Starting phenix.real_space_refine on Fri Mar 14 00:03:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pr1_13607/03_2025/7pr1_13607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pr1_13607/03_2025/7pr1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pr1_13607/03_2025/7pr1_13607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pr1_13607/03_2025/7pr1_13607.map" model { file = "/net/cci-nas-00/data/ceres_data/7pr1_13607/03_2025/7pr1_13607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pr1_13607/03_2025/7pr1_13607.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.81, per 1000 atoms: 0.63 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: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.08 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: 2.93 Time building geometry restraints manager: 2.74 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: 5105 17.30 - 34.60: 438 34.60 - 51.90: 69 51.90 - 69.19: 16 69.19 - 86.49: 22 Dihedral angle restraints: 5650 sinusoidal: 2248 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 5647 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: 0.05 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.060 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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= 0.412 Angle : 0.951 22.218 12760 Z= 0.607 Chirality : 0.051 0.283 1486 Planarity : 0.005 0.078 1608 Dihedral : 14.353 86.493 3458 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.002 TRP A 675 HIS 0.007 0.001 HIS A 132 PHE 0.013 0.002 PHE A 259 TYR 0.014 0.002 TYR A 274 ARG 0.009 0.001 ARG B 170 *********************** 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 : 0.954 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: 1.8067 time to fit residues: 219.0139 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 : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3707 r_free = 0.3707 target = 0.145056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117210 restraints weight = 11407.271| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.30 r_work: 0.3299 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9396 Z= 0.241 Angle : 0.603 11.977 12760 Z= 0.312 Chirality : 0.043 0.160 1486 Planarity : 0.004 0.047 1608 Dihedral : 6.630 57.684 1348 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.34 % Allowed : 10.70 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1170 helix: 1.25 (0.18), residues: 788 sheet: -1.37 (0.58), residues: 66 loop : -0.58 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 110 HIS 0.005 0.001 HIS A 557 PHE 0.010 0.001 PHE B 316 TYR 0.015 0.001 TYR A 642 ARG 0.003 0.000 ARG A 405 *********************** 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 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.168 Fit side-chains REVERT: A 190 LYS cc_start: 0.7207 (mttm) cc_final: 0.6840 (mtpm) REVERT: A 248 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7647 (mp) REVERT: A 289 ARG cc_start: 0.6826 (ttp80) cc_final: 0.6566 (ttp-110) REVERT: A 425 ARG cc_start: 0.8051 (ptp-110) cc_final: 0.7840 (ptp90) REVERT: B 190 LYS cc_start: 0.7199 (mttm) cc_final: 0.6827 (mtpm) REVERT: B 248 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7668 (mp) REVERT: B 289 ARG cc_start: 0.6833 (ttp80) cc_final: 0.6582 (ttp-110) REVERT: B 425 ARG cc_start: 0.8082 (ptp-110) cc_final: 0.7880 (ptp90) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 1.7815 time to fit residues: 178.4523 Evaluate side-chains 81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.144766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116859 restraints weight = 11734.083| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.33 r_work: 0.3273 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9396 Z= 0.218 Angle : 0.570 10.747 12760 Z= 0.290 Chirality : 0.042 0.153 1486 Planarity : 0.003 0.036 1608 Dihedral : 6.358 57.373 1348 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.37 % Allowed : 11.73 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1170 helix: 1.62 (0.18), residues: 788 sheet: -1.31 (0.59), residues: 66 loop : -0.51 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.005 0.001 HIS A 557 PHE 0.009 0.001 PHE B 396 TYR 0.017 0.001 TYR A 642 ARG 0.004 0.000 ARG A 289 *********************** 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 103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.976 Fit side-chains REVERT: A 190 LYS cc_start: 0.7119 (mttm) cc_final: 0.6767 (mtpm) REVERT: A 248 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7575 (mp) REVERT: A 425 ARG cc_start: 0.8118 (ptp-110) cc_final: 0.7686 (ptp90) REVERT: B 190 LYS cc_start: 0.7155 (mttm) cc_final: 