Starting phenix.real_space_refine on Thu Jun 4 04:02:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itg_60861/06_2026/9itg_60861.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itg_60861/06_2026/9itg_60861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itg_60861/06_2026/9itg_60861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itg_60861/06_2026/9itg_60861.map" model { file = "/net/cci-nas-00/data/ceres_data/9itg_60861/06_2026/9itg_60861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itg_60861/06_2026/9itg_60861.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 42 5.16 5 C 6932 2.51 5 N 1653 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10451 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4960 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 582} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4967 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 583} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'1T9': 1, '3PE': 2, 'CLR': 1, 'IHP': 1, 'PLM': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'1T9': 1, '3PE': 2, 'CLR': 1, 'IHP': 1, 'PLM': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.98, per 1000 atoms: 0.29 Number of scatterers: 10451 At special positions: 0 Unit cell: (104.34, 125.06, 101.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 20 15.00 O 1804 8.00 N 1653 7.00 C 6932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 550.0 milliseconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 77.1% alpha, 0.0% 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 2 through 10 Processing helix chain 'A' and resid 12 through 16 Processing helix chain 'A' and resid 21 through 35 Processing helix chain 'A' and resid 46 through 101 removed outlier: 3.644A pdb=" N ALA A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 168 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 230 through 256 removed outlier: 3.575A pdb=" N LEU A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.283A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.655A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 404 through 420 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 453 through 471 Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.096A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.504A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TRP A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 Processing helix chain 'A' and resid 587 through 620 Proline residue: A 598 - end of helix removed outlier: 3.618A pdb=" N VAL A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 602 " --> pdb=" O PRO A 598 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 619 " --> pdb=" O GLU A 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 12 through 16 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 46 through 101 removed outlier: 3.676A pdb=" N ALA B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 168 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 190 through 206 Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 230 through 256 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.284A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.656A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 404 through 420 Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 453 through 471 Processing helix chain 'B' and resid 472 through 502 removed outlier: 4.039A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.504A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TRP B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 Processing helix chain 'B' and resid 586 through 620 removed outlier: 4.026A pdb=" N ASP B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.618A pdb=" N VAL B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 602 " --> pdb=" O PRO B 598 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 612 " --> pdb=" O ASN B 608 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 2037 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: 1.60 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1571 1.32 - 1.44: 3055 1.44 - 1.57: 6022 1.57 - 1.69: 22 1.69 - 1.81: 60 Bond restraints: 10730 Sorted by residual: bond pdb=" OBB 1T9 A 808 " pdb=" PAX 1T9 A 808 " ideal model delta sigma weight residual 1.726 1.611 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" OBB 