Starting phenix.real_space_refine on Fri Aug 22 22:35:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tu9_41620/08_2025/8tu9_41620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tu9_41620/08_2025/8tu9_41620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tu9_41620/08_2025/8tu9_41620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tu9_41620/08_2025/8tu9_41620.map" model { file = "/net/cci-nas-00/data/ceres_data/8tu9_41620/08_2025/8tu9_41620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tu9_41620/08_2025/8tu9_41620.cif" } resolution = 3.26 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= 0.006 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 38 5.16 5 C 5524 2.51 5 N 1348 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8390 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4102 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 26, 'TRANS': 506} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 6, 'TRP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ACO': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B Time building chain proxies: 3.62, per 1000 atoms: 0.43 Number of scatterers: 8390 At special positions: 0 Unit cell: (77.35, 121.55, 105.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 6 15.00 O 1474 8.00 N 1348 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 79 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS B 334 " distance=2.05 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 434 " distance=2.02 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 434 " distance=2.02 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 Links applied NAG-ASN " NAG A 702 " - " ASN A 134 " " NAG A 703 " - " ASN A 433 " " NAG A 704 " - " ASN A 114 " " NAG B 702 " - " ASN B 134 " " NAG B 703 " - " ASN B 433 " " NAG B 704 " - " ASN B 114 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 506.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 50.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.641A pdb=" N PHE A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 260 removed outlier: 3.836A pdb=" N ASP A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 302 removed outlier: 4.283A pdb=" N TRP A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 3.989A pdb=" N GLY A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 removed outlier: 3.686A pdb=" N PHE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 410 removed outlier: 4.165A pdb=" N LEU A 394 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.672A pdb=" N GLY A 429 " --> pdb=" O GLY A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.523A pdb=" N ILE A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 475 through 496 Processing helix chain 'A' and resid 499 through 523 removed outlier: 3.982A pdb=" N ILE A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 558 removed outlier: 3.744A pdb=" N SER A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 4.334A pdb=" N ASN A 578 " --> pdb=" O TYR A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 589 Processing helix chain 'A' and resid 604 through 629 removed outlier: 3.608A pdb=" N HIS A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.642A pdb=" N PHE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.836A pdb=" N ASP B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 280 through 302 removed outlier: 4.282A pdb=" N TRP B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 286 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 328 removed outlier: 3.989A pdb=" N GLY B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 366 removed outlier: 3.686A pdb=" N PHE B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 389 through 410 removed outlier: 4.165A pdb=" N LEU B 394 " --> pdb=" O TRP B 390 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.672A pdb=" N GLY B 429 " --> pdb=" O GLY B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 removed outlier: 3.524A pdb=" N ILE B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 475 through 496 Processing helix chain 'B' and resid 499 through 523 removed outlier: 3.982A pdb=" N ILE B 503 " --> pdb=" O ARG B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 558 removed outlier: 3.745A pdb=" N SER B 548 " --> pdb=" O THR B 544 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.335A