Starting phenix.real_space_refine on Thu Jul 2 16:51:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pr1_13607/07_2026/7pr1_13607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pr1_13607/07_2026/7pr1_13607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pr1_13607/07_2026/7pr1_13607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pr1_13607/07_2026/7pr1_13607.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pr1_13607/07_2026/7pr1_13607.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pr1_13607/07_2026/7pr1_13607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pr1_13607/07_2026/7pr1_13607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pr1_13607/07_2026/7pr1_13607.map" } resolution = 2.81 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= 0.124 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 26 5.16 5 C 5888 2.51 5 N 1604 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9222 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4579 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 17, 'TRANS': 569} Chain: "B" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4579 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 17, 'TRANS': 569} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.32, per 1000 atoms: 0.25 Number of scatterers: 9222 At special positions: 0 Unit cell: (74.048, 90.688, 139.776, 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 26 16.00 P 6 15.00 Mg 2 11.99 O 1696 8.00 N 1604 7.00 C 5888 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: 0.97 Conformation dependent library (CDL) restraints added in 399.5 milliseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 6 sheets defined 73.2% alpha, 8.3% 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 92 through 101 removed outlier: 3.874A pdb=" N ILE A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 110 through 146 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 159 through 205 removed outlier: 4.152A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 215 through 240 removed outlier: 3.925A pdb=" N THR A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 259 removed outlier: 3.501A pdb=" N THR A 244 " --> pdb=" O HIS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 309 removed outlier: 4.184A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 318 through 372 removed outlier: 3.573A pdb=" N PHE A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 400 Proline residue: A 393 - end of helix Processing helix chain 'A' and resid 400 through 420 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 504 through 508 removed outlier: 3.777A pdb=" N VAL A 508 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 609 through 628 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 660 through 668 Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 110 through 146 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 159 through 205 removed outlier: 4.152A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 215 through 240 removed outlier: 3.925A pdb=" N THR B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 259 removed outlier: 3.501A pdb=" N THR B 244 " --> pdb=" O HIS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 309 removed outlier: 4.184A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 318 through 372 removed outlier: 3.574A pdb=" N PHE B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 400 Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 400 through 420 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 504 through 508 removed outlier: 3.777A pdb=" N VAL B 508 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 530 through 537 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 556 through 563 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 595 Processing helix chain 'B' and resid 609 through 628 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 660 through 668 Processing helix chain 'B' and resid 669 through 677 Processing sheet with id=AA1, first strand: chain 'A' and resid 457 through 460 removed outlier: 5.435A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460 removed outlier: 5.435A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 446 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN A 495 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 517 through 520 removed outlier: 6.611A pdb=" N LEU A 599 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 634 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 601 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS A 469 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE A 648 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 