1T9 B 808 " pdb=" PAX 1T9 B 808 " ideal model delta sigma weight residual 1.726 1.611 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C5 IHP B 802 " pdb=" O15 IHP B 802 " ideal model delta sigma weight residual 1.389 1.466 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 IHP A 802 " pdb=" O15 IHP A 802 " ideal model delta sigma weight residual 1.389 1.466 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N VAL A 220 " pdb=" CA VAL A 220 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.34e+01 ... (remaining 10725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 9163 1.36 - 2.72: 3940 2.72 - 4.08: 1250 4.08 - 5.44: 143 5.44 - 6.80: 27 Bond angle restraints: 14523 Sorted by residual: angle pdb=" N ALA A 52 " pdb=" CA ALA A 52 " pdb=" C ALA A 52 " ideal model delta sigma weight residual 113.01 106.75 6.26 1.20e+00 6.94e-01 2.72e+01 angle pdb=" N ALA B 52 " pdb=" CA ALA B 52 " pdb=" C ALA B 52 " ideal model delta sigma weight residual 113.01 106.84 6.17 1.20e+00 6.94e-01 2.65e+01 angle pdb=" N LYS B 556 " pdb=" CA LYS B 556 " pdb=" C LYS B 556 " ideal model delta sigma weight residual 113.28 107.01 6.27 1.22e+00 6.72e-01 2.64e+01 angle pdb=" N LYS A 556 " pdb=" CA LYS A 556 " pdb=" C LYS A 556 " ideal model delta sigma weight residual 113.28 107.04 6.24 1.22e+00 6.72e-01 2.62e+01 angle pdb=" N ILE A 579 " pdb=" CA ILE A 579 " pdb=" C ILE A 579 " ideal model delta sigma weight residual 111.91 107.49 4.42 8.90e-01 1.26e+00 2.46e+01 ... (remaining 14518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 6050 22.82 - 45.63: 425 45.63 - 68.45: 98 68.45 - 91.26: 8 91.26 - 114.08: 6 Dihedral angle restraints: 6587 sinusoidal: 3009 harmonic: 3578 Sorted by residual: dihedral pdb=" CA PHE A 474 " pdb=" C PHE A 474 " pdb=" N PRO A 475 " pdb=" CA PRO A 475 " ideal model delta harmonic sigma weight residual 0.00 20.82 -20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE B 474 " pdb=" C PHE B 474 " pdb=" N PRO B 475 " pdb=" CA PRO B 475 " ideal model delta harmonic sigma weight residual 0.00 20.04 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CAU 1T9 A 808 " pdb=" CAT 1T9 A 808 " pdb=" CBC 1T9 A 808 " pdb=" CBD 1T9 A 808 " ideal model delta sinusoidal sigma weight residual 177.21 -68.71 -114.08 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 6584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 505 0.058 - 0.116: 677 0.116 - 0.174: 324 0.174 - 0.232: 56 0.232 - 0.290: 6 Chirality restraints: 1568 Sorted by residual: chirality pdb=" C13 CLR B 803 " pdb=" C12 CLR B 803 " pdb=" C14 CLR B 803 " pdb=" C17 CLR B 803 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C13 CLR A 803 " pdb=" C12 CLR A 803 " pdb=" C14 CLR A 803 " pdb=" C17 CLR A 803 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C1 IHP B 802 " pdb=" C2 IHP B 802 " pdb=" C6 IHP B 802 " pdb=" O11 IHP B 802 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1565 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAC 1T9 B 808 " 0.033 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" CAD 1T9 B 808 " -0.078 2.00e-02 2.50e+03 pdb=" CAE 1T9 B 808 " 0.078 2.00e-02 2.50e+03 pdb=" CAQ 1T9 B 808 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAC 1T9 A 808 " -0.033 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" CAD 1T9 A 808 " 0.078 2.00e-02 2.50e+03 pdb=" CAE 1T9 A 808 " -0.078 2.00e-02 2.50e+03 pdb=" CAQ 1T9 A 808 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 466 " -0.244 9.50e-02 1.11e+02 1.09e-01 7.43e+00 pdb=" NE ARG B 466 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 466 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 466 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 466 " -0.007 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 4176 2.91 - 3.41: 11165 3.41 - 3.91: 18226 3.91 - 4.40: 20425 4.40 - 4.90: 33480 Nonbonded interactions: 87472 Sorted by model distance: nonbonded pdb=" O VAL A 478 " pdb=" OH TYR A 524 " model vdw 2.416 3.040 nonbonded pdb=" O ARG A 604 " pdb=" ND2 ASN A 608 " model vdw 2.425 3.120 nonbonded pdb=" O ARG B 604 " pdb=" ND2 ASN B 608 " model vdw 2.425 3.120 nonbonded pdb=" O PRO A 37 " pdb=" C SER A 38 " model vdw 2.438 3.270 nonbonded pdb=" O VAL B 478 " pdb=" OH TYR B 524 " model vdw 2.475 3.040 ... (remaining 87467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 