Starting phenix.real_space_refine on Wed Feb 4 08:21:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtm_37836/02_2026/8wtm_37836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtm_37836/02_2026/8wtm_37836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wtm_37836/02_2026/8wtm_37836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtm_37836/02_2026/8wtm_37836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wtm_37836/02_2026/8wtm_37836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtm_37836/02_2026/8wtm_37836.map" } resolution = 2.65 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= -0.001 sd= 0.111 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6298 2.51 5 N 1622 2.21 5 O 1718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9680 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4825 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 3 Chain: "B" Number of atoms: 4825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4825 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 3 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'JAA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.11, per 1000 atoms: 0.22 Number of scatterers: 9680 At special positions: 0 Unit cell: (80.51, 100.43, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1718 8.00 N 1622 7.00 C 6298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 646 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 646 " - pdb=" SG CYS B 687 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 476.8 milliseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 60.3% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.670A pdb=" N ARG A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.793A pdb=" N VAL A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.543A pdb=" N SER A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 325 removed outlier: 3.838A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.584A pdb=" N LYS A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 369 removed outlier: 3.867A pdb=" N LYS A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.549A pdb=" N SER A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.607A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 468 Processing helix chain 'A' and resid 474 through 495 removed outlier: 3.577A pdb=" N GLN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 493 " --> pdb=" O MET A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.729A pdb=" N GLU A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 514 removed outlier: 3.502A pdb=" N ARG A 512 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.504A pdb=" N VAL A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 552 removed outlier: 4.742A pdb=" N TRP A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 582 Processing helix chain 'A' and resid 587 through 605 Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.556A pdb=" N HIS A 623 " --> pdb=" O TRP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 649 through 655 removed outlier: 3.679A pdb=" N LEU A 653 " --> pdb=" O GLY A 650 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 654 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP A 655 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 679 removed outlier: 3.754A pdb=" N ARG A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 678 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 Processing helix chain 'A' and resid 704 through 733 removed outlier: 3.717A pdb=" N SER A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 199 through 214 Processing helix chain 'B' and resid 233 through 246 removed outlier: 3.670A pdb=" N ARG B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.793A pdb=" N VAL B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 298 removed outlier: 3.542A pdb=" N SER B 297 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 318 through 325 removed outlier: 3.838A pdb=" N GLY B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 354 through 365 removed outlier: 3.584A pdb=" N LYS B 363 " --> pdb=" O GLU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 369 removed outlier: 3.867A pdb=" N LYS B 369 " --> pdb=" O GLU B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 387 through 399 removed outlier: 3.549A pdb=" N SER B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 445 removed outlier: 3.607A pdb=" N ILE B 432 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 468 Processing helix chain 'B' and resid 474 through 495 removed outlier: 3.578A pdb=" N GLN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 