471 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 650 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 473 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 657 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS A 651 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 457 through 460 removed outlier: 5.435A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 457 through 460 removed outlier: 5.435A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL B 446 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 495 " --> pdb=" O VAL B 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 517 through 520 removed outlier: 6.611A pdb=" N LEU B 599 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL B 634 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE B 601 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS B 469 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE B 648 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 471 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU B 650 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 473 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 657 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 651 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1950 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: 1.62 Time building geometry restraints manager: 1.20 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: 2905 1.34 - 1.45: 1236 1.45 - 1.57: 5197 1.57 - 1.69: 10 1.69 - 1.80: 48 Bond restraints: 9396 Sorted by residual: bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.66e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.98e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.96e+01 bond pdb=" C5 ATP B 801 " pdb=" N7 ATP B 801 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.33e+01 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 12676 4.44 - 8.89: 78 8.89 - 13.33: 0 13.33 - 17.77: 4 17.77 - 22.22: 2 Bond angle restraints: 12760 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 117.65 22.22 1.00e+00 1.00e+00 4.94e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 117.67 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 120.00 16.83 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 120.02 16.81 1.00e+00 1.00e+00 2.82e+02 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.53 8.27 1.00e+00 1.00e+00 6.84e+01 ... (remaining 12755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5071 17.30 - 34.60: 418 34.60 - 51.90: 61 51.90 - 69.19: 16 69.19 - 86.49: 22 Dihedral angle restraints: 5588 sinusoidal: 2186 harmonic: 3402 Sorted by residual: dihedral pdb=" CA ARG B 489 " pdb=" C ARG B 489 " pdb=" N SER B 490 " pdb=" CA SER B 490 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG A 489 " pdb=" C ARG A 489 " pdb=" N SER A 490 " pdb=" CA SER A 490 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" N GLU A 412 " pdb=" C GLU A 412 " pdb=" CA GLU A 412 " pdb=" CB GLU A 412 " ideal model delta harmonic sigma weight residual 122.80 131.50 -8.70 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1159 0.057 - 0.113: 278 0.113 - 0.170: 39 0.170 - 0.226: 6 0.226 - 0.283: 4 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CB ILE A 171 " pdb=" CA ILE A 171 " pdb=" CG1 ILE A 171 " pdb=" CG2 ILE A 171 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE B 171 " pdb=" CA ILE B 171 " pdb=" CG1 ILE B 171 " pdb=" CG2 ILE B 171 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA GLU A 412 " pdb=" N GLU A 412 " pdb=" C GLU A 412 " pdb=" CB GLU A 412 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1483 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 427 " 0.053 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO B 428 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 427 " 0.053 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO A 428 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 596 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 597 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 597 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 597 " -0.021 5.00e-02 4.00e+02 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 110 2.62 - 3.19: 8434 3.19 - 3.76: 15330 3.76 - 4.33: 20456 4.33 - 4.90: 34298 Nonbonded interactions: 78628 Sorted by model distance: nonbonded pdb=" NE2 GLN B 522 " pdb="MG MG B 802 " model vdw 2.053 2.250 nonbonded pdb=" OD2 ASP A 207 " pdb=" OG1 THR A 423 " model vdw 2.215 3.040 nonbonded pdb=" OD2 ASP B 207 " pdb=" OG1 THR B 423 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 306 " pdb=" OE1 GLU B 322 " model vdw 2.229 3.040 nonbonded pdb=" OG SER A 306 " pdb=" OE1 GLU A 322 " model vdw 2.229 3.040 ... (remaining 78623 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: 0.02 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: 2.320 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.530 Find NCS groups from input model: 0.210 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:6.640 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.007 0.082 9396 Z= 0.327 Angle : 0.951 22.218 12760 Z= 0.607 Chirality : 0.051 0.283 1486 Planarity : 0.005 0.078 1608 Dihedral : 14.131 86.493 3396 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.18 (0.23), residues: 1170 helix: 0.36 (0.17), residues: 788 sheet: -1.18 (0.55), residues: 66 loop : -0.80 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 170 TYR 0.014 0.002 TYR A 274 PHE 0.013 0.002 PHE A 259 TRP 0.017 0.002 TRP A 675 HIS 0.007 0.001 HIS A 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.33 ( 9396) covalent geometry : angle 0.95110 / 0.61 (12760) hydrogen bonds : bond 0.14173 / 9.64 ( 662) hydrogen bonds : angle 6.11466 / 4.52 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.356 Fit side-chains REVERT: A 190 LYS cc_start: 0.7544 (mttm) cc_final: 0.7213 (mtpm) REVERT: A 425 ARG cc_start: 0.8006 (ptp-110) cc_final: 0.7737 (ptp90) REVERT: B 190 LYS cc_start: 0.7544 (mttm) cc_final: 0.7204 (mtpm) REVERT: B 425 ARG cc_start: 0.8008 (ptp-110) cc_final: 0.7747 (ptp90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.7865 time to fit residues: 95.3902 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN A 552 GLN B 495 GLN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119510 restraints weight = 11538.727| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.28 r_work: 0.3268 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9396 Z= 0.146 Angle : 0.588 11.923 12760 Z= 0.303 Chirality : 0.042 0.160 1486 Planarity : 0.004 0.046 1608 Dihedral : 5.076 53.956 1286 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.23 % Allowed : 10.39 % Favored : 88.37 % 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: 0.91 (0.24), residues: 1170 helix: 1.30 (0.18), residues: 788 sheet: -1.24 (0.59), residues: 66 loop : -0.59 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.015 0.001 TYR A 642 PHE 0.008 0.001 PHE B 239 TRP 0.010 0.001 TRP B 110 HIS 0.006 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 9396) covalent geometry : angle 0.58781 / 0.30 (12760) hydrogen bonds : bond 0.05115 / 3.45 ( 662) hydrogen bonds : angle 4.42057 / 3.33 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.354 Fit side-chains REVERT: A 190 LYS cc_start: 0.7101 (mttm) cc_final: 0.6738 (mtpm) REVERT: A 248 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7602 (mp) REVERT: A 289 ARG cc_start: 0.6738 (ttp80) cc_final: 0.6518 (ttp-110) REVERT: A 425 ARG cc_start: 0.8042 (ptp-110) cc_final: 0.7837 (ptp90) REVERT: B 190 LYS cc_start: 0.7126 (mttm) cc_final: 0.6747 (mtpm) REVERT: B 248 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7629 (mp) REVERT: B 289 ARG cc_start: 0.6735 (ttp80) cc_final: 0.6513 (ttp-110) REVERT: B 425 ARG cc_start: 0.8059 (ptp-110) cc_final: 0.7503 (ptp90) REVERT: B 605 THR cc_start: 0.8406 (p) cc_final: 0.8108 (p) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 0.5706 time to fit residues: 59.0039 Evaluate side-chains 85 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 562 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 51 optimal weight: 0.0060 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 0.0010 chunk 92 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120543 restraints weight = 11492.921| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.29 r_work: 0.3329 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9396 Z= 0.128 Angle : 0.547 10.460 12760 Z= 0.278 Chirality : 0.041 0.147 1486 Planarity : 0.003 0.034 1608 Dihedral : 4.689 50.818 1286 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.26 % Allowed : 11.52 % Favored : 86.21 % 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: 1.38 (0.24), residues: 1170 helix: 1.71 (0.18), residues: 788 sheet: -1.19 (0.59), residues: 66 loop : -0.56 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.017 0.001 TYR B 642 PHE 0.010 0.001 PHE B 396 TRP 0.007 0.001 TRP B 110 HIS 0.005 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9396) covalent geometry : angle 0.54742 / 0.28 (12760) hydrogen bonds : bond 0.04608 / 3.09 ( 662) hydrogen bonds : angle 4.16086 / 3.14 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.344 Fit side-chains REVERT: A 190 LYS cc_start: 0.7124 (mttm) cc_final: 0.6743 (mtpm) REVERT: A 248 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7527 (mp) REVERT: A 425 