0.6779 (mtpm) REVERT: B 248 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 296 ASP cc_start: 0.8450 (t0) cc_final: 0.8237 (t0) REVERT: B 425 ARG cc_start: 0.8121 (ptp-110) cc_final: 0.7691 (ptp90) REVERT: B 662 ARG cc_start: 0.7334 (ttp-110) cc_final: 0.7086 (ttp-110) outliers start: 23 outliers final: 4 residues processed: 95 average time/residue: 1.3122 time to fit residues: 133.5915 Evaluate side-chains 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 622 GLU 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 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 59 optimal weight: 0.0030 chunk 84 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.147723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119881 restraints weight = 11452.956| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.34 r_work: 0.3323 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9396 Z= 0.173 Angle : 0.549 11.961 12760 Z= 0.276 Chirality : 0.041 0.195 1486 Planarity : 0.003 0.033 1608 Dihedral : 6.052 55.322 1348 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.26 % Allowed : 12.24 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1170 helix: 1.91 (0.18), residues: 788 sheet: -1.19 (0.59), residues: 66 loop : -0.49 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 675 HIS 0.003 0.001 HIS A 211 PHE 0.008 0.001 PHE B 239 TYR 0.017 0.001 TYR A 642 ARG 0.009 0.000 ARG A 662 *********************** 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 111 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.7148 (mttm) cc_final: 0.6763 (mtpm) REVERT: A 425 ARG cc_start: 0.8089 (ptp-110) cc_final: 0.7669 (ptp90) REVERT: B 190 LYS cc_start: 0.7140 (mttm) cc_final: 0.6765 (mtpt) REVERT: B 296 ASP cc_start: 0.8420 (t0) cc_final: 0.8184 (t0) REVERT: B 425 ARG cc_start: 0.8084 (ptp-110) cc_final: 0.7669 (ptp90) outliers start: 22 outliers final: 5 residues processed: 102 average time/residue: 1.2850 time to fit residues: 140.2805 Evaluate side-chains 81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 622 GLU 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 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.146644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118876 restraints weight = 11511.018| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.34 r_work: 0.3302 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1779 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= 0.196 Angle : 0.559 11.193 12760 Z= 0.282 Chirality : 0.041 0.162 1486 Planarity : 0.003 0.027 1608 Dihedral : 6.108 57.512 1348 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.16 % Allowed : 13.99 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.25), residues: 1170 helix: 2.01 (0.18), residues: 788 sheet: -1.21 (0.59), residues: 66 loop : -0.49 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 364 HIS 0.003 0.001 HIS A 211 PHE 0.011 0.001 PHE A 396 TYR 0.018 0.001 TYR B 642 ARG 0.002 0.000 ARG B 180 *********************** 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 103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 1.055 Fit side-chains REVERT: A 190 LYS cc_start: 0.7120 (mttm) cc_final: 0.6732 (mtpm) REVERT: A 425 ARG cc_start: 0.8091 (ptp-110) cc_final: 0.7871 (ptp90) REVERT: A 673 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: B 190 LYS cc_start: 0.7140 (mttm) cc_final: 0.6766 (mtpt) REVERT: B 296 ASP cc_start: 0.8263 (t0) cc_final: 0.8037 (t0) REVERT: B 425 ARG cc_start: 0.8088 (ptp-110) cc_final: 0.7865 (ptp90) REVERT: B 673 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7685 (mt-10) outliers start: 21 outliers final: 11 residues processed: 92 average time/residue: 1.3229 time to fit residues: 130.4783 Evaluate side-chains 93 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 673 GLU 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 Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 103 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.145221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117056 restraints weight = 11459.917| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.33 r_work: 0.3277 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1832 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= 0.229 Angle : 0.566 10.832 12760 Z= 0.287 Chirality : 0.042 0.179 1486 Planarity : 0.003 0.025 1608 Dihedral : 6.285 58.891 1348 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.16 % Allowed : 14.71 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.25), residues: 1170 helix: 2.04 (0.18), residues: 788 sheet: -1.27 (0.58), residues: 66 loop : -0.50 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 364 HIS 