493 " --> pdb=" O MET B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.729A pdb=" N GLU B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 514 removed outlier: 3.502A pdb=" N ARG B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 532 removed outlier: 3.504A pdb=" N VAL B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 552 removed outlier: 4.742A pdb=" N TRP B 549 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 582 Processing helix chain 'B' and resid 587 through 605 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.555A pdb=" N HIS B 623 " --> pdb=" O TRP B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 640 Processing helix chain 'B' and resid 649 through 655 removed outlier: 3.678A pdb=" N LEU B 653 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 654 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP B 655 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 679 removed outlier: 3.754A pdb=" N ARG B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 673 " --> pdb=" O ARG B 669 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 678 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 704 through 733 removed outlier: 3.717A pdb=" N SER B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS B 732 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 116 removed outlier: 6.627A pdb=" N ASP A 109 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR A 79 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE A 111 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 78 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS A 148 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170 removed outlier: 6.103A pdb=" N ALA A 168 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 121 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 302 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 313 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE A 304 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 116 removed outlier: 6.627A pdb=" N ASP B 109 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR B 79 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE B 111 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU B 78 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS B 148 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 170 removed outlier: 6.102A pdb=" N ALA B 168 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 121 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 302 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER B 313 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE B 304 " --> pdb=" O VAL B 311 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1452 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: 1.41 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: 1.17 - 1.29: 1500 1.29 - 1.42: 2626 1.42 - 1.55: 5670 1.55 - 1.68: 18 1.68 - 1.81: 74 Bond restraints: 9888 Sorted by residual: bond pdb=" C04 JAA A 802 " pdb=" C05 JAA A 802 " ideal model delta sigma weight residual 1.534 1.346 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C04 JAA A 801 " pdb=" C05 JAA A 801 " ideal model delta sigma weight residual 1.534 1.346 0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" C07 JAA A 802 " pdb=" C08 JAA A 802 " ideal model delta sigma weight residual 1.514 1.342 0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C07 JAA A 801 " pdb=" C08 JAA A 801 " ideal model delta sigma weight residual 1.514 1.343 0.171 2.00e-02 2.50e+03 7.34e+01 bond pdb=" C05 JAA A 802 " pdb=" C08 JAA A 802 " ideal model delta sigma weight residual 1.515 1.684 -0.169 2.00e-02 2.50e+03 7.16e+01 ... (remaining 9883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 12980 2.28 - 4.57: 315 4.57 - 6.85: 59 6.85 - 9.13: 14 9.13 - 11.42: 2 Bond angle restraints: 13370 Sorted by residual: angle pdb=" C GLN A 172 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C GLN B 172 " pdb=" N ASP B 173 " pdb=" CA ASP B 173 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C LYS A 105 " pdb=" N THR A 106 " pdb=" CA THR A 106 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C LYS B 105 " pdb=" N THR B 106 " pdb=" CA THR B 106 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CA THR B 106 " pdb=" CB THR B 106 " pdb=" CG2 THR B 106 " ideal model delta sigma weight residual 110.50 117.01 -6.51 1.70e+00 3.46e-01 1.47e+01 ... (remaining 13365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5355 17.88 - 35.75: 442 35.75 - 53.63: 65 53.63 - 71.50: 14 71.50 - 89.38: 8 Dihedral angle restraints: 5884 sinusoidal: 2364 harmonic: 3520 