Starting phenix.real_space_refine on Wed Feb 12 21:20:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tu9_41620/02_2025/8tu9_41620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tu9_41620/02_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_41620/02_2025/8tu9_41620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tu9_41620/02_2025/8tu9_41620.map" model { file = "/net/cci-nas-00/data/ceres_data/8tu9_41620/02_2025/8tu9_41620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tu9_41620/02_2025/8tu9_41620.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'HIS: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: 8.03, per 1000 atoms: 0.96 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=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 79 " distance=2.03 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 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: 2.10 Conformation dependent library (CDL) restraints added in 989.5 milliseconds 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: 0.91 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: 2.30 Time building geometry restraints manager: 2.41 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: 4531 17.01 - 34.02: 429 34.02 - 51.02: 84 51.02 - 68.03: 26 68.03 - 85.04: 8 Dihedral angle restraints: 5078 sinusoidal: 2000 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 5075 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: 2.02 - 2.60: 24 2.60 - 3.17: 6474 3.17 - 3.75: 12013 3.75 - 4.32: 15516 4.32 - 4.90: 27408 Nonbonded interactions: 61435 Sorted by model distance: nonbonded pdb=" SG CYS B 415 " pdb=" SG CYS B 434 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS B 76 " pdb=" SG CYS B 79 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS A 334 " pdb=" SG CYS B 334 " model vdw 2.047 3.760 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 ... (remaining 61430 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.140 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.050 ------------------------------------------------------------------------------- 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 8626 Z= 0.717 Angle : 1.677 73.855 11798 Z= 0.825 Chirality : 0.078 0.721 1370 Planarity : 0.017 0.233 1434 Dihedral : 14.551 85.038 3104 Min Nonbonded Distance : 2.023 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 TRP 0.025 0.002 TRP A 403 HIS 0.016 0.004 HIS A 586 PHE 0.043 0.003 PHE B 246 TYR 0.052 0.003 TYR A 127 ARG 0.030 0.005 ARG A 506 *********************** 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 : 0.917 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1463 time to fit residues: 14.8698 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 : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 A 605 HIS B 59 HIS B 258 ASN B 605 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.163941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130270 restraints weight = 10262.098| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.93 r_work: 0.3433 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8626 Z= 0.395 Angle : 0.784 8.806 11798 Z= 0.424 Chirality : 0.052 0.378 1370 Planarity : 0.007 0.096 1434 Dihedral : 10.420 87.552 1368 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.83 % Allowed : 5.78 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1058 helix: 1.66 (0.22), residues: 482 sheet: 0.56 (0.46), residues: 126 loop : -2.55 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 403 HIS 0.007 0.002 HIS B 608 PHE 0.040 0.003 PHE A 246 TYR 0.034 0.002 TYR A 453 ARG 0.005 0.001 ARG A 506 *********************** 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 74 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.848 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 0.1769 time to fit residues: 18.5164 Evaluate side-chains 61 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 88 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.165433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131003 restraints weight = 10564.318| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.05 r_work: 0.3439 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8626 Z= 0.269 Angle : 0.646 7.958 11798 Z= 0.346 Chirality : 0.047 0.258 1370 Planarity : 0.006 0.061 1434 Dihedral : 9.556 85.386 1368 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.30 % Allowed : 8.14 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1058 helix: 2.08 (0.23), residues: 480 sheet: 1.17 (0.46), residues: 122 loop : -2.44 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 403 HIS 0.004 0.001 HIS B 608 PHE 0.025 0.002 PHE B 573 TYR 0.022 0.002 TYR B 453 ARG 0.002 0.000 ARG B 344 *********************** 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 74 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.931 Fit side-chains REVERT: A 465 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6549 (mp0) REVERT: B 465 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6556 (mp0) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.1580 time to fit residues: 18.0863 Evaluate side-chains 65 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 77 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.163646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129429 