582 or resid 584 through 808)) } 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.840 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.012 0.115 10732 Z= 0.896 Angle : 1.571 6.798 14527 Z= 1.222 Chirality : 0.098 0.290 1568 Planarity : 0.009 0.109 1740 Dihedral : 15.650 114.080 4259 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.76 % Allowed : 7.81 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.49 (0.21), residues: 1191 helix: -1.28 (0.15), residues: 902 sheet: None (None), residues: 0 loop : -2.34 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 176 TYR 0.017 0.002 TYR A 352 PHE 0.020 0.002 PHE A 517 TRP 0.027 0.002 TRP A 514 HIS 0.009 0.002 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.01243 / 0.90 (10730) covalent geometry : angle 1.57146 / 1.22 (14523) SS BOND : bond 0.00444 / 0.23 ( 2) SS BOND : angle 0.60854 / 0.28 ( 4) hydrogen bonds : bond 0.23977 / 15.89 ( 687) hydrogen bonds : angle 8.10740 / 5.99 ( 2037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 0.410 Fit side-chains REVERT: A 11 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7419 (mt) REVERT: A 126 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7954 (mmt180) REVERT: A 302 ILE cc_start: 0.8929 (mt) cc_final: 0.8666 (mt) REVERT: A 468 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7171 (ttm170) REVERT: A 475 PRO cc_start: 0.8389 (OUTLIER) cc_final: 0.8044 (Cg_endo) REVERT: A 627 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8683 (mtm-85) REVERT: A 631 VAL cc_start: 0.7582 (p) cc_final: 0.6873 (t) REVERT: B 11 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7405 (mt) REVERT: B 302 ILE cc_start: 0.8765 (mt) cc_final: 0.8525 (mt) REVERT: B 466 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7935 (mtp85) REVERT: B 468 ARG cc_start: 0.7745 (ttt180) cc_final: 0.6962 (ttm170) REVERT: B 631 VAL cc_start: 0.7490 (p) cc_final: 0.6483 (t) outliers start: 39 outliers final: 6 residues processed: 300 average time/residue: 0.1327 time to fit residues: 52.5914 Evaluate side-chains 128 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 475 PRO Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 627 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 204 ASN A 387 HIS A 399 GLN A 504 HIS B 70 ASN B 89 ASN B 150 ASN B 204 ASN B 387 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.161330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125742 restraints weight = 14492.552| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.05 r_work: 0.3443 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10732 Z= 0.148 Angle : 0.608 9.883 14527 Z= 0.315 Chirality : 0.041 0.317 1568 Planarity : 0.004 0.041 1740 Dihedral : 12.208 108.372 1992 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.45 % Allowed : 13.02 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.74 (0.25), residues: 1191 helix: 1.12 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -1.48 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 171 TYR 0.029 0.002 TYR B 412 PHE 0.023 0.002 PHE A 3 TRP 0.023 0.002 TRP A 607 HIS 0.008 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (10730) covalent geometry : angle 0.60822 / 0.31 (14523) SS BOND : bond 0.00080 / 0.04 ( 2) SS BOND : angle 0.85797 / 0.42 ( 4) hydrogen bonds : bond 0.06317 / 4.22 ( 687) hydrogen bonds : angle 4.09000 / 3.02 ( 2037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.388 Fit side-chains REVERT: A 11 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 129 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8117 (tptp) REVERT: A 422 LYS cc_start: 0.7871 (tptp) cc_final: 0.7549 (pttp) REVERT: A 468 ARG cc_start: 0.7536 (ttt180) cc_final: 0.6689 (ttm110) REVERT: B 11 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7799 (mt) REVERT: B 129 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8079 (tptp) REVERT: B 422 LYS cc_start: 0.7842 (tptp) cc_final: 0.7526 (pttp) REVERT: B 468 ARG cc_start: 0.7540 (ttt180) cc_final: 0.6672 (ttm110) outliers start: 15 outliers final: 5 residues processed: 180 average time/residue: 0.1137 time to fit residues: 28.3244 Evaluate side-chains 133 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 627 ARG Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 544 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 204 ASN B 92 GLN B 204 