Starting phenix.real_space_refine on Wed Sep 17 15:15:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pr1_13607/09_2025/7pr1_13607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pr1_13607/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pr1_13607/09_2025/7pr1_13607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pr1_13607/09_2025/7pr1_13607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pr1_13607/09_2025/7pr1_13607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pr1_13607/09_2025/7pr1_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-2.0-5805/lib/python3.9/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: 0.89 Conformation dependent library (CDL) restraints added in 364.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 1.77 Time building geometry restraints manager: 1.14 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: 0.02 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: 3.290 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.770 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.560 ------------------------------------------------------------------------------- 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= 0.327 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00655 ( 9396) covalent geometry : angle 0.95110 (12760) hydrogen bonds : bond 0.14173 ( 662) hydrogen bonds : angle 6.11466 ( 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 : 0.366 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: 0.8583 time to fit residues: 103.6836 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 : 0.357 ------------------------------------------------------------------------------- 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... 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 = 0.3728 r_free = 0.3728 target = 0.146865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119312 restraints weight = 11527.534| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.29 r_work: 0.3266 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9396 Z= 0.149 Angle : 0.591 11.927 12760 Z= 0.305 Chirality : 0.042 0.156 1486 Planarity : 0.004 0.044 1608 Dihedral : 6.479 56.860 1348 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.34 % Allowed : 10.29 % 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 aren not related in a simple way. whole: 0.91 (0.24), residues: 1170 helix: 1.30 (0.18), residues: 788 sheet: -1.26 (0.58), residues: 66 loop : -0.60 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 405 TYR 0.014 0.001 TYR A 642 PHE 0.008 0.001 PHE B 316 TRP 0.011 0.001 TRP B 110 HIS 0.005 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9396) covalent geometry : angle 0.59072 (12760) hydrogen bonds : bond 0.05090 ( 662) hydrogen bonds : angle 4.44207 ( 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 101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.365 Fit side-chains REVERT: A 190 LYS cc_start: 0.7112 (mttm) cc_final: 0.6749 (mtpm) REVERT: A 248 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7599 (mp) REVERT: A 425 ARG cc_start: 0.8047 (ptp-110) cc_final: 0.7841 (ptp90) REVERT: B 190 LYS cc_start: 0.7143 (mttm) cc_final: 0.6763 (mtpm) REVERT: B 248 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7642 (mp) REVERT: B 425 ARG cc_start: 0.8051 (ptp-110) cc_final: 0.7849 (ptp90) REVERT: B 605 THR cc_start: 0.8402 (p) cc_final: 0.8101 (p) outliers start: 13 outliers final: 8 residues processed: 96 average time/residue: 0.6212 time to fit residues: 63.9241 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 : 0.371 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 0.0470 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.145957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118568 restraints weight = 11530.352| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.28 r_work: 0.3295 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9396 Z= 0.142 Angle : 0.563 11.054 12760 Z= 0.286 Chirality : 0.042 0.147 1486 Planarity : 0.003 0.036 1608 Dihedral : 6.250 57.234 1348 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.57 % Allowed : 11.32 % Favored : 86.11 % 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 aren not related in a simple way. whole: 1.33 (0.24), residues: 1170 helix: 1.66 (0.18), residues: 788 sheet: -1.25 (0.59), residues: 66 loop : -0.55 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.016 0.001 TYR B 642 PHE 0.009 0.001 PHE A 316 TRP 0.007 0.001 TRP B 110 HIS 0.006 0.001 HIS A 557 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9396) covalent geometry : angle 0.56305 (12760) hydrogen bonds : bond 0.04782 ( 662) hydrogen bonds : angle 4.18902 ( 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 105 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.7154 (mttm) cc_final: 0.6777 (mtpm) REVERT: A 248 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7566 (mp) REVERT: A 425 ARG cc_start: 0.8125 (ptp-110) cc_final: 0.7688 (ptp90) REVERT: B 190 LYS cc_start: 0.7170 (mttm) cc_final: 0.6786 (mtpm) REVERT: B 248 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7567 (mp) REVERT: B 425 ARG cc_start: 0.8105 (ptp-110) cc_final: 0.7676 (ptp90) REVERT: B 426 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8084 (mt-10) REVERT: B 662 ARG cc_start: 0.7335 (ttp-110) cc_final: 0.7080 (ttp-110) outliers start: 25 outliers final: 3 residues processed: 96 average time/residue: 0.6929 time to fit residues: 70.9525 Evaluate side-chains 76 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 2.9990 chunk 82 