Sorted by residual: dihedral pdb=" CA GLN B 172 " pdb=" C GLN B 172 " pdb=" N ASP B 173 " pdb=" CA ASP B 173 " ideal model delta harmonic sigma weight residual 180.00 148.31 31.69 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA GLN A 172 " pdb=" C GLN A 172 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " ideal model delta harmonic sigma weight residual 180.00 148.32 31.68 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CB CYS A 646 " pdb=" SG CYS A 646 " pdb=" SG CYS A 687 " pdb=" CB CYS A 687 " ideal model delta sinusoidal sigma weight residual 93.00 139.00 -46.00 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 5881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1221 0.064 - 0.129: 281 0.129 - 0.193: 38 0.193 - 0.257: 2 0.257 - 0.321: 2 Chirality restraints: 1544 Sorted by residual: chirality pdb=" C05 JAA A 801 " pdb=" C04 JAA A 801 " pdb=" C08 JAA A 801 " pdb=" C09 JAA A 801 " both_signs ideal model delta sigma weight residual False 2.50 2.82 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C05 JAA A 802 " pdb=" C04 JAA A 802 " pdb=" C08 JAA A 802 " pdb=" C09 JAA A 802 " both_signs ideal model delta sigma weight residual False 2.50 2.82 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA THR A 106 " pdb=" N THR A 106 " pdb=" C THR A 106 " pdb=" CB THR A 106 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1541 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 67 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO B 68 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 68 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 68 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 67 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 68 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 507 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C ARG A 507 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG A 507 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 508 " -0.015 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2394 2.78 - 3.31: 8329 3.31 - 3.84: 15597 3.84 - 4.37: 19914 4.37 - 4.90: 32759 Nonbonded interactions: 78993 Sorted by model distance: nonbonded pdb=" O LEU A 163 " pdb=" OG SER A 167 " model vdw 2.256 3.040 nonbonded pdb=" O LEU B 163 " pdb=" OG SER B 167 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" OH TYR A 592 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR B 494 " pdb=" OH TYR B 592 " model vdw 2.300 3.040 nonbonded pdb=" O ILE A 277 " pdb=" OG SER A 280 " model vdw 2.331 3.040 ... (remaining 78988 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 67 through 733) 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: 1.700 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.780 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.008 0.188 9890 Z= 0.368 Angle : 0.915 11.417 13374 Z= 0.489 Chirality : 0.055 0.321 1544 Planarity : 0.007 0.066 1668 Dihedral : 13.621 89.378 3610 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.19 % Allowed : 5.11 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.17), residues: 1212 helix: -4.00 (0.09), residues: 670 sheet: 0.28 (0.59), residues: 66 loop : -2.06 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 507 TYR 0.011 0.003 TYR A 630 PHE 0.015 0.002 PHE A 75 TRP 0.009 0.002 TRP B 621 HIS 0.007 0.002 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00820 ( 9888) covalent geometry : angle 0.91524 (13370) SS BOND : bond 0.00324 ( 2) SS BOND : angle 1.24976 ( 4) hydrogen bonds : bond 0.29568 ( 494) hydrogen bonds : angle 9.18213 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8276 (tpt) cc_final: 0.8068 (mmm) REVERT: A 237 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7469 (mtp180) REVERT: A 269 MET cc_start: 0.7112 (tpt) cc_final: 0.6584 (tpt) REVERT: A 272 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7276 (mtpp) REVERT: A 307 ARG cc_start: 0.7817 (ptp-170) cc_final: 0.7478 (ptp90) REVERT: A 342 ASP cc_start: 0.7400 (t0) cc_final: 0.7101 (t0) REVERT: A 511 MET cc_start: 0.7817 (mtm) cc_final: 0.7174 (mmt) REVERT: A 528 HIS cc_start: 0.8249 (t-90) cc_final: 0.8011 (t-170) REVERT: A 598 ILE cc_start: 0.8408 (mt) cc_final: 0.8147 (tp) REVERT: B 187 MET cc_start: 0.8279 (tpt) cc_final: 0.8076 (mmm) REVERT: B 237 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7443 (mtp180) REVERT: B 269 MET cc_start: 0.7104 (tpt) cc_final: 0.6675 (tpt) REVERT: B 272 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7296 (mtpp) REVERT: B 307 ARG cc_start: 0.7808 (ptp-170) cc_final: 0.7466 (ptp90) REVERT: B 342 ASP cc_start: 0.7379 (t0) cc_final: 