ASN B 614 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.157973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124045 restraints weight = 14456.644| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.12 r_work: 0.3393 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10732 Z= 0.139 Angle : 0.546 10.433 14527 Z= 0.280 Chirality : 0.040 0.270 1568 Planarity : 0.004 0.030 1740 Dihedral : 11.402 95.358 1976 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.64 % Allowed : 13.98 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.25), residues: 1191 helix: 2.02 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -1.27 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 171 TYR 0.030 0.002 TYR A 412 PHE 0.020 0.002 PHE B 54 TRP 0.021 0.001 TRP A 607 HIS 0.007 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (10730) covalent geometry : angle 0.54568 / 0.28 (14523) SS BOND : bond 0.00095 / 0.05 ( 2) SS BOND : angle 0.58938 / 0.27 ( 4) hydrogen bonds : bond 0.05983 / 4.01 ( 687) hydrogen bonds : angle 3.68445 / 2.75 ( 2037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8070 (mt) REVERT: A 129 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8152 (tptp) REVERT: A 175 TRP cc_start: 0.7808 (t60) cc_final: 0.7571 (t60) REVERT: A 419 LEU cc_start: 0.8631 (mt) cc_final: 0.8426 (tt) REVERT: A 422 LYS cc_start: 0.7863 (tptp) cc_final: 0.7486 (pttp) REVERT: A 468 ARG cc_start: 0.7614 (ttt180) cc_final: 0.6656 (ttm110) REVERT: B 11 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 129 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8104 (tptp) REVERT: B 422 LYS cc_start: 0.7901 (tptp) cc_final: 0.7469 (pttp) REVERT: B 452 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7877 (tp40) REVERT: B 468 ARG cc_start: 0.7602 (ttt180) cc_final: 0.6692 (ttm110) outliers start: 17 outliers final: 9 residues processed: 153 average time/residue: 0.1183 time to fit residues: 24.8702 Evaluate side-chains 131 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 631 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.152590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116694 restraints weight = 14531.480| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.03 r_work: 0.3315 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10732 Z= 0.222 Angle : 0.644 10.995 14527 Z= 0.331 Chirality : 0.044 0.265 1568 Planarity : 0.005 0.033 1740 Dihedral : 12.411 89.749 1972 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.22 % Allowed : 14.27 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.24), residues: 1191 helix: 1.81 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -1.20 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 171 TYR 0.038 0.002 TYR A 412 PHE 0.034 0.002 PHE B 54 TRP 0.027 0.002 TRP A 607 HIS 0.006 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (10730) covalent geometry : angle 0.64415 / 0.33 (14523) SS BOND : bond 0.00136 / 0.07 ( 2) SS BOND : angle 0.56033 / 0.28 ( 4) hydrogen bonds : bond 0.07292 / 4.87 ( 687) hydrogen bonds : angle 3.87522 / 2.88 ( 2037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8197 (tptp) REVERT: A 227 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6843 (pt0) REVERT: A 412 TYR cc_start: 0.8146 (t80) cc_final: 0.7367 (t80) REVERT: A 468 ARG cc_start: 0.7707 (ttt180) cc_final: 0.6407 (mtm180) REVERT: A 471 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8294 (mmmm) REVERT: B 129 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8170 (ttpp) REVERT: B 227 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6743 (pt0) REVERT: B 412 TYR cc_start: 0.8313 (t80) cc_final: 0.7815 (t80) REVERT: B 468 ARG cc_start: 0.7753 (ttt180) cc_final: 0.6421 (mtm180) REVERT: B 471 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8213 (mmmm) outliers start: 23 outliers final: 15 residues processed: 139 average time/residue: 0.1151 time to fit residues: 22.1628 Evaluate side-chains 125 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 631 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 102 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 GLN A 399 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119966 restraints weight = 14337.896| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.04 r_work: 0.3357 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10732 