ARG cc_start: 0.8112 (ptp-110) cc_final: 0.7675 (ptp90) REVERT: B 190 LYS cc_start: 0.7122 (mttm) cc_final: 0.6752 (mtpt) REVERT: B 248 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7549 (mp) REVERT: B 425 ARG cc_start: 0.8121 (ptp-110) cc_final: 0.7719 (ptp90) REVERT: B 662 ARG cc_start: 0.7297 (ttp-110) cc_final: 0.7018 (ttp-110) outliers start: 22 outliers final: 3 residues processed: 99 average time/residue: 0.6454 time to fit residues: 68.3427 Evaluate side-chains 78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 114 optimal weight: 0.0040 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118570 restraints weight = 11676.437| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.34 r_work: 0.3301 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9396 Z= 0.144 Angle : 0.559 12.319 12760 Z= 0.281 Chirality : 0.041 0.157 1486 Planarity : 0.003 0.045 1608 Dihedral : 4.478 44.599 1286 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.95 % Allowed : 12.65 % Favored : 85.39 % 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: 1.62 (0.25), residues: 1170 helix: 1.92 (0.18), residues: 788 sheet: -1.22 (0.59), residues: 66 loop : -0.53 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 662 TYR 0.017 0.001 TYR A 642 PHE 0.009 0.001 PHE A 316 TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 9396) covalent geometry : angle 0.55917 / 0.28 (12760) hydrogen bonds : bond 0.04605 / 3.10 ( 662) hydrogen bonds : angle 4.05195 / 3.05 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.359 Fit side-chains REVERT: A 190 LYS cc_start: 0.7110 (mttm) cc_final: 0.6719 (mtpm) REVERT: A 296 ASP cc_start: 0.8323 (t0) cc_final: 0.8110 (t0) REVERT: A 425 ARG cc_start: 0.8115 (ptp-110) cc_final: 0.7904 (ptp90) REVERT: B 190 LYS cc_start: 0.7134 (mttm) cc_final: 0.6763 (mtpt) REVERT: B 296 ASP cc_start: 0.8311 (t0) cc_final: 0.8094 (t0) REVERT: B 425 ARG cc_start: 0.8103 (ptp-110) cc_final: 0.7888 (ptp90) REVERT: B 605 THR cc_start: 0.8428 (p) cc_final: 0.8116 (p) outliers start: 19 outliers final: 10 residues processed: 94 average time/residue: 0.5250 time to fit residues: 52.9172 Evaluate side-chains 87 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117184 restraints weight = 11554.217| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.34 r_work: 0.3281 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9396 Z= 0.156 Angle : 0.571 11.283 12760 Z= 0.287 Chirality : 0.042 0.169 1486 Planarity : 0.003 0.028 1608 Dihedral : 4.426 38.874 1286 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.37 % Allowed : 13.27 % Favored : 84.36 % 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: 1.65 (0.25), residues: 1170 helix: 1.94 (0.18), residues: 788 sheet: -1.31 (0.58), residues: 66 loop : -0.48 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.018 0.001 TYR B 642 PHE 0.011 0.001 PHE A 396 TRP 0.006 0.001 TRP A 364 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 9396) covalent geometry : angle 0.57053 / 0.29 (12760) hydrogen bonds : bond 0.04681 / 3.15 ( 662) hydrogen bonds : angle 4.04290 / 3.04 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.233 Fit side-chains REVERT: A 190 LYS cc_start: 0.7217 (mttm) cc_final: 0.6840 (mtpm) REVERT: A 296 ASP cc_start: 0.8399 (t0) cc_final: 0.8180 (t0) REVERT: A 425 ARG cc_start: 0.8101 (ptp-110) cc_final: 0.7848 (ptp90) REVERT: A 662 ARG cc_start: 0.7224 (mmt180) cc_final: 0.6957 (mmm160) REVERT: B 190 LYS cc_start: 0.7208 (mttm) cc_final: 0.6829 (mtpm) REVERT: B 296 ASP cc_start: 0.8404 (t0) cc_final: 0.8177 (t0) REVERT: B 425 ARG cc_start: 0.8115 (ptp-110) cc_final: 0.7858 (ptp90) outliers start: 23 outliers final: 14 residues processed: 95 average time/residue: 0.4923 time to fit residues: 50.4477 Evaluate side-chains 93 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 0.0980 chunk 94 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118177 restraints weight = 11506.680| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.33 r_work: 0.3303 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9396 Z= 0.134 Angle : 0.546 10.205 12760 Z= 0.277 Chirality : 0.041 0.169 1486 Planarity : 0.003 0.026 1608 Dihedral : 4.334 37.221 1286 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.26 % Allowed : 14.51 % Favored : 83.23 % 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: 1.76 (0.25), residues: 1170 helix: 2.03 (0.18), residues: 788 sheet: -1.17 (0.58), residues: 66 loop : -0.48 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.018 0.001 TYR A 642 PHE 0.008 0.001 PHE B 600 TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9396) covalent geometry : angle 0.54594 / 0.28 (12760) hydrogen bonds : bond 