pdb=" N ASN B 578 " --> pdb=" O TYR B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 589 Processing helix chain 'B' and resid 604 through 629 removed outlier: 3.608A pdb=" N HIS B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 104 removed outlier: 3.600A pdb=" N LEU A 57 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 150 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 148 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 85 removed outlier: 3.506A pdb=" N GLN A 82 " --> pdb=" O TRP A 71 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 69 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS A 123 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 104 removed outlier: 3.600A pdb=" N LEU B 57 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 150 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B 148 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 85 removed outlier: 3.506A pdb=" N GLN B 82 " --> pdb=" O TRP B 71 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 69 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 123 " --> pdb=" O LEU B 113 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1230 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: 1.38 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 2 1.13 - 1.31: 1266 1.31 - 1.49: 3704 1.49 - 1.66: 3602 1.66 - 1.84: 52 Bond restraints: 8626 Sorted by residual: bond pdb=" CB PRO A 371 " pdb=" CG PRO A 371 " ideal model delta sigma weight residual 1.492 0.953 0.539 5.00e-02 4.00e+02 1.16e+02 bond pdb=" CB PRO B 371 " pdb=" CG PRO B 371 " ideal model delta sigma weight residual 1.492 0.953 0.539 5.00e-02 4.00e+02 1.16e+02 bond pdb=" CG PRO A 371 " pdb=" CD PRO A 371 " ideal model delta sigma weight residual 1.503 1.232 0.271 3.40e-02 8.65e+02 6.34e+01 bond pdb=" CG PRO B 371 " pdb=" CD PRO B 371 " ideal model delta sigma weight residual 1.503 1.233 0.270 3.40e-02 8.65e+02 6.33e+01 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.11e+00 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 11792 14.77 - 29.54: 4 29.54 - 44.31: 0 44.31 - 59.08: 0 59.08 - 73.85: 2 Bond angle restraints: 11798 Sorted by residual: angle pdb=" CB PRO A 371 " pdb=" CG PRO A 371 " pdb=" CD PRO A 371 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CB PRO B 371 " pdb=" CG PRO B 371 " pdb=" CD PRO B 371 " ideal model delta sigma weight residual 106.10 179.93 -73.83 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO B 371 " pdb=" CD PRO B 371 " pdb=" CG PRO B 371 " ideal model delta sigma weight residual 103.20 77.97 25.23 1.50e+00 4.44e-01 2.83e+02 angle pdb=" N PRO A 371 " pdb=" CD PRO A 371 " pdb=" CG PRO A 371 " ideal model delta sigma weight residual 103.20 77.99 25.21 1.50e+00 4.44e-01 2.82e+02 angle pdb=" CA PRO A 371 " pdb=" CB PRO A 371 " pdb=" CG PRO A 371 " ideal model delta sigma weight residual 104.50 75.99 28.51 1.90e+00 2.77e-01 2.25e+02 ... (remaining 11793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 4539 17.01 - 34.02: 430 34.02 - 51.02: 84 51.02 - 68.03: 26 68.03 - 85.04: 8 Dihedral angle restraints: 5087 sinusoidal: 2009 harmonic: 3078 Sorted by residual: dihedral pdb=" CA LYS A 600 " pdb=" C LYS A 600 " pdb=" N ASP A 601 " pdb=" CA ASP A 601 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LYS B 600 " pdb=" C LYS B 600 " pdb=" N ASP B 601 " pdb=" CA ASP B 601 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LYS B 564 " pdb=" C LYS B 564 " pdb=" N GLY B 565 " pdb=" CA GLY B 565 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1300 0.144 - 0.289: 60 0.289 - 0.433: 6 0.433 - 0.577: 2 0.577 - 0.721: 2 Chirality restraints: 1370 Sorted by residual: chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 114 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 114 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 433 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 1367 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 531 " -0.111 5.00e-02 4.00e+02 1.65e-01 4.37e+01 pdb=" N PRO B 532 " 0.286 5.00e-02 4.00e+02 pdb=" CA PRO B 532 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO B 532 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 531 " 0.111 5.00e-02 4.00e+02 1.65e-01 4.36e+01 pdb=" N PRO A 532 " -0.286 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " 0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 