Z= 0.144 Angle : 0.541 11.051 14527 Z= 0.277 Chirality : 0.039 0.214 1568 Planarity : 0.004 0.032 1740 Dihedral : 11.522 92.429 1968 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.12 % Allowed : 14.85 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.17 (0.25), residues: 1191 helix: 2.26 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -1.10 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 171 TYR 0.021 0.002 TYR A 412 PHE 0.026 0.002 PHE B 54 TRP 0.020 0.001 TRP A 607 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10730) covalent geometry : angle 0.54116 / 0.28 (14523) SS BOND : bond 0.00068 / 0.03 ( 2) SS BOND : angle 0.42785 / 0.19 ( 4) hydrogen bonds : bond 0.05856 / 3.92 ( 687) hydrogen bonds : angle 3.59677 / 2.68 ( 2037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8133 (ttpp) REVERT: A 175 TRP cc_start: 0.7905 (t60) cc_final: 0.7472 (t60) REVERT: A 372 PHE cc_start: 0.8180 (m-10) cc_final: 0.7936 (m-10) REVERT: A 412 TYR cc_start: 0.8241 (t80) cc_final: 0.7645 (t80) REVERT: A 468 ARG cc_start: 0.7679 (ttt180) cc_final: 0.6415 (mtm180) REVERT: A 471 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8291 (mmmm) REVERT: B 1 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6398 (ttp) REVERT: B 129 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8076 (ttpp) REVERT: B 175 TRP cc_start: 0.7888 (t60) cc_final: 0.7508 (t60) REVERT: B 372 PHE cc_start: 0.8139 (m-10) cc_final: 0.7901 (m-10) REVERT: B 412 TYR cc_start: 0.8303 (t80) cc_final: 0.7801 (t80) REVERT: B 468 ARG cc_start: 0.7690 (ttt180) cc_final: 0.6661 (ttm110) REVERT: B 471 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8209 (mmmm) outliers start: 22 outliers final: 14 residues processed: 141 average time/residue: 0.1124 time to fit residues: 22.2099 Evaluate side-chains 132 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 631 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.154811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119209 restraints weight = 14410.266| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.00 r_work: 0.3347 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10732 Z= 0.155 Angle : 0.550 11.064 14527 Z= 0.283 Chirality : 0.040 0.192 1568 Planarity : 0.004 0.034 1740 Dihedral : 11.513 90.115 1968 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.22 % Allowed : 15.53 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.30 (0.25), residues: 1191 helix: 2.34 (0.17), residues: 887 sheet: None (None), residues: 0 loop : -1.04 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 171 TYR 0.020 0.002 TYR A 412 PHE 0.028 0.002 PHE B 54 TRP 0.021 0.001 TRP B 607 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (10730) covalent geometry : angle 0.55021 / 0.28 (14523) SS BOND : bond 0.00078 / 0.04 ( 2) SS BOND : angle 0.47335 / 0.24 ( 4) hydrogen bonds : bond 0.05964 / 3.99 ( 687) hydrogen bonds : angle 3.60822 / 2.68 ( 2037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8118 (ttpp) REVERT: A 412 TYR cc_start: 0.8280 (t80) cc_final: 0.7669 (t80) REVERT: A 468 ARG cc_start: 0.7650 (ttt180) cc_final: 0.6351 (mtm180) REVERT: A 471 LYS cc_start: 0.8572 (mmmt) cc_final: 0.8365 (mmmm) REVERT: B 1 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6389 (ttp) REVERT: B 129 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8084 (ttpp) REVERT: B 175 TRP cc_start: 0.7919 (t60) cc_final: 0.7454 (t60) REVERT: B 349 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8182 (tt) REVERT: B 372 PHE cc_start: 0.8158 (m-10) cc_final: 0.7917 (m-10) REVERT: B 412 TYR cc_start: 0.8325 (t80) cc_final: 0.7496 (t80) REVERT: B 468 ARG cc_start: 0.7715 (ttt180) cc_final: 0.6667 (ttm110) REVERT: B 471 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8310 (mmmm) outliers start: 23 outliers final: 15 residues processed: 144 average time/residue: 0.1102 time to fit residues: 22.1811 Evaluate side-chains 134 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 631 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 163 HIS A 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118522 restraints weight = 14288.820| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.98 r_work: 0.3334 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10732 Z= 0.173 Angle : 0.569 11.242 14527 Z= 0.293 Chirality : 0.041 0.202 1568 