0.7115 (t0) REVERT: B 511 MET cc_start: 0.7813 (mtm) cc_final: 0.7184 (mmt) REVERT: B 528 HIS cc_start: 0.8240 (t-90) cc_final: 0.8002 (t-170) REVERT: B 589 MET cc_start: 0.8589 (tpt) cc_final: 0.8289 (tpt) REVERT: B 598 ILE cc_start: 0.8414 (mt) cc_final: 0.8158 (tp) outliers start: 2 outliers final: 2 residues processed: 160 average time/residue: 0.6579 time to fit residues: 111.0416 Evaluate side-chains 122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 182 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.0870 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 248 HIS A 611 ASN A 617 GLN B 81 ASN B 248 HIS B 611 ASN B 617 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.174842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105009 restraints weight = 9269.039| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.72 r_work: 0.2931 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9890 Z= 0.119 Angle : 0.558 6.061 13374 Z= 0.298 Chirality : 0.040 0.136 1544 Planarity : 0.005 0.073 1668 Dihedral : 6.277 66.087 1366 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.23 % Allowed : 11.17 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.22), residues: 1212 helix: -1.07 (0.17), residues: 702 sheet: 0.88 (0.53), residues: 82 loop : -1.74 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 301 TYR 0.013 0.002 TYR A 494 PHE 0.012 0.001 PHE B 562 TRP 0.007 0.001 TRP B 572 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9888) covalent geometry : angle 0.55784 (13370) SS BOND : bond 0.00004 ( 2) SS BOND : angle 1.16144 ( 4) hydrogen bonds : bond 0.04649 ( 494) hydrogen bonds : angle 4.17290 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.230 Fit side-chains REVERT: A 114 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7105 (tm-30) REVERT: A 237 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7451 (mtp180) REVERT: A 272 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7202 (mtpp) REVERT: A 307 ARG cc_start: 0.8018 (ptp-170) cc_final: 0.7807 (ptp-170) REVERT: A 338 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6212 (tm-30) REVERT: A 444 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7503 (ttm-80) REVERT: A 511 MET cc_start: 0.8717 (mtm) cc_final: 0.7991 (mmt) REVERT: A 528 HIS cc_start: 0.8527 (t-90) cc_final: 0.8324 (t-170) REVERT: A 598 ILE cc_start: 0.8430 (mt) cc_final: 0.8193 (tp) REVERT: A 680 MET cc_start: 0.5953 (mtp) cc_final: 0.5556 (ptt) REVERT: B 114 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7084 (tm-30) REVERT: B 237 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7446 (mtp180) REVERT: B 272 LYS cc_start: 0.7599 (ttpt) cc_final: 0.7175 (mtpp) REVERT: B 307 ARG cc_start: 0.8007 (ptp-170) cc_final: 0.7794 (ptp-170) REVERT: B 338 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: B 444 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7489 (ttm-80) REVERT: B 511 MET cc_start: 0.8735 (mtm) cc_final: 0.8001 (mmt) REVERT: B 598 ILE cc_start: 0.8430 (mt) cc_final: 0.8198 (tp) outliers start: 13 outliers final: 1 residues processed: 142 average time/residue: 0.5407 time to fit residues: 81.9348 Evaluate side-chains 113 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 72 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 617 GLN B 81 ASN B 528 HIS B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.104591 restraints weight = 9332.100| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.92 r_work: 0.2859 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9890 Z= 0.212 Angle : 0.635 8.311 13374 Z= 0.328 Chirality : 0.046 0.155 1544 Planarity : 0.005 0.067 1668 Dihedral : 6.184 62.843 1364 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.50 % Allowed : 12.78 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1212 helix: 0.21 (0.19), residues: 698 sheet: 0.47 (0.55), residues: 66 loop : -1.61 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 301 TYR 0.018 0.002 TYR A 601 PHE 0.016 0.002 PHE A 562 TRP 0.007 0.001 TRP B 621 HIS 0.005 0.002 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 9888) covalent geometry : angle 0.63455 (13370) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.75384 ( 4) hydrogen bonds : bond 0.05873 ( 494) hydrogen bonds : angle 3.97783 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.314 Fit side-chains REVERT: A 114 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7162 (tm-30) REVERT: A 173 ASP cc_start: 0.6918 (m-30) cc_final: 0.6478 (t0) REVERT: A 218 ASN cc_start: 0.7233 (p0) cc_final: 0.6569 (p0) REVERT: A 236 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: A 237 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7598 (mtp-110) REVERT: A 272 LYS cc_start: 0.7655 (ttpt) cc_final: 0.7218 (mtpp) REVERT: A 307 ARG cc_start: 0.8010 (ptp-170) cc_final: 0.7797 (ptp-170) REVERT: A 428 PHE cc_start: 0.8035 (t80) cc_final: 0.7804 (t80) REVERT: A 511 MET cc_start: 0.8854 (mtm) cc_final: 0.8099 (mmt) REVERT: A 528 HIS cc_start: 0.8605 (t-90) cc_final: 0.8357 (t-170) REVERT: A 598 ILE cc_start: 0.8575 (mt) cc_final: 0.8304 (tp) REVERT: B 114 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: B 173 ASP cc_start: 0.6912 (m-30) cc_final: 0.6473 (t0) REVERT: B 218 ASN cc_start: 0.7232 (p0) cc_final: 0.6592 (p0) REVERT: B 236 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: B 237 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7615 (mtp-110) REVERT: B 272 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7202 (mtpp) REVERT: B 307 ARG cc_start: 0.7993 (ptp-170) cc_final: 0.7782 (ptp-170) REVERT: B 342 ASP cc_start: 0.7297 (t0) cc_final: 0.6976 (t0) REVERT: B 428 PHE cc_start: 0.8034 (t80) cc_final: 0.7803 (t80) REVERT: B 511 MET cc_start: 0.8866 (mtm) cc_final: 0.8107 (mmt) REVERT: B 598 ILE cc_start: 0.8570 (mt) cc_final: 0.8299 (tp) outliers start: 37 outliers final: 18 residues processed: 146 average time/residue: 0.5828 time to fit residues: 90.5436 Evaluate side-chains 142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 617 GLN B 81 ASN B 528 HIS B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.172282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.102274 restraints weight = 9304.113| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.36 r_work: 0.2804 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9890 Z= 0.159 Angle : 0.581 9.716 13374 Z= 0.299 Chirality : 0.044 0.142 1544 Planarity : 0.004 0.054 1668 Dihedral : 5.885 55.197 1364 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.45 % Allowed : 13.64 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1212 helix: 0.89 (0.20), residues: 688 sheet: 0.62 (0.53), residues: 94 loop : -1.39 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 301 TYR 0.012 0.002 TYR A 630 PHE 0.012 0.001 PHE A 562 TRP 0.006 0.001 TRP B 621 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9888) covalent geometry : angle 0.58047 (13370) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.75767 ( 4) hydrogen bonds : bond 0.04844 ( 494) hydrogen bonds : angle 3.75176 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.377 Fit side-chains REVERT: A 114 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7032 (tm-30) REVERT: A 236 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: A 237 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7591 (mtp-110) REVERT: A 260 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.8072 (p) REVERT: A 272 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7263 (mtpp) REVERT: A 307 ARG cc_start: 0.7981 (ptp-170) cc_final: 0.7754 (ptp-170) REVERT: A 428 PHE cc_start: 0.8028 (t80) cc_final: 0.7800 (t80) REVERT: A 511 MET cc_start: 0.8813 (mtm) cc_final: 0.8096 (mmt) REVERT: A 528 HIS cc_start: 0.8588 (t-90) cc_final: 0.8387 (t-170) REVERT: A 598 ILE cc_start: 0.8553 (mt) cc_final: 0.8309 (tp) REVERT: A 680 MET cc_start: 0.6057 (mtp) cc_final: 0.5630 (ptt) REVERT: B 114 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: B 236 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: B 237 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7604 (mtp-110) REVERT: B 260 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.8067 (p) REVERT: B 272 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7251 (mtpp) REVERT: B 307 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7734 (ptp-170) REVERT: B 428 PHE cc_start: 0.8026 (t80) cc_final: 0.7795 (t80) REVERT: B 511 MET cc_start: 0.8819 (mtm) cc_final: 0.8102 (mmt) REVERT: B 598 ILE cc_start: 0.8549 (mt) cc_final: 0.8308 (tp) REVERT: B 680 MET cc_start: 0.6059 (mtp) cc_final: 0.5637 (ptt) outliers start: 47 outliers final: 18 residues processed: 157 average time/residue: 0.5371 time to fit residues: 90.1226 Evaluate side-chains 136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 91 optimal weight: 0.0370 chunk 94 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 617 GLN B 81 ASN B 528 HIS B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.173185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101663 restraints weight = 9347.694| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.16 r_work: 0.2835 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9890 Z= 0.130 Angle : 0.554 10.584 