restraints weight = 10563.924| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.08 r_work: 0.3414 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8626 Z= 0.274 Angle : 0.635 7.017 11798 Z= 0.339 Chirality : 0.047 0.235 1370 Planarity : 0.005 0.046 1434 Dihedral : 9.098 77.267 1368 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.12 % Allowed : 10.38 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1058 helix: 2.15 (0.23), residues: 480 sheet: 1.30 (0.45), residues: 122 loop : -2.40 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 390 HIS 0.004 0.001 HIS A 608 PHE 0.025 0.002 PHE B 573 TYR 0.018 0.001 TYR A 453 ARG 0.002 0.000 ARG B 444 *********************** 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 85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.847 Fit side-chains REVERT: A 600 LYS cc_start: 0.7817 (pttm) cc_final: 0.7369 (ptmm) REVERT: B 600 LYS cc_start: 0.7802 (pttm) cc_final: 0.7354 (ptmm) outliers start: 18 outliers final: 12 residues processed: 83 average time/residue: 0.1839 time to fit residues: 22.5840 Evaluate side-chains 78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 76 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 Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.166912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134812 restraints weight = 10397.205| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.94 r_work: 0.3490 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8626 Z= 0.173 Angle : 0.553 6.801 11798 Z= 0.291 Chirality : 0.043 0.224 1370 Planarity : 0.004 0.037 1434 Dihedral : 8.704 76.406 1368 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.12 % Allowed : 11.67 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1058 helix: 2.56 (0.23), residues: 480 sheet: 1.45 (0.45), residues: 122 loop : -2.28 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 390 HIS 0.003 0.001 HIS B 608 PHE 0.018 0.001 PHE B 573 TYR 0.014 0.001 TYR A 542 ARG 0.001 0.000 ARG A 351 *********************** 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 79 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.952 Fit side-chains REVERT: A 564 LYS cc_start: 0.8788 (ptmm) cc_final: 0.8287 (ptpt) REVERT: A 600 LYS cc_start: 0.7843 (pttm) cc_final: 0.7406 (ptmm) REVERT: B 564 LYS cc_start: 0.8783 (ptmm) cc_final: 0.8289 (ptpt) REVERT: B 600 LYS cc_start: 0.7841 (pttm) cc_final: 0.7398 (ptmm) outliers start: 18 outliers final: 12 residues processed: 75 average time/residue: 0.1717 time to fit residues: 19.5229 Evaluate side-chains 69 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 586 HIS 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 586 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.160913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126655 restraints weight = 10503.633| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.02 r_work: 0.3380 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8626 Z= 0.364 Angle : 0.677 6.074 11798 Z= 0.361 Chirality : 0.048 0.246 1370 Planarity : 0.005 0.038 1434 Dihedral : 8.546 53.998 1368 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.36 % Allowed : 12.38 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1058 helix: 2.07 (0.23), residues: 480 sheet: 1.44 (0.46), residues: 122 loop : -2.40 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 403 HIS 0.005 0.002 HIS B 608 PHE 0.026 0.002 PHE A 573 TYR 0.019 0.002 TYR B 453 ARG 0.003 0.000 ARG A 351 *********************** 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 80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.860 Fit side-chains REVERT: A 600 LYS cc_start: 0.7964 (pttm) cc_final: 0.7591 (ptmm) REVERT: B 600 LYS cc_start: 0.7915 (pttm) cc_final: 0.7554 (ptmm) outliers start: 20 outliers final: 13 residues processed: 78 average time/residue: 0.1814 time to fit residues: 20.8179 Evaluate side-chains 73 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.168008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136395 restraints weight = 10356.561| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.91 r_work: 0.3512 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8626 Z= 0.162 Angle : 0.540 6.522 11798 Z= 0.282 Chirality : 0.043 0.223 1370 Planarity : 0.004 0.034 1434 Dihedral : 8.029 51.930 1368 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.53 % Allowed : 13.44 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1058 helix: 2.65 (0.23), residues: 480 sheet: 1.63 (0.45), residues: 122 loop : -2.24 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 597 HIS 0.003 0.001 HIS B 586 PHE 0.013 0.001 PHE A 573 TYR 0.014 0.001 TYR B 77 ARG 0.001 0.000 ARG A 444 *********************** 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 70 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.861 Fit side-chains REVERT: A 564 LYS cc_start: 0.8790 (ptmm) cc_final: 0.8319 (ptpt) REVERT: A 600 LYS cc_start: 0.7873 (pttm) cc_final: 0.7538 (ptmm) REVERT: B 564 LYS cc_start: 0.8714 (ptmm) cc_final: 0.8194 (ptpt) REVERT: B 600 LYS cc_start: 0.7900 (pttm) cc_final: 0.7560 (ptmm) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.1742 time to fit residues: 17.7823 Evaluate