0.003 0.001 HIS A 211 PHE 0.010 0.001 PHE A 316 TYR 0.018 0.001 TYR A 642 ARG 0.003 0.000 ARG B 180 *********************** 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 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.004 Fit side-chains REVERT: A 190 LYS cc_start: 0.7221 (mttm) cc_final: 0.6843 (mtpm) REVERT: A 425 ARG cc_start: 0.8090 (ptp-110) cc_final: 0.7843 (ptp90) REVERT: B 190 LYS cc_start: 0.7208 (mttm) cc_final: 0.6825 (mtpm) REVERT: B 271 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5693 (mtt) REVERT: B 296 ASP cc_start: 0.8341 (t0) cc_final: 0.8128 (t0) REVERT: B 425 ARG cc_start: 0.8090 (ptp-110) cc_final: 0.7832 (ptp90) REVERT: B 673 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7706 (mt-10) outliers start: 21 outliers final: 13 residues processed: 95 average time/residue: 1.1522 time to fit residues: 118.1643 Evaluate side-chains 90 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 233 LEU 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 271 MET 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 Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.145328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117267 restraints weight = 11618.239| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.35 r_work: 0.3285 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1938 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= 0.218 Angle : 0.555 10.949 12760 Z= 0.282 Chirality : 0.042 0.180 1486 Planarity : 0.003 0.025 1608 Dihedral : 6.283 57.993 1348 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.67 % Allowed : 14.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.25), residues: 1170 helix: 2.07 (0.18), residues: 788 sheet: -1.24 (0.58), residues: 66 loop : -0.47 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 364 HIS 0.003 0.001 HIS B 211 PHE 0.010 0.001 PHE A 396 TYR 0.018 0.001 TYR B 642 ARG 0.003 0.000 ARG A 180 *********************** 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 103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.960 Fit side-chains REVERT: A 190 LYS cc_start: 0.7204 (mttm) cc_final: 0.6827 (mtpm) REVERT: A 248 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7474 (mp) REVERT: A 271 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5683 (mtt) REVERT: A 425 ARG cc_start: 0.8098 (ptp-110) cc_final: 0.7852 (ptp90) REVERT: B 190 LYS cc_start: 0.7200 (mttm) cc_final: 0.6817 (mtpm) REVERT: B 425 ARG cc_start: 0.8052 (ptp-110) cc_final: 0.7803 (ptp90) REVERT: B 673 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7685 (mt-10) outliers start: 26 outliers final: 11 residues processed: 96 average time/residue: 1.2076 time to fit residues: 124.7933 Evaluate side-chains 87 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.145285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117311 restraints weight = 11655.878| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.34 r_work: 0.3282 rms_B_bonded: 3.07 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: 0.7634 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9396 Z= 0.227 Angle : 0.567 10.730 12760 Z= 0.289 Chirality : 0.042 0.180 1486 Planarity : 0.003 0.026 1608 Dihedral : 6.347 58.410 1348 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.26 % Allowed : 15.74 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1170 helix: 2.07 (0.18), residues: 788 sheet: -1.24 (0.58), residues: 66 loop : -0.45 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 364 HIS 0.003 0.001 HIS B 211 PHE 0.014 0.001 PHE B 600 TYR 0.019 0.001 TYR A 642 ARG 0.003 0.000 ARG B 180 *********************** 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 97 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.976 Fit side-chains REVERT: A 248 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 271 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.5674 (mtt) REVERT: A 425 ARG cc_start: 0.8081 (ptp-110) cc_final: 0.7830 (ptp90) REVERT: B 190 LYS cc_start: 0.7214 (mttm) cc_final: 0.6835 (mtpm) REVERT: B 248 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7540 (mp) REVERT: B 271 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5672 (mtt) REVERT: B 425 ARG cc_start: 0.8053 (ptp-110) cc_final: 0.7795 (ptp90) REVERT: B 673 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7661 (mt-10) outliers start: 22 outliers final: 13 residues processed: 88 average time/residue: 1.2125 time to fit residues: 114.8827 Evaluate side-chains 91 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 248 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 313 VAL 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 Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 113 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116706 restraints weight = 11467.499| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.32 r_work: 0.3277 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9396 Z= 0.242 Angle : 0.579 11.786 12760 Z= 0.294 Chirality : 0.042 0.191 1486 Planarity : 0.003 0.026 1608 Dihedral : 6.583 59.992 1348 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.16 % Allowed : 16.