Planarity : 0.004 0.034 1740 Dihedral : 11.763 89.306 1968 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.03 % Allowed : 15.72 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.27 (0.25), residues: 1191 helix: 2.32 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -1.01 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 171 TYR 0.017 0.002 TYR A 412 PHE 0.030 0.002 PHE B 54 TRP 0.021 0.001 TRP B 607 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (10730) covalent geometry : angle 0.56880 / 0.29 (14523) SS BOND : bond 0.00088 / 0.04 ( 2) SS BOND : angle 0.42990 / 0.21 ( 4) hydrogen bonds : bond 0.06176 / 4.14 ( 687) hydrogen bonds : angle 3.65453 / 2.71 ( 2037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6390 (t80) REVERT: A 349 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8248 (tt) REVERT: A 372 PHE cc_start: 0.8215 (m-10) cc_final: 0.8012 (m-10) REVERT: A 412 TYR cc_start: 0.8287 (t80) cc_final: 0.7701 (t80) REVERT: A 468 ARG cc_start: 0.7694 (ttt180) cc_final: 0.6360 (mtm180) REVERT: B 1 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6506 (ttp) REVERT: B 175 TRP cc_start: 0.7932 (t60) cc_final: 0.7447 (t60) REVERT: B 335 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6479 (t80) REVERT: B 349 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8206 (tt) REVERT: B 412 TYR cc_start: 0.8335 (t80) cc_final: 0.7606 (t80) REVERT: B 468 ARG cc_start: 0.7757 (ttt180) cc_final: 0.6691 (ttm110) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 0.1037 time to fit residues: 19.9976 Evaluate side-chains 131 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 631 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 42 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.157992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122867 restraints weight = 14197.309| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.00 r_work: 0.3392 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10732 Z= 0.115 Angle : 0.502 10.923 14527 Z= 0.257 Chirality : 0.038 0.196 1568 Planarity : 0.004 0.034 1740 Dihedral : 11.004 91.538 1968 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.64 % Allowed : 16.10 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.25), residues: 1191 helix: 2.68 (0.17), residues: 887 sheet: None (None), residues: 0 loop : -0.93 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 171 TYR 0.012 0.001 TYR A 412 PHE 0.032 0.001 PHE B 54 TRP 0.016 0.001 TRP B 607 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (10730) covalent geometry : angle 0.50191 / 0.26 (14523) SS BOND : bond 0.00028 / 0.01 ( 2) SS BOND : angle 0.36416 / 0.18 ( 4) hydrogen bonds : bond 0.04888 / 3.28 ( 687) hydrogen bonds : angle 3.42442 / 2.53 ( 2037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6280 (t80) REVERT: A 349 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8110 (tt) REVERT: A 372 PHE cc_start: 0.8055 (m-10) cc_final: 0.7830 (m-10) REVERT: A 412 TYR cc_start: 0.8256 (t80) cc_final: 0.7379 (t80) REVERT: A 468 ARG cc_start: 0.7525 (ttt180) cc_final: 0.6233 (mtm180) REVERT: B 1 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6297 (ttp) REVERT: B 335 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.6269 (t80) REVERT: B 412 TYR cc_start: 0.8301 (t80) cc_final: 0.7570 (t80) REVERT: B 468 ARG cc_start: 0.7687 (ttt180) cc_final: 0.6618 (ttm110) outliers start: 17 outliers final: 12 residues processed: 131 average time/residue: 0.1030 time to fit residues: 19.5130 Evaluate side-chains 126 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 631 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121371 restraints weight = 14272.102| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.98 r_work: 0.3375 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10732 Z= 0.130 Angle : 0.532 11.375 14527 Z= 0.271 Chirality : 0.039 0.203 1568 Planarity : 0.004 0.033 1740 Dihedral : 11.004 89.502 1968 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.74 % Allowed : 16.39 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.25), residues: 1191 helix: 2.69 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -0.93 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 171 TYR 0.013 0.001 TYR A 412 PHE 0.029 0.002 PHE B 54 TRP 0.018 0.001 TRP B 607 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10730) covalent