side-chains 65 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 586 HIS 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 586 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 0.0040 chunk 11 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.7492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 463 HIS B 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.167580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135068 restraints weight = 10450.414| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.97 r_work: 0.3492 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8626 Z= 0.169 Angle : 0.537 6.300 11798 Z= 0.281 Chirality : 0.043 0.218 1370 Planarity : 0.004 0.034 1434 Dihedral : 7.761 52.232 1368 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.77 % Allowed : 13.33 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1058 helix: 2.66 (0.23), residues: 488 sheet: 1.68 (0.45), residues: 122 loop : -2.15 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 403 HIS 0.003 0.001 HIS A 586 PHE 0.016 0.001 PHE A 573 TYR 0.014 0.001 TYR B 542 ARG 0.001 0.000 ARG A 351 *********************** 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 73 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.935 Fit side-chains REVERT: A 139 VAL cc_start: 0.7289 (p) cc_final: 0.6961 (m) REVERT: A 600 LYS cc_start: 0.7917 (pttm) cc_final: 0.7573 (ptmm) REVERT: B 600 LYS cc_start: 0.7887 (pttm) cc_final: 0.7556 (ptmm) outliers start: 15 outliers final: 15 residues processed: 70 average time/residue: 0.1614 time to fit residues: 17.7582 Evaluate side-chains 69 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 566 LEU 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 26 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.160801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128651 restraints weight = 10640.857| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.92 r_work: 0.3415 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8626 Z= 0.298 Angle : 0.626 5.907 11798 Z= 0.332 Chirality : 0.046 0.236 1370 Planarity : 0.004 0.035 1434 Dihedral : 8.076 55.511 1368 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.12 % Allowed : 13.68 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1058 helix: 2.23 (0.22), residues: 488 sheet: 1.54 (0.45), residues: 122 loop : -2.25 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 390 HIS 0.005 0.001 HIS B 608 PHE 0.024 0.002 PHE A 573 TYR 0.018 0.002 TYR B 542 ARG 0.002 0.000 ARG A 351 *********************** 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 72 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.882 Fit side-chains REVERT: A 139 VAL cc_start: 0.7378 (p) cc_final: 0.7109 (m) REVERT: A 600 LYS cc_start: 0.7895 (pttm) cc_final: 0.7563 (ptmm) REVERT: B 600 LYS cc_start: 0.7861 (pttm) cc_final: 0.7544 (ptmm) outliers start: 18 outliers final: 15 residues processed: 67 average time/residue: 0.1831 time to fit residues: 18.5674 Evaluate side-chains 69 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 370 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.164716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131743 restraints weight = 10526.144| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.96 r_work: 0.3452 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8626 Z= 0.211 Angle : 0.570 6.111 11798 Z= 0.300 Chirality : 0.044 0.228 1370 Planarity : 0.004 0.034 1434 Dihedral : 7.937 55.103 1368 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.00 % Allowed : 14.50 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1058 helix: 2.41 (0.23), residues: 488 sheet: 1.54 (0.44), residues: 122 loop : -2.18 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 403 HIS 0.004 0.001 HIS B 586 PHE 0.018 0.001 PHE B 573 TYR 0.017 0.001 TYR B 542 ARG 0.002 0.000 ARG B 351 ********************** 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 69 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.981 Fit side-chains REVERT: A 139 VAL cc_start: 0.7370 (p) cc_final: 0.7109 (m) REVERT: A 600 LYS cc_start: 0.7841 (pttm) cc_final: 0.7558 (ptmm) REVERT: B 600 LYS cc_start: 0.7850 (pttm) cc_final: 0.7577 (ptmm) outliers start: 17 outliers final: 14 residues processed: 64 average time/residue: 0.1450 time to fit residues: 15.2666 Evaluate side-chains 64 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.158438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126416 restraints weight = 10726.544| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.91 r_work: 0.3386 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 8626 Z= 0.377 Angle : 0.675 5.701 11798 Z= 0.360 Chirality : 0.048 0.248 1370 Planarity : 0.005 0.036 1434 Dihedral : 8.273 57.773 1368 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.65 % Allowed : 14.98 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1058 helix: 1.93 (0.22), residues: 488 sheet: 1.44 (0.45), residues: 122 loop : -2.36 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 390 HIS 0.006 0.002 HIS B 608 PHE 0.027 0.002 PHE A 573 TYR 0.020 0.002 TYR A 453 ARG 0.002 0.001 ARG B 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4018.60 seconds wall clock time: 72 minutes 8.55 seconds (4328.55 seconds total)