), residues: 726 sheet: 1.34 (0.74), residues: 50 loop : -0.95 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 223 TYR 0.018 0.001 TYR A 345 PHE 0.037 0.002 PHE A 262 TRP 0.009 0.002 TRP A 314 HIS 0.003 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8422) covalent geometry : angle 0.52035 (11462) hydrogen bonds : bond 0.05203 ( 610) hydrogen bonds : angle 3.81056 ( 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 163 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.8195 (tpp) cc_final: 0.7924 (mmm) REVERT: A 324 LYS cc_start: 0.8794 (tmmt) cc_final: 0.8413 (ttmm) REVERT: A 339 ASN cc_start: 0.7942 (m-40) cc_final: 0.7574 (m110) REVERT: A 345 TYR cc_start: 0.8875 (m-80) cc_final: 0.8608 (m-80) REVERT: A 427 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6640 (tp) REVERT: A 493 PHE cc_start: 0.7160 (m-10) cc_final: 0.6826 (m-10) REVERT: B 324 LYS cc_start: 0.8660 (tmmt) cc_final: 0.8206 (ttmm) REVERT: B 427 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6670 (tt) REVERT: B 530 TYR cc_start: 0.6494 (m-80) cc_final: 0.6184 (m-10) REVERT: B 663 ILE cc_start: 0.8121 (mt) cc_final: 0.7798 (mt) outliers start: 33 outliers final: 28 residues processed: 142 average time/residue: 0.0622 time to fit residues: 13.6917 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 : 0.240 ------------------------------------------------------------------------------- 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 279 MET 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 427 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 466 THR 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 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 386 SER 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 Chi-restraints excluded: chain B residue 631 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.160432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.135590 restraints weight = 11740.467| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.96 r_work: 0.3585 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2940 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= 0.159 Angle : 0.551 7.433 11462 Z= 0.291 Chirality : 0.041 0.215 1374 Planarity : 0.003 0.024 1456 Dihedral : 6.809 59.297 1246 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.94 % Allowed : 16.71 % Favored : 79.36 % 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: 2.68 (0.26), residues: 1092 helix: 2.94 (0.19), residues: 724 sheet: 1.32 (0.75), 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 0.014 0.002 PHE B 385 TRP 0.009 0.002 TRP A 314 HIS 0.005 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8422) covalent geometry : angle 0.55091 (11462) hydrogen bonds : bond 0.05746 ( 610) hydrogen bonds : angle 3.90818 ( 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 164 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.8096 (tpp) cc_final: 0.7804 (mmm) REVERT: A 324 LYS cc_start: 0.8787 (tmmt) cc_final: 0.8465 (ttmm) REVERT: A 339 ASN cc_start: 0.8037 (m-40) cc_final: 0.7684 (m110) REVERT: A 345 TYR cc_start: 0.8928 (m-80) cc_final: 0.8708 (m-80) REVERT: A 427 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6964 (tp) REVERT: A 493 PHE cc_start: 0.7090 (m-10) cc_final: 0.6712 (m-10) REVERT: B 324 LYS cc_start: 0.8696 (tmmt) cc_final: 0.8265 (ttmm) REVERT: B 427 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6933 (tt) REVERT: B 530 TYR cc_start: 0.6559 (m-80) cc_final: 0.6214 (m-10) REVERT: B 663 ILE cc_start: 0.8168 (mt) cc_final: 0.7851 (mt) outliers start: 33 outliers final: 28 residues processed: 142 average time/residue: 0.0637 time to fit residues: 13.7794 Evaluate side-chains 159 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 279 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 314 TRP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 466 THR 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 222 ILE 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 386 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 61 optimal weight: 0.7980 chunk 80 optimal weight: 0.0980 chunk 52 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.164922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140049 restraints weight = 11677.742| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.04 r_work: 0.3668 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8422 Z= 0.122 Angle : 0.530 9.091 11462 Z= 0.275 Chirality : 0.040 0.228 1374 Planarity : 0.003 0.023 1456 Dihedral : 6.497 52.834 1246 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.22 % Allowed : 17.90 % Favored : 78.88 % 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: 2.85 (0.26), residues: 1092 helix: 3.05 (0.19), residues: 726 sheet: 1.30 (0.75), residues: 50 loop : -0.96 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 223 TYR 0.017 0.001 TYR A 345 PHE 0.016 0.001 PHE A 214 TRP 0.010 0.002 TRP B 314 HIS 0.002 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8422) covalent geometry : angle 0.52961 (11462) hydrogen bonds : bond 0.04967 ( 610) hydrogen bonds : angle 3.74509 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.72 seconds wall clock time: 34 minutes 45.69 seconds (2085.69 seconds total)