optimal weight: 0.8980 chunk 114 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.147102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119206 restraints weight = 11640.916| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.34 r_work: 0.3313 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9396 Z= 0.136 Angle : 0.556 12.316 12760 Z= 0.280 Chirality : 0.041 0.154 1486 Planarity : 0.003 0.031 1608 Dihedral : 6.115 57.097 1348 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.16 % Allowed : 12.55 % Favored : 85.29 % 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 aren not related in a simple way. whole: 1.63 (0.25), residues: 1170 helix: 1.92 (0.18), residues: 788 sheet: -1.22 (0.59), residues: 66 loop : -0.50 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 180 TYR 0.017 0.001 TYR A 642 PHE 0.008 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 covalent geometry : bond 0.00301 ( 9396) covalent geometry : angle 0.55617 (12760) hydrogen bonds : bond 0.04540 ( 662) hydrogen bonds : angle 4.05699 ( 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 108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.362 Fit side-chains REVERT: A 190 LYS cc_start: 0.7153 (mttm) cc_final: 0.6769 (mtpm) REVERT: A 425 ARG cc_start: 0.8137 (ptp-110) cc_final: 0.7894 (ptp90) REVERT: A 426 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 673 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: B 190 LYS cc_start: 0.7168 (mttm) cc_final: 0.6793 (mtpt) REVERT: B 425 ARG cc_start: 0.8075 (ptp-110) cc_final: 0.7648 (ptp90) outliers start: 21 outliers final: 8 residues processed: 99 average time/residue: 0.6633 time to fit residues: 70.1898 Evaluate side-chains 84 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 673 GLU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 408 LEU 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: 0.9980 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.144723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116800 restraints weight = 11615.745| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.34 r_work: 0.3280 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9396 Z= 0.160 Angle : 0.576 11.051 12760 Z= 0.291 Chirality : 0.042 0.163 1486 Planarity : 0.003 0.041 1608 Dihedral : 6.311 59.514 1348 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.78 % Allowed : 13.17 % Favored : 84.05 % 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 aren not related in a simple way. whole: 1.64 (0.25), residues: 1170 helix: 1.94 (0.18), residues: 788 sheet: -1.32 (0.58), residues: 66 loop : -0.49 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 662 TYR 0.018 0.001 TYR A 642 PHE 0.011 0.001 PHE A 396 TRP 0.005 0.001 TRP A 364 HIS 0.003 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9396) covalent geometry : angle 0.57574 (12760) hydrogen bonds : bond 0.04695 ( 662) hydrogen bonds : angle 4.04430 ( 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 108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.394 Fit side-chains REVERT: A 190 LYS cc_start: 0.7223 (mttm) cc_final: 0.6841 (mtpm) REVERT: A 425 ARG cc_start: 0.8082 (ptp-110) cc_final: 0.7827 (ptp90) REVERT: A 426 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8313 (mt-10) REVERT: B 190 LYS cc_start: 0.7225 (mttm) cc_final: 0.6840 (mtpm) REVERT: B 271 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.5731 (mtt) REVERT: B 425 ARG cc_start: 0.8158 (ptp-110) cc_final: 0.7920 (ptp90) REVERT: B 673 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7707 (mt-10) outliers start: 27 outliers final: 15 residues processed: 94 average time/residue: 0.6478 time to fit residues: 65.2544 Evaluate side-chains 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 353 ILE 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 353 ILE 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 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 38 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 59 optimal weight: 0.0000 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 30.0000 chunk 49 optimal weight: 0.5980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.146490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118733 restraints weight = 11489.638| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.33 r_work: 0.3304 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1876 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= 0.132 Angle : 0.553 10.720 12760 Z= 0.280 Chirality : 0.041 0.166 1486 Planarity : 0.003 0.025 1608 Dihedral : 6.076 55.955 1348 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.67 % Allowed : 14.09 % 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 aren not related in a simple way. whole: 1.84 (0.25), residues: 1170 helix: 2.10 (0.18), residues: 788 sheet: -1.14 (0.58), residues: 66 loop : -0.50 (0.36), 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 0.007 0.001 PHE A 316 TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9396) covalent geometry : angle 0.55274 (12760) hydrogen bonds : bond 0.04421 ( 662) hydrogen bonds : angle 3.94151 ( 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 110 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.371 Fit side-chains REVERT: A 190 LYS cc_start: 0.7160 (mttm) cc_final: 0.6794 (mtpt) REVERT: A 425 ARG cc_start: 0.8101 (ptp-110) cc_final: 0.7853 (ptp90) REVERT: A 426 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8267 (mt-10) REVERT: A 662 ARG cc_start: 0.7228 (mmt180) cc_final: 0.6956 (mmm160) REVERT: B 190 