506 " -0.519 9.50e-02 1.11e+02 2.33e-01 3.63e+01 pdb=" NE ARG A 506 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 506 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 506 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 506 " -0.007 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1922 2.80 - 3.32: 7298 3.32 - 3.85: 12775 3.85 - 4.37: 13704 4.37 - 4.90: 25727 Nonbonded interactions: 61426 Sorted by model distance: nonbonded pdb=" OG1 THR A 568 " pdb=" OG1 THR A 570 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR B 568 " pdb=" OG1 THR B 570 " model vdw 2.275 3.040 nonbonded pdb=" O PRO B 88 " pdb=" OG SER B 97 " model vdw 2.414 3.040 nonbonded pdb=" O PRO A 88 " pdb=" OG SER A 97 " model vdw 2.415 3.040 nonbonded pdb=" O LEU B 540 " pdb=" OG1 THR B 544 " model vdw 2.420 3.040 ... (remaining 61421 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.011 0.539 8637 Z= 0.389 Angle : 1.695 73.855 11826 Z= 0.829 Chirality : 0.078 0.721 1370 Planarity : 0.017 0.233 1434 Dihedral : 14.551 85.038 3104 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.24), residues: 1058 helix: 1.05 (0.21), residues: 482 sheet: 0.88 (0.53), residues: 114 loop : -2.58 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.005 ARG A 506 TYR 0.052 0.003 TYR A 127 PHE 0.043 0.003 PHE B 246 TRP 0.025 0.002 TRP A 403 HIS 0.016 0.004 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.01123 ( 8626) covalent geometry : angle 1.67696 (11798) SS BOND : bond 0.00903 ( 5) SS BOND : angle 3.30721 ( 10) hydrogen bonds : bond 0.18882 ( 418) hydrogen bonds : angle 6.68832 ( 1230) link_NAG-ASN : bond 0.01821 ( 6) link_NAG-ASN : angle 6.19463 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.317 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0738 time to fit residues: 7.4170 Evaluate side-chains 50 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 258 ASN B 59 HIS B 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.168254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134431 restraints weight = 10405.130| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.03 r_work: 0.3513 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8637 Z= 0.177 Angle : 0.686 8.610 11826 Z= 0.367 Chirality : 0.048 0.287 1370 Planarity : 0.007 0.091 1434 Dihedral : 10.414 87.528 1368 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.83 % Allowed : 4.95 % Favored : 94.22 % 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: 0.24 (0.25), residues: 1058 helix: 2.07 (0.22), residues: 482 sheet: 0.68 (0.46), residues: 126 loop : -2.29 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 124 TYR 0.027 0.002 TYR A 453 PHE 0.033 0.002 PHE A 246 TRP 0.015 0.001 TRP A 403 HIS 0.006 0.002 HIS B 608 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8626) covalent geometry : angle 0.67699 (11798) SS BOND : bond 0.00587 ( 5) SS BOND : angle 1.21796 ( 10) hydrogen bonds : bond 0.07922 ( 418) hydrogen bonds : angle 5.01869 ( 1230) link_NAG-ASN : bond 0.00646 ( 6) link_NAG-ASN : angle 2.83882 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.319 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.0705 time to fit residues: 7.2985 Evaluate side-chains 54 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 586 HIS B 59 HIS B 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130313 restraints weight = 10319.121| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.99 r_work: 0.3439 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8637 Z= 0.187 Angle : 0.665 7.416 11826 Z= 0.354 Chirality : 0.048 0.243 1370 Planarity : 0.005 0.062 1434 Dihedral : 9.499 84.936 1368 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.42 % Allowed : 7.78 % Favored : 90.80 % 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: 0.43 (0.25), residues: 1058 helix: 2.15 (0.23), residues: 480 sheet: 1.29 (0.46), residues: 122 loop : -2.24 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 344 TYR 0.027 0.002 TYR B 453 PHE 0.027 0.002 PHE A 573 TRP 0.012 0.001 TRP A 403 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8626) covalent geometry : angle 0.65899 (11798) SS BOND : bond 0.00591 ( 5) SS BOND : angle 0.83469 ( 10) hydrogen bonds : bond 0.08332 ( 418) hydrogen bonds : angle 4.80551 ( 1230) link_NAG-ASN : bond 0.00582 ( 6) link_NAG-ASN : angle 2.32545 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.321 Fit side-chains REVERT: A 465 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6565 (mp0) REVERT: B 465 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6583 (mp0) REVERT: B 581 LEU cc_start: 0.8241 (mt) cc_final: 0.7874 (tt) outliers start: 12 outliers final: 10 residues processed: 71 average time/residue: 0.0639 time to fit residues: 7.3870 Evaluate side-chains 66 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 605 HIS B 59 HIS B 605 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.160497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126862 restraints weight = 10504.421| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.98 r_work: 0.3381 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 8637 Z= 0.228 Angle : 0.692 6.921 11826 Z= 0.369 Chirality : 0.049 0.246 1370 Planarity : 0.005 0.048 1434 Dihedral : 9.035 69.725 1368 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.30 % Allowed : 10.97 % Favored : 87.74 % 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: 0.17 (0.25), residues: 1058 helix: 1.89 (0.22), residues: 480 sheet: 1.24 (0.45), residues: 124 loop : -2.36 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.021 0.002 TYR B 453 PHE 0.028 0.002 PHE B 573 TRP 0.012 0.002 TRP B 403 HIS 0.005 0.002 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 8626) covalent geometry : angle 0.68619 (11798) SS BOND : bond 0.00595 ( 5) SS BOND : angle 0.82270 ( 10) hydrogen bonds : bond 0.09350 ( 418) hydrogen bonds : angle 4.90573 ( 1230) link_NAG-ASN : bond 0.00559 ( 6) link_NAG-ASN : angle 2.30214 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.330 Fit side-chains REVERT: A 600 LYS cc_start: 0.7840 (pttm) cc_final: 0.7429 (ptmm) REVERT: B 581 LEU cc_start: 0.8254 (mt) cc_final: 0.7882 (tt) REVERT: B 600 LYS cc_start: 0.7829 (pttm) cc_final: 0.7420 (ptmm) outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 0.0840 time to fit residues: 8.5883 Evaluate side-chains 63 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.165472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131909 restraints weight = 10569.975| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.02 r_work: 0.3448 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8637 Z= 0.151 Angle : 0.591 6.625 11826 Z= 0.312 Chirality : 0.045 0.235 1370 Planarity : 0.004 0.040 1434 Dihedral : 8.548 65.811 1368 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.48 % Allowed : 11.20 % Favored : 86.32 % 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: 0.59 (0.25), residues: 1058 helix: 2.34 (0.23), residues: 480 sheet: 1.51 (0.45), residues: 122 loop : -2.27 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 444 TYR 0.016 0.001 TYR A 542 PHE 0.019 0.001 PHE B 573 TRP 0.008 0.001 TRP B 403 HIS 0.004 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8626) covalent geometry : angle 0.58630 (11798) SS BOND : bond 0.00412 ( 5) SS BOND : angle 0.71815 ( 10) hydrogen bonds : bond 0.07021 ( 418) hydrogen bonds : angle 4.53048 ( 1230) link_NAG-ASN : bond 0.00525 ( 6) link_NAG-ASN : angle 1.96473 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.321 Fit side-chains REVERT: A 600 LYS cc_start: 0.7897 (pttm) cc_final: 0.7572 (ptmm) REVERT: B 581 LEU cc_start: 0.8244 (mt) cc_final: 0.7953 (tt) REVERT: B 600 LYS cc_start: 0.7889 (pttm) cc_final: 0.7566 (ptmm) outliers start: 21 outliers final: 13 residues processed: 71 average time/residue: 0.0667 time to fit residues: 7.6905 Evaluate side-chains 66 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130483 restraints weight = 10439.738| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.92 r_work: 0.3435 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8637 Z= 0.165 Angle : 0.600 6.229 11826 Z= 0.318 Chirality : 0.045 0.233 1370 Planarity : 0.004 0.039 1434 Dihedral : 8.237 54.661 1368 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.48 % Allowed : 11.56 % Favored : 85.97 % 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: 0.62 (0.25), residues: 1058 helix: 2.36 (0.23), residues: 480 sheet: 1.50 (0.45), residues: 122 loop : -2.23 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 444 TYR 0.017 0.001 TYR B 542 PHE 0.021 0.002 PHE B 573 TRP 0.010 0.001 TRP B 403 HIS 0.004 