geometry : angle 0.53220 / 0.27 (14523) SS BOND : bond 0.00043 / 0.02 ( 2) SS BOND : angle 0.37136 / 0.18 ( 4) hydrogen bonds : bond 0.05196 / 3.49 ( 687) hydrogen bonds : angle 3.47216 / 2.57 ( 2037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 372 PHE cc_start: 0.8113 (m-10) cc_final: 0.7875 (m-10) REVERT: A 412 TYR cc_start: 0.8299 (t80) cc_final: 0.7780 (t80) REVERT: A 468 ARG cc_start: 0.7538 (ttt180) cc_final: 0.6201 (mtm180) REVERT: A 471 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8305 (mmmm) REVERT: B 1 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6340 (ttp) REVERT: B 349 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 372 PHE cc_start: 0.8092 (m-10) cc_final: 0.7868 (m-10) REVERT: B 412 TYR cc_start: 0.8334 (t80) cc_final: 0.7596 (t80) REVERT: B 468 ARG cc_start: 0.7694 (ttt180) cc_final: 0.6633 (ttm110) REVERT: B 471 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8203 (mmmm) outliers start: 18 outliers final: 12 residues processed: 130 average time/residue: 0.1084 time to fit residues: 20.0395 Evaluate side-chains 127 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 529 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.5968 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.159184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124472 restraints weight = 14277.351| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.97 r_work: 0.3416 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10732 Z= 0.114 Angle : 0.515 11.001 14527 Z= 0.262 Chirality : 0.038 0.199 1568 Planarity : 0.004 0.034 1740 Dihedral : 10.701 90.153 1968 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.45 % Allowed : 16.78 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.96 (0.25), residues: 1191 helix: 2.85 (0.17), residues: 887 sheet: None (None), residues: 0 loop : -0.87 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 171 TYR 0.011 0.001 TYR A 412 PHE 0.032 0.001 PHE A 54 TRP 0.015 0.001 TRP B 607 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10730) covalent geometry : angle 0.51500 / 0.26 (14523) SS BOND : bond 0.00039 / 0.02 ( 2) SS BOND : angle 0.37217 / 0.17 ( 4) hydrogen bonds : bond 0.04632 / 3.12 ( 687) hydrogen bonds : angle 3.40137 / 2.51 ( 2037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8157 (tt) REVERT: A 372 PHE cc_start: 0.8065 (m-10) cc_final: 0.7843 (m-10) REVERT: A 412 TYR cc_start: 0.8274 (t80) cc_final: 0.7430 (t80) REVERT: A 468 ARG cc_start: 0.7529 (ttt180) cc_final: 0.6216 (mtm180) REVERT: A 471 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8311 (mmmm) REVERT: B 1 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6402 (ttp) REVERT: B 349 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8020 (tt) REVERT: B 468 ARG cc_start: 0.7666 (ttt180) cc_final: 0.6612 (ttm110) REVERT: B 471 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8238 (mmmm) outliers start: 15 outliers final: 11 residues processed: 130 average time/residue: 0.1030 time to fit residues: 19.2296 Evaluate side-chains 126 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 529 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN B 163 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.157075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121923 restraints weight = 14426.732| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.99 r_work: 0.3381 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10732 Z= 0.131 Angle : 0.537 11.129 14527 Z= 0.272 Chirality : 0.039 0.203 1568 Planarity : 0.004 0.033 1740 Dihedral : 10.878 88.576 1968 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.45 % Allowed : 17.16 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.25), residues: 1191 helix: 2.76 (0.17), residues: 886 sheet: None (None), residues: 0 loop : -0.85 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.033 0.001 TYR B 412 PHE 0.032 0.002 PHE A 54 TRP 0.018 0.001 TRP B 607 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10730) covalent geometry : angle 0.53690 / 0.27 (14523) SS BOND : bond 0.00039 / 0.02 ( 2) SS BOND : angle 0.28228 / 0.16 ( 4) hydrogen bonds : bond 0.05130 / 3.44 ( 687) hydrogen bonds : angle 3.46527 / 2.56 ( 2037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.09 seconds wall clock time: 57 minutes 56.48 seconds (3476.48 seconds total)