13374 Z= 0.284 Chirality : 0.042 0.133 1544 Planarity : 0.004 0.044 1668 Dihedral : 5.561 45.273 1364 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.88 % Allowed : 14.20 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1212 helix: 1.29 (0.20), residues: 690 sheet: 0.75 (0.52), residues: 94 loop : -1.31 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 649 TYR 0.014 0.002 TYR A 494 PHE 0.010 0.001 PHE B 562 TRP 0.005 0.001 TRP B 572 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9888) covalent geometry : angle 0.55376 (13370) SS BOND : bond 0.00074 ( 2) SS BOND : angle 1.26541 ( 4) hydrogen bonds : bond 0.04306 ( 494) hydrogen bonds : angle 3.59594 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.231 Fit side-chains REVERT: A 114 GLU cc_start: 0.7763 (tm-30) cc_final: 0.6941 (tm-30) REVERT: A 171 MET cc_start: 0.8504 (mtp) cc_final: 0.7884 (mmm) REVERT: A 237 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7553 (mtp-110) REVERT: A 260 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.8053 (p) REVERT: A 272 LYS cc_start: 0.7536 (ttpt) cc_final: 0.7210 (mtpp) REVERT: A 307 ARG cc_start: 0.7951 (ptp-170) cc_final: 0.7698 (ptp-170) REVERT: A 511 MET cc_start: 0.8735 (mtm) cc_final: 0.7994 (mmt) REVERT: A 554 GLU cc_start: 0.8481 (tp30) cc_final: 0.8269 (mm-30) REVERT: A 598 ILE cc_start: 0.8515 (mt) cc_final: 0.8279 (tp) REVERT: A 680 MET cc_start: 0.6046 (mtp) cc_final: 0.5650 (ptt) REVERT: B 114 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7002 (tm-30) REVERT: B 171 MET cc_start: 0.8483 (mtp) cc_final: 0.7874 (mmm) REVERT: B 237 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7573 (mtp-110) REVERT: B 272 LYS cc_start: 0.7520 (ttpt) cc_final: 0.7194 (mtpp) REVERT: B 307 ARG cc_start: 0.7944 (ptp-170) cc_final: 0.7694 (ptp-170) REVERT: B 511 MET cc_start: 0.8754 (mtm) cc_final: 0.8001 (mmt) REVERT: B 598 ILE cc_start: 0.8514 (mt) cc_final: 0.8283 (tp) REVERT: B 642 ASP cc_start: 0.6978 (m-30) cc_final: 0.6755 (t0) REVERT: B 680 MET cc_start: 0.6039 (mtp) cc_final: 0.5645 (ptt) outliers start: 41 outliers final: 22 residues processed: 154 average time/residue: 0.5499 time to fit residues: 90.1527 Evaluate side-chains 133 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 109 optimal weight: 3.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 528 HIS A 617 GLN B 528 HIS B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.170977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099598 restraints weight = 9334.132| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.19 r_work: 0.2825 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9890 Z= 0.190 Angle : 0.623 11.535 13374 Z= 0.314 Chirality : 0.046 0.150 1544 Planarity : 0.004 0.040 1668 Dihedral : 5.628 34.598 1364 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.69 % Allowed : 14.39 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1212 helix: 1.23 (0.20), residues: 692 sheet: 0.70 (0.52), residues: 94 loop : -1.33 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 649 TYR 0.017 0.002 TYR A 494 PHE 0.013 0.002 PHE A 562 TRP 0.006 0.001 TRP B 621 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9888) covalent geometry : angle 0.62258 (13370) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.87267 ( 4) hydrogen bonds : bond 0.05187 ( 494) hydrogen bonds : angle 3.71440 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7850 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 218 ASN cc_start: 0.7298 (p0) cc_final: 0.6800 (p0) REVERT: A 260 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8117 (p) REVERT: A 272 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7242 (mtpp) REVERT: A 307 ARG cc_start: 0.7966 (ptp-170) cc_final: 0.7730 (ptp-170) REVERT: A 342 ASP cc_start: 0.7293 (t0) cc_final: 0.7019 (t0) REVERT: A 511 MET cc_start: 0.8802 (mtm) cc_final: 0.8057 (mmt) REVERT: A 598 ILE cc_start: 0.8572 (mt) cc_final: 0.8303 (tp) REVERT: A 680 MET cc_start: 0.6027 (mtp) cc_final: 0.5602 (ptt) REVERT: B 114 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: B 218 ASN cc_start: 0.7296 (p0) cc_final: 0.6799 (p0) REVERT: B 272 LYS cc_start: 0.7649 (ttpt) cc_final: 0.7242 (mtpp) REVERT: B 307 ARG cc_start: 0.7958 (ptp-170) cc_final: 0.7722 (ptp-170) REVERT: B 342 ASP cc_start: 0.7298 (t0) cc_final: 0.7002 (t0) REVERT: B 511 MET cc_start: 0.8811 (mtm) cc_final: 0.8067 (mmt) REVERT: B 598 ILE cc_start: 0.8562 (mt) cc_final: 0.8296 (tp) REVERT: B 642 ASP cc_start: 0.6983 (m-30) cc_final: 0.6772 (t0) REVERT: B 680 MET cc_start: 0.6006 (mtp) cc_final: 0.5600 (ptt) outliers start: 39 outliers