0.04484 / 2.99 ( 662) hydrogen bonds : angle 3.96957 / 2.99 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.349 Fit side-chains REVERT: A 190 LYS cc_start: 0.7197 (mttm) cc_final: 0.6818 (mtpm) REVERT: A 296 ASP cc_start: 0.8383 (t0) cc_final: 0.8162 (t0) REVERT: A 425 ARG cc_start: 0.8098 (ptp-110) cc_final: 0.7875 (ptp-110) REVERT: A 662 ARG cc_start: 0.7217 (mmt180) cc_final: 0.6985 (mmm160) REVERT: B 190 LYS cc_start: 0.7195 (mttm) cc_final: 0.6825 (mtpt) REVERT: B 296 ASP cc_start: 0.8403 (t0) cc_final: 0.8173 (t0) REVERT: B 605 THR cc_start: 0.8376 (p) cc_final: 0.8057 (p) outliers start: 22 outliers final: 12 residues processed: 98 average time/residue: 0.5345 time to fit residues: 56.6575 Evaluate side-chains 89 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.145092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116920 restraints weight = 11627.525| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.34 r_work: 0.3281 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9396 Z= 0.155 Angle : 0.557 11.290 12760 Z= 0.282 Chirality : 0.042 0.183 1486 Planarity : 0.003 0.028 1608 Dihedral : 4.353 31.886 1286 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.98 % Allowed : 14.40 % Favored : 82.61 % 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: 1.77 (0.25), residues: 1170 helix: 2.04 (0.18), residues: 788 sheet: -1.24 (0.57), residues: 66 loop : -0.46 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 425 TYR 0.018 0.001 TYR A 642 PHE 0.011 0.001 PHE A 316 TRP 0.005 0.001 TRP B 364 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 9396) covalent geometry : angle 0.55730 / 0.28 (12760) hydrogen bonds : bond 0.04575 / 3.09 ( 662) hydrogen bonds : angle 3.95534 / 2.98 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.337 Fit side-chains REVERT: A 190 LYS cc_start: 0.7201 (mttm) cc_final: 0.6827 (mtpm) REVERT: A 248 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7462 (mp) REVERT: A 271 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.5675 (mtt) REVERT: A 296 ASP cc_start: 0.8407 (t0) cc_final: 0.8191 (t0) REVERT: A 425 ARG cc_start: 0.8087 (ptp-110) cc_final: 0.7832 (ptp90) REVERT: A 662 ARG cc_start: 0.7209 (mmt180) cc_final: 0.6981 (mmm160) REVERT: B 190 LYS cc_start: 0.7181 (mttm) cc_final: 0.6813 (mtpt) REVERT: B 248 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7503 (mp) REVERT: B 296 ASP cc_start: 0.8407 (t0) cc_final: 0.8194 (t0) outliers start: 29 outliers final: 16 residues processed: 99 average time/residue: 0.5299 time to fit residues: 56.6139 Evaluate side-chains 97 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 614 GLN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 614 GLN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117971 restraints weight = 11402.747| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.32 r_work: 0.3295 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9396 Z= 0.143 Angle : 0.557 10.888 12760 Z= 0.282 Chirality : 0.042 0.183 1486 Planarity : 0.003 0.049 1608 Dihedral : 4.288 29.262 1286 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.78 % Allowed : 15.12 % Favored : 82.10 % 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: 1.84 (0.25), residues: 1170 helix: 2.10 (0.18), residues: 788 sheet: -1.18 (0.58), residues: 66 loop : -0.46 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 425 TYR 0.019 0.001 TYR A 642 PHE 0.017 0.001 PHE B 600 TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9396) covalent geometry : angle 0.55677 / 0.28 (12760) hydrogen bonds : bond 0.04456 / 3.01 ( 662) hydrogen bonds : angle 3.90811 / 2.94 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.345 Fit side-chains REVERT: A 100 MET cc_start: 0.7189 (ttt) cc_final: 0.6981 (tmm) REVERT: A 190 LYS cc_start: 0.7185 (mttm) cc_final: 0.6810 (mtpm) REVERT: A 248 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7487 (mp) REVERT: A 271 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5630 (mtt) REVERT: A 425 ARG cc_start: 0.8057 (ptp-110) cc_final: 0.7815 (ptp90) REVERT: A 662 ARG cc_start: 0.7199 (mmt180) cc_final: 0.6981 (mmm160) REVERT: B 190 LYS cc_start: 0.7184 (mttm) cc_final: 0.6812 (mtpt) REVERT: B 248 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7514 (mp) REVERT: B 271 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.5733 (mtt) REVERT: B 605 THR cc_start: 0.8373 (p) cc_final: 0.8060 (p) outliers start: 27 outliers final: 18 residues processed: 96 average time/residue: 0.4635 time to fit residues: 48.1461 Evaluate side-chains 95 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117980 restraints weight = 11460.237| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.32 