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8626) covalent geometry : angle 0.59592 (11798) SS BOND : bond 0.00422 ( 5) SS BOND : angle 0.69892 ( 10) hydrogen bonds : bond 0.07554 ( 418) hydrogen bonds : angle 4.52898 ( 1230) link_NAG-ASN : bond 0.00504 ( 6) link_NAG-ASN : angle 1.87790 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.329 Fit side-chains REVERT: A 139 VAL cc_start: 0.7388 (p) cc_final: 0.7121 (m) REVERT: A 600 LYS cc_start: 0.7909 (pttm) cc_final: 0.7561 (ptmm) REVERT: B 581 LEU cc_start: 0.8263 (mt) cc_final: 0.7985 (tt) REVERT: B 600 LYS cc_start: 0.7918 (pttm) cc_final: 0.7577 (ptmm) outliers start: 21 outliers final: 15 residues processed: 75 average time/residue: 0.0904 time to fit residues: 9.7711 Evaluate side-chains 68 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 TRP Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 36 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.135979 restraints weight = 10443.913| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.96 r_work: 0.3508 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8637 Z= 0.118 Angle : 0.534 6.279 11826 Z= 0.279 Chirality : 0.043 0.220 1370 Planarity : 0.004 0.036 1434 Dihedral : 7.821 54.975 1368 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.77 % Allowed : 12.50 % Favored : 85.73 % 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: 0.95 (0.26), residues: 1058 helix: 2.63 (0.23), residues: 484 sheet: 1.64 (0.46), residues: 122 loop : -2.11 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 444 TYR 0.013 0.001 TYR A 542 PHE 0.015 0.001 PHE A 573 TRP 0.006 0.001 TRP A 597 HIS 0.004 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8626) covalent geometry : angle 0.53043 (11798) SS BOND : bond 0.00307 ( 5) SS BOND : angle 0.61774 ( 10) hydrogen bonds : bond 0.05446 ( 418) hydrogen bonds : angle 4.24182 ( 1230) link_NAG-ASN : bond 0.00505 ( 6) link_NAG-ASN : angle 1.62451 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.354 Fit side-chains REVERT: A 139 VAL cc_start: 0.7378 (p) cc_final: 0.7150 (m) REVERT: A 600 LYS cc_start: 0.7882 (pttm) cc_final: 0.7580 (ptmm) REVERT: B 581 LEU cc_start: 0.8217 (mt) cc_final: 0.8006 (tt) REVERT: B 600 LYS cc_start: 0.7871 (pttm) cc_final: 0.7573 (ptmm) outliers start: 15 outliers final: 15 residues processed: 68 average time/residue: 0.0661 time to fit residues: 7.3686 Evaluate side-chains 66 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 586 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 102 optimal weight: 0.0060 chunk 28 optimal weight: 3.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 332 ASN B 59 HIS B 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138670 restraints weight = 10396.680| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.95 r_work: 0.3540 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8637 Z= 0.109 Angle : 0.514 5.914 11826 Z= 0.267 Chirality : 0.042 0.204 1370 Planarity : 0.004 0.034 1434 Dihedral : 7.497 57.348 1368 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.30 % Allowed : 13.21 % Favored : 85.50 % 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: 1.22 (0.26), residues: 1058 helix: 2.84 (0.23), residues: 484 sheet: 1.86 (0.46), residues: 118 loop : -1.93 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 241 TYR 0.012 0.001 TYR B 542 PHE 0.014 0.001 PHE A 573 TRP 0.007 0.001 TRP B 403 HIS 0.004 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8626) covalent geometry : angle 0.51177 (11798) SS BOND : bond 0.00287 ( 5) SS BOND : angle 0.59957 ( 10) hydrogen bonds : bond 0.04950 ( 418) hydrogen bonds : angle 4.09790 ( 1230) link_NAG-ASN : bond 0.00448 ( 6) link_NAG-ASN : angle 1.41705 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.342 Fit side-chains REVERT: A 139 VAL cc_start: 0.7402 (OUTLIER) cc_final: 0.7196 (m) REVERT: A 600 LYS cc_start: 0.7877 (pttm) cc_final: 0.7604 (ptmm) REVERT: B 600 LYS cc_start: 0.7865 (pttm) cc_final: 0.7598 (ptmm) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.0723 time to fit residues: 7.5833 Evaluate side-chains 64 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 586 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 87 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 34 optimal weight: 0.0570 overall best weight: 1.