final: 24 residues processed: 148 average time/residue: 0.6039 time to fit residues: 95.2824 Evaluate side-chains 144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 2 optimal weight: 9.9990 chunk 78 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 71 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS A 617 GLN B 528 HIS B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.175559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.107808 restraints weight = 9283.676| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.05 r_work: 0.2921 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9890 Z= 0.101 Angle : 0.539 12.709 13374 Z= 0.270 Chirality : 0.041 0.128 1544 Planarity : 0.004 0.034 1668 Dihedral : 5.210 28.846 1364 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.46 % Allowed : 16.57 % Favored : 80.97 % 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 are not related in a simple way. whole: 0.96 (0.25), residues: 1212 helix: 1.65 (0.20), residues: 700 sheet: 0.81 (0.51), residues: 94 loop : -1.17 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 301 TYR 0.013 0.001 TYR A 494 PHE 0.008 0.001 PHE A 75 TRP 0.007 0.001 TRP A 572 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9888) covalent geometry : angle 0.53854 (13370) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.77077 ( 4) hydrogen bonds : bond 0.03477 ( 494) hydrogen bonds : angle 3.41775 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.390 Fit side-chains REVERT: A 114 GLU cc_start: 0.7790 (tm-30) cc_final: 0.6970 (tm-30) REVERT: A 171 MET cc_start: 0.8492 (mtp) cc_final: 0.7937 (mmm) REVERT: A 272 LYS cc_start: 0.7568 (ttpt) cc_final: 0.7168 (mtpp) REVERT: A 307 ARG cc_start: 0.7959 (ptp-170) cc_final: 0.7697 (ptp-170) REVERT: A 452 MET cc_start: 0.8090 (tpt) cc_final: 0.7815 (mmp) REVERT: A 511 MET cc_start: 0.8621 (mtm) cc_final: 0.7906 (mmt) REVERT: A 554 GLU cc_start: 0.8483 (tp30) cc_final: 0.8241 (mm-30) REVERT: A 680 MET cc_start: 0.5999 (mtp) cc_final: 0.5631 (ptt) REVERT: B 114 GLU cc_start: 0.7834 (tm-30) cc_final: 0.6998 (tm-30) REVERT: B 171 MET cc_start: 0.8472 (mtp) cc_final: 0.7928 (mmm) REVERT: B 272 LYS cc_start: 0.7544 (ttpt) cc_final: 0.7137 (mtpp) REVERT: B 307 ARG cc_start: 0.7981 (ptp-170) cc_final: 0.7719 (ptp-170) REVERT: B 452 MET cc_start: 0.8081 (tpt) cc_final: 0.7805 (mmp) REVERT: B 511 MET cc_start: 0.8628 (mtm) cc_final: 0.7913 (mmt) REVERT: B 554 GLU cc_start: 0.8462 (tp30) cc_final: 0.8120 (mm-30) REVERT: B 680 MET cc_start: 0.5966 (mtp) cc_final: 0.5599 (ptt) outliers start: 26 outliers final: 12 residues processed: 136 average time/residue: 0.6470 time to fit residues: 93.9068 Evaluate side-chains 128 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 502 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 528 HIS A 617 GLN B 81 ASN B 528 HIS B 617 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.172967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.105455 restraints weight = 9282.006| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.24 r_work: 0.2863 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9890 Z= 0.144 Angle : 0.585 13.160 13374 Z= 0.292 Chirality : 0.043 0.141 1544 Planarity : 0.004 0.035 1668 Dihedral : 5.238 28.968 1364 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.65 % Allowed : 16.95 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1212 helix: 1.51 (0.20), residues: 706 sheet: 0.75 (0.50), residues: 94 loop : -1.16 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 649 TYR 0.017 0.002 TYR B 494 PHE 0.011 0.001 PHE B 75 TRP 0.005 0.001 TRP A 621 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9888) covalent geometry : angle 0.58494 (13370) SS BOND : bond 0.00002 ( 2) SS BOND : angle 0.67947 ( 4) hydrogen bonds : bond 0.04475 ( 494) hydrogen bonds : angle 3.53238 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.415 Fit side-chains REVERT: A 114 GLU cc_start: 0.7843 (tm-30) cc_final: 0.6998 (tm-30) REVERT: A 141 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6757 (mtt-85) REVERT: A 171 MET cc_start: 0.8528 (mtp) cc_final: 0.7938 (mmm) REVERT: A 236 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: A 272 LYS cc_start: 0.7581 (ttpt) cc_final: 0.7239 (mtpp) REVERT: A 307 ARG cc_start: 0.7927 (ptp-170) cc_final: 0.7664 (ptp-170) REVERT: A 389 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8211 (mmtm) REVERT: A 511 MET cc_start: 0.8742 (mtm) cc_final: 0.7905 (mmt) REVERT: A 680 MET cc_start: 0.5984 (mtp) cc_final: 0.5586 (ptt) REVERT: B 114 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 