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1170 helix: 2.05 (0.18), residues: 788 sheet: -1.26 (0.58), residues: 66 loop : -0.46 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS B 661 PHE 0.017 0.001 PHE A 600 TYR 0.019 0.001 TYR B 642 ARG 0.003 0.000 ARG A 180 *********************** 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 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.070 Fit side-chains REVERT: A 190 LYS cc_start: 0.7257 (ttmm) cc_final: 0.6952 (mtpm) REVERT: A 271 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5623 (mtt) REVERT: A 425 ARG cc_start: 0.8088 (ptp-110) cc_final: 0.7836 (ptp90) REVERT: B 190 LYS cc_start: 0.7205 (mttm) cc_final: 0.6828 (mtpm) REVERT: B 248 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7436 (mp) REVERT: B 271 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5620 (mtt) REVERT: B 425 ARG cc_start: 0.8068 (ptp-110) cc_final: 0.7803 (ptp90) REVERT: B 673 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7633 (mt-10) outliers start: 21 outliers final: 14 residues processed: 91 average time/residue: 1.3058 time to fit residues: 128.3095 Evaluate side-chains 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 313 VAL 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 248 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 313 VAL 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 Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3709 r_free = 0.3709 target = 0.145210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117198 restraints weight = 11676.173| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.34 r_work: 0.3280 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9396 Z= 0.228 Angle : 0.578 11.904 12760 Z= 0.292 Chirality : 0.042 0.191 1486 Planarity : 0.003 0.026 1608 Dihedral : 6.542 58.482 1348 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.06 % Allowed : 16.46 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1170 helix: 2.08 (0.18), residues: 788 sheet: -1.19 (0.58), residues: 66 loop : -0.45 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS B 211 PHE 0.013 0.001 PHE B 600 TYR 0.020 0.001 TYR B 642 ARG 0.003 0.000 ARG A 180 ********************** 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 100 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.485 Fit side-chains REVERT: A 190 LYS cc_start: 0.7274 (ttmm) cc_final: 0.6955 (mtpm) REVERT: A 271 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.5620 (mtt) REVERT: A 425 ARG cc_start: 0.8091 (ptp-110) cc_final: 0.7836 (ptp90) REVERT: B 248 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7479 (mp) REVERT: B 271 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.5588 (mtt) REVERT: B 425 ARG cc_start: 0.8077 (ptp-110) cc_final: 0.7807 (ptp90) REVERT: B 673 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7636 (mt-10) outliers start: 20 outliers final: 14 residues processed: 92 average time/residue: 1.6314 time to fit residues: 161.2813 Evaluate side-chains 93 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 313 VAL 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 248 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 313 VAL 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 Chi-restraints excluded: chain B residue 673 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3704 r_free = 0.3704 target = 0.144771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116700 restraints weight = 11517.616| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.32 r_work: 0.3276 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9396 Z= 0.239 Angle : 0.593 11.992 12760 Z= 0.299 Chirality : 0.042 0.192 1486 Planarity : 0.004 0.061 1608 Dihedral : 6.615 59.177 1348 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.95 % Allowed : 16.67 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1170 helix: 2.08 (0.18), residues: 788 sheet: -1.18 (0.58), residues: 66 loop : -0.44 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.004 0.001 HIS B 661 PHE 0.011 0.001 PHE B 396 TYR 0.020 0.001 TYR A 642 ARG 0.015 0.000 ARG B 662 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6136.99 seconds wall clock time: 109 minutes 21.14 seconds (6561.14 seconds total)