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.163100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129504 restraints weight = 10486.943| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.00 r_work: 0.3418 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8637 Z= 0.187 Angle : 0.610 5.855 11826 Z= 0.323 Chirality : 0.045 0.229 1370 Planarity : 0.004 0.035 1434 Dihedral : 7.989 59.961 1368 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.53 % Allowed : 13.68 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.25), residues: 1058 helix: 2.49 (0.22), residues: 480 sheet: 1.64 (0.45), residues: 122 loop : -2.05 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.016 0.001 TYR A 542 PHE 0.023 0.002 PHE B 573 TRP 0.008 0.001 TRP B 619 HIS 0.005 0.002 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8626) covalent geometry : angle 0.60460 (11798) SS BOND : bond 0.00454 ( 5) SS BOND : angle 0.80957 ( 10) hydrogen bonds : bond 0.08101 ( 418) hydrogen bonds : angle 4.48657 ( 1230) link_NAG-ASN : bond 0.00424 ( 6) link_NAG-ASN : angle 2.08102 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.323 Fit side-chains REVERT: A 139 VAL cc_start: 0.7404 (p) cc_final: 0.7173 (m) REVERT: A 600 LYS cc_start: 0.7903 (pttm) cc_final: 0.6305 (mmtm) REVERT: B 600 LYS cc_start: 0.7907 (pttm) cc_final: 0.6305 (mmtm) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.0802 time to fit residues: 7.4214 Evaluate side-chains 59 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 1 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.164400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132510 restraints weight = 10320.511| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.92 r_work: 0.3471 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8637 Z= 0.136 Angle : 0.554 6.013 11826 Z= 0.291 Chirality : 0.043 0.222 1370 Planarity : 0.004 0.034 1434 Dihedral : 7.793 59.138 1368 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.42 % Allowed : 13.92 % Favored : 84.67 % 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: 1.03 (0.26), residues: 1058 helix: 2.68 (0.23), residues: 480 sheet: 1.67 (0.45), residues: 122 loop : -1.99 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 351 TYR 0.015 0.001 TYR A 542 PHE 0.018 0.001 PHE B 573 TRP 0.007 0.001 TRP B 403 HIS 0.005 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8626) covalent geometry : angle 0.54996 (11798) SS BOND : bond 0.00360 ( 5) SS BOND : angle 0.65573 ( 10) hydrogen bonds : bond 0.06437 ( 418) hydrogen bonds : angle 4.31404 ( 1230) link_NAG-ASN : bond 0.00500 ( 6) link_NAG-ASN : angle 1.87082 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.326 Fit side-chains REVERT: A 139 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7134 (m) REVERT: A 600 LYS cc_start: 0.7898 (pttm) cc_final: 0.6344 (mmtm) REVERT: B 600 LYS cc_start: 0.7894 (pttm) cc_final: 0.6347 (mmtm) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.0732 time to fit residues: 6.5365 Evaluate side-chains 59 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 49 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 0.0070 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.172969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141187 restraints weight = 10421.449| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.99 r_work: 0.3562 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8637 Z= 0.103 Angle : 0.502 6.223 11826 Z= 0.260 Chirality : 0.041 0.205 1370 Planarity : 0.003 0.032 1434 Dihedral : 7.472 56.978 1368 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.18 % Allowed : 14.50 % Favored : 84.32 % 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 (0.26), residues: 1058 helix: 2.94 (0.23), residues: 484 sheet: 1.88 (0.45), residues: 114 loop : -1.84 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 241 TYR 0.009 0.001 TYR A 542 PHE 0.014 0.001 PHE B 573 TRP 0.006 0.001 TRP B 265 HIS 0.004 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8626) covalent geometry : angle 0.49831 (11798) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.58886 ( 10) hydrogen bonds : bond 0.04314 ( 418) hydrogen bonds : angle 4.05906 ( 1230) link_NAG-ASN : bond 0.00520 ( 6) link_NAG-ASN : angle 1.60044 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.75 seconds wall clock time: 38 minutes 54.09 seconds (2334.09 seconds total)