171 MET cc_start: 0.8565 (mtp) cc_final: 0.7915 (mmm) REVERT: B 236 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: B 272 LYS cc_start: 0.7549 (ttpt) cc_final: 0.7142 (mtpp) REVERT: B 307 ARG cc_start: 0.7927 (ptp-170) cc_final: 0.7666 (ptp-170) REVERT: B 511 MET cc_start: 0.8750 (mtm) cc_final: 0.7918 (mmt) REVERT: B 680 MET cc_start: 0.5860 (mtp) cc_final: 0.5577 (ptt) outliers start: 28 outliers final: 16 residues processed: 139 average time/residue: 0.6959 time to fit residues: 102.5920 Evaluate side-chains 130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 0 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.0270 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS A 617 GLN B 81 ASN B 528 HIS B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.173150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102810 restraints weight = 9193.111| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.38 r_work: 0.2829 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9890 Z= 0.137 Angle : 0.576 13.180 13374 Z= 0.290 Chirality : 0.043 0.139 1544 Planarity : 0.004 0.035 1668 Dihedral : 5.226 29.072 1364 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.27 % Allowed : 17.42 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1212 helix: 1.52 (0.20), residues: 706 sheet: 0.36 (0.53), residues: 78 loop : -1.07 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 649 TYR 0.018 0.002 TYR B 494 PHE 0.010 0.001 PHE B 75 TRP 0.006 0.001 TRP A 549 HIS 0.003 0.001 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9888) covalent geometry : angle 0.57559 (13370) SS BOND : bond 0.00001 ( 2) SS BOND : angle 0.72405 ( 4) hydrogen bonds : bond 0.04322 ( 494) hydrogen bonds : angle 3.51450 ( 1452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.306 Fit side-chains REVERT: A 114 GLU cc_start: 0.7820 (tm-30) cc_final: 0.6947 (tm-30) REVERT: A 141 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6741 (mtt180) REVERT: A 171 MET cc_start: 0.8553 (mtp) cc_final: 0.7893 (mmm) REVERT: A 272 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7238 (mtpp) REVERT: A 307 ARG cc_start: 0.7909 (ptp-170) cc_final: 0.7650 (ptp-170) REVERT: A 389 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8165 (mmtm) REVERT: A 511 MET cc_start: 0.8727 (mtm) cc_final: 0.7983 (mmt) REVERT: A 680 MET cc_start: 0.5968 (mtp) cc_final: 0.5551 (ptt) REVERT: B 114 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7024 (tm-30) REVERT: B 171 MET cc_start: 0.8532 (mtp) cc_final: 0.7876 (mmm) REVERT: B 272 LYS cc_start: 0.7559 (ttpt) cc_final: 0.7145 (mtpp) REVERT: B 307 ARG cc_start: 0.7914 (ptp-170) cc_final: 0.7656 (ptp-170) REVERT: B 389 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8180 (mmtm) REVERT: B 511 MET cc_start: 0.8736 (mtm) cc_final: 0.7995 (mmt) REVERT: B 680 MET cc_start: 0.5952 (mtp) cc_final: 0.5516 (ptt) outliers start: 24 outliers final: 17 residues processed: 132 average time/residue: 0.5885 time to fit residues: 82.7113 Evaluate side-chains 131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 1 optimal weight: 0.0970 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 528 HIS A 617 GLN B 528 HIS B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.174437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.106744 restraints weight = 9237.169| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.29 r_work: 0.2840 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9890 Z= 0.117 Angle : 0.560 13.286 13374 Z= 0.281 Chirality : 0.042 0.131 1544 Planarity : 0.004 0.035 1668 Dihedral : 5.102 28.526 1364 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.89 % Allowed : 17.71 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1212 helix: 1.71 (0.20), residues: 700 sheet: 0.76 (0.50), residues: 94 loop : -1.03 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 649 TYR 0.016 0.001 TYR B 494 PHE 0.009 0.001 PHE B 75 TRP 0.006 0.001 TRP A 572 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9888) covalent geometry : angle 0.55967 (13370) SS BOND : bond 0.00000 ( 2) SS BOND : angle 0.72841 ( 4) hydrogen bonds : bond 0.03910 ( 494) hydrogen bonds : angle 3.42806 ( 1452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.302 Fit side-chains REVERT: A 114 GLU cc_start: 0.7809 (tm-30) cc_final: 0.6958 (tm-30) REVERT: A 171 MET cc_start: 0.8526 (mtp) cc_final: 0.7906 (mmm) REVERT: A 272 LYS cc_start: 0.7584 (ttpt) cc_final: 0.7163 (mtpp) REVERT: A 307 ARG cc_start: 0.7922 (ptp-170) cc_final: 0.7665 (ptp-170) REVERT: A 389 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8174 (mmtm) REVERT