r_work: 0.3293 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9396 Z= 0.143 Angle : 0.564 11.697 12760 Z= 0.285 Chirality : 0.042 0.184 1486 Planarity : 0.003 0.028 1608 Dihedral : 4.275 26.434 1286 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.88 % Allowed : 15.84 % Favored : 81.28 % 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: 1.86 (0.25), residues: 1170 helix: 2.10 (0.18), residues: 788 sheet: -1.18 (0.58), residues: 66 loop : -0.43 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 425 TYR 0.020 0.001 TYR B 642 PHE 0.015 0.001 PHE A 600 TRP 0.006 0.001 TRP A 364 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9396) covalent geometry : angle 0.56353 / 0.29 (12760) hydrogen bonds : bond 0.04470 / 3.01 ( 662) hydrogen bonds : angle 3.91545 / 2.94 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.217 Fit side-chains REVERT: A 190 LYS cc_start: 0.7218 (mttm) cc_final: 0.6844 (mtpt) REVERT: A 248 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7474 (mp) REVERT: A 271 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5633 (mtt) REVERT: A 425 ARG cc_start: 0.8057 (ptp-110) cc_final: 0.7825 (ptp90) REVERT: A 662 ARG cc_start: 0.7224 (mmt180) cc_final: 0.7008 (mmm160) REVERT: B 190 LYS cc_start: 0.7204 (mttm) cc_final: 0.6833 (mtpt) REVERT: B 248 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7484 (mp) REVERT: B 271 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.5768 (mtt) outliers start: 28 outliers final: 17 residues processed: 95 average time/residue: 0.5103 time to fit residues: 52.0874 Evaluate side-chains 95 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 562 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 0.0070 chunk 27 optimal weight: 0.8980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 GLN B 544 GLN B 614 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120111 restraints weight = 11538.045| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.32 r_work: 0.3320 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9396 Z= 0.126 Angle : 0.562 11.915 12760 Z= 0.283 Chirality : 0.041 0.182 1486 Planarity : 0.003 0.054 1608 Dihedral : 4.173 27.255 1286 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.95 % Allowed : 17.28 % Favored : 80.76 % 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: 1.96 (0.25), residues: 1170 helix: 2.19 (0.18), residues: 788 sheet: -1.03 (0.59), residues: 66 loop : -0.43 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 425 TYR 0.020 0.001 TYR B 642 PHE 0.012 0.001 PHE B 600 TRP 0.007 0.001 TRP B 364 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 9396) covalent geometry : angle 0.56205 / 0.28 (12760) hydrogen bonds : bond 0.04253 / 2.85 ( 662) hydrogen bonds : angle 3.86351 / 2.90 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.215 Fit side-chains REVERT: A 190 LYS cc_start: 0.7092 (mttm) cc_final: 0.6719 (mtpt) REVERT: A 271 MET cc_start: 0.5758 (OUTLIER) cc_final: 0.5464 (mtt) REVERT: A 425 ARG cc_start: 0.8061 (ptp-110) cc_final: 0.7790 (ptp-110) REVERT: A 662 ARG cc_start: 0.7234 (mmt180) cc_final: 0.7019 (mmm160) REVERT: B 190 LYS cc_start: 0.7103 (mttm) cc_final: 0.6732 (mtpt) REVERT: B 425 ARG cc_start: 0.7973 (ptp-110) cc_final: 0.7663 (ptp-110) outliers start: 19 outliers final: 11 residues processed: 102 average time/residue: 0.4381 time to fit residues: 48.2291 Evaluate side-chains 91 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 562 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 97 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 GLN B 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120422 restraints weight = 11327.894| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.29 r_work: 0.3323 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9396 Z= 0.131 Angle : 0.580 12.013 12760 Z= 0.291 Chirality : 0.041 0.182 1486 Planarity : 0.004 0.061 1608 Dihedral : 4.175 26.382 1286 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.75 % Allowed : 17.80 % Favored : 80.45 % 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: 2.00 (0.25), residues: 1170 helix: 2.21 (0.18), residues: 788 sheet: -0.97 (0.59), residues: 66 loop : -0.39 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 425 TYR 0.020 0.001 TYR B 642 PHE 0.013 0.001 PHE A 600 TRP 0.007 0.001 TRP A 364 HIS 0.004 0.001 HIS B 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9396) covalent geometry : angle 0.58044 / 0.29 (12760) hydrogen bonds : bond 0.04274 / 2.87 ( 662) hydrogen bonds : angle 3.92093 / 2.94 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2725.97 seconds wall clock time: 47 minutes 21.36 seconds (2841.36 seconds total)