LYS cc_start: 0.7200 (mttm) cc_final: 0.6827 (mtpt) REVERT: B 248 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7579 (mp) REVERT: B 271 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.5532 (mtt) REVERT: B 425 ARG cc_start: 0.8079 (ptp-110) cc_final: 0.7821 (ptp90) REVERT: B 673 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7696 (mt-10) outliers start: 26 outliers final: 10 residues processed: 100 average time/residue: 0.5785 time to fit residues: 62.2890 Evaluate side-chains 88 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 ILE 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 622 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 353 ILE 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 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 99 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 100 optimal weight: 0.0070 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.146199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118287 restraints weight = 11571.051| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.34 r_work: 0.3298 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9396 Z= 0.146 Angle : 0.554 10.691 12760 Z= 0.283 Chirality : 0.041 0.174 1486 Planarity : 0.003 0.025 1608 Dihedral : 6.187 57.720 1348 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.98 % Allowed : 14.71 % Favored : 82.30 % 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 aren not related in a simple way. whole: 1.81 (0.25), residues: 1170 helix: 2.07 (0.18), residues: 788 sheet: -1.16 (0.58), residues: 66 loop : -0.46 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.019 0.001 TYR A 642 PHE 0.010 0.001 PHE B 396 TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9396) covalent geometry : angle 0.55443 (12760) hydrogen bonds : bond 0.04505 ( 662) hydrogen bonds : angle 3.95259 ( 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 110 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.7220 (mttm) cc_final: 0.6852 (mtpt) REVERT: A 425 ARG cc_start: 0.8074 (ptp-110) cc_final: 0.7841 (ptp90) REVERT: A 426 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8272 (mt-10) REVERT: A 662 ARG cc_start: 0.7226 (mmt180) cc_final: 0.6996 (mmm160) REVERT: B 190 LYS cc_start: 0.7202 (mttm) cc_final: 0.6831 (mtpt) REVERT: B 248 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7584 (mp) REVERT: B 271 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.5585 (mtt) REVERT: B 425 ARG cc_start: 0.8054 (ptp-110) cc_final: 0.7798 (ptp90) outliers start: 29 outliers final: 16 residues processed: 100 average time/residue: 0.5001 time to fit residues: 54.0585 Evaluate side-chains 95 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 353 ILE 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 622 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 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 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: 1.9990 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 0.0040 chunk 71 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118491 restraints weight = 11442.270| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.32 r_work: 0.3299 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2029 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= 0.147 Angle : 0.560 10.962 12760 Z= 0.285 Chirality : 0.042 0.180 1486 Planarity : 0.003 0.026 1608 Dihedral : 6.215 57.697 1348 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.88 % Allowed : 15.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.25), residues: 1170 helix: 2.11 (0.18), residues: 788 sheet: -1.15 (0.58), residues: 66 loop : -0.46 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.019 0.001 TYR A 642 PHE 0.017 0.001 PHE A 600 TRP 0.006 0.001 TRP B 364 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9396) covalent geometry : angle 0.55951 (12760) hydrogen bonds : bond 0.04458 ( 662) hydrogen bonds : angle 3.91834 ( 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 108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.378 Fit side-chains REVERT: A 190 LYS cc_start: 0.7196 (mttm) cc_final: 0.6826 (mtpt) REVERT: A 248 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7543 (mp) REVERT: A 271 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5668 (mtt) REVERT: A 425 ARG cc_start: 0.8066 (ptp-110) cc_final: 0.7834 (ptp90) REVERT: A 426 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8261 (mt-10) REVERT: A 662 ARG cc_start: 0.7222 (mmt180) cc_final: 0.6996 (mmm160) REVERT: B 190 LYS cc_start: 0.7199 (mttm) cc_final: 0.6821 (mtpt) REVERT: B 248 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7552 (mp) REVERT: B 271 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5529 (mtt) REVERT: B 425 ARG cc_start: 0.8048 (ptp-110) cc_final: 0.7791 (ptp90) REVERT: B 605 THR cc_start: 0.8346 (p) cc_final: 0.8034 (p) outliers start: 28 outliers final: 17 residues processed: 99 average time/residue: 0.6182 time to fit residues: 65.6762 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 : 0.305 ------------------------------------------------------------------------------- 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 342 THR Chi-restraints excluded: chain A residue 353 ILE 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 248 ILE Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 353 ILE 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 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: 0.9990 chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116986 restraints weight = 11507.469| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.32 r_work: 0.3277 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: 0.7629 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9396 Z= 0.163 Angle : 0.578 11.359 12760 Z= 0.295 Chirality : 0.043 0.186 1486 Planarity : 0.003 0.028 1608 Dihedral : 6.503 59.687 1348 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.98 % Allowed : 15.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.25), residues: 1170 helix: 2.08 (0.18), residues: 788 sheet: -1.21 (0.58), residues: 66 loop : -0.45 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.019 0.001 TYR A 642 PHE 0.018 0.001 PHE B 600 TRP 0.005 0.001 TRP A 261 HIS 0.003 0.001 HIS B 661 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9396) covalent geometry : angle 0.57805 (12760) hydrogen bonds : bond 0.04605 ( 662) hydrogen bonds : angle 3.96359 ( 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 109 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.336 Fit side-chains REVERT: A 190 LYS cc_start: 0.7209 (mttm) cc_final: 0.6831 (mtpm) REVERT: A 271 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5669 (mtt) REVERT: A 425 ARG cc_start: 0.8102 (ptp-110) cc_final: 0.7860 (ptp90) REVERT: A 426 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8269 (mt-10) REVERT: A 662 ARG cc_start: 0.7213 (mmt180) cc_final: 0.7006 (mmm160) REVERT: B 190 LYS cc_start: 0.7186 (mttm) cc_final: 0.6809 (mtpt) REVERT: B 248 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7526 (mp) REVERT: B 271 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5525 (mtt) REVERT: B 411 MET cc_start: 0.4713 (tpt) cc_final: 0.4371 (mtm) REVERT: B 425 ARG cc_start: 0.8063 (ptp-110) cc_final: 0.7799 (ptp90) REVERT: B 605 THR cc_start: 0.8353 (p) cc_final: 0.7955 (p) outliers start: 29 outliers final: 19 residues processed: 102 average time/residue: 0.6287 time to fit residues: 68.4959 Evaluate side-chains 100 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 342 THR Chi-restraints excluded: chain A residue 353 ILE 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 342 THR Chi-restraints excluded: chain B residue 353 ILE 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 Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.144775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116911 restraints weight = 11636.421| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.33 r_work: 0.3278 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2116 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= 0.160 Angle : 0.585 12.045 12760 Z= 0.297 Chirality : 0.043 0.193 1486 Planarity : 0.003 0.039 1608 Dihedral : 6.569 59.389 1348 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.37 % Allowed : 16.46 % Favored : 81.17 % 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 aren not related in a simple way. whole: 1.81 (0.25), residues: 1170 helix: 2.06 (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 ARG 0.008 0.000 ARG A 170 TYR 0.020 0.001 TYR B 642 PHE 0.013 0.001 PHE A 600 TRP 0.005 0.001 TRP B 364 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9396) covalent geometry : angle 0.58497 (12760) hydrogen bonds : bond 0.04570 ( 662) hydrogen bonds : angle 3.97698 ( 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 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.367 Fit side-chains REVERT: A 425 ARG cc_start: 0.8110 (ptp-110) cc_final: 0.7859 (ptp90) REVERT: A 426 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 662 ARG cc_start: 0.7185 (mmt180) cc_final: 0.6976 (mmm160) REVERT: B 190 LYS cc_start: 0.7188 (mttm) cc_final: 0.6811 (mtpt) REVERT: B 248 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7503 (mp) REVERT: B 271 MET cc_start: 0.5786 (OUTLIER) cc_final: 0.5527 (mtt) REVERT: B 425 ARG cc_start: 0.8075 (ptp-110) cc_final: 0.7817 (ptp90) outliers start: 23 outliers final: 18 residues processed: 97 average time/residue: 0.6188 time to fit residues: 64.4073 Evaluate side-chains 97 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 353 ILE 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 342 THR Chi-restraints excluded: chain B residue 353 ILE 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 Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 97 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 76 optimal weight: 0.5980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.147019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119558 restraints weight = 11431.592| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.31 r_work: 0.3313 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9396 Z= 0.131 Angle : 0.576 12.044 12760 Z= 0.291 Chirality : 0.041 0.183 1486 Planarity : 0.004 0.059 1608 Dihedral : 6.325 55.697 1348 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.65 % Allowed : 17.49 % Favored : 80.86 % 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 aren not related in a simple way. whole: 1.93 (0.25), residues: 1170 helix: 2.17 (0.18), residues: 788 sheet: -1.07 (0.59), residues: 66 loop : -0.44 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 662 TYR 0.020 0.001 TYR A 642 PHE 0.014 0.001 PHE B 600 TRP 0.007 0.001 TRP A 364 HIS 0.005 0.001 HIS B 661 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9396) covalent geometry : angle 0.57594 (12760) hydrogen bonds : bond 0.04315 ( 662) hydrogen bonds : angle 3.91465 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.41 seconds wall clock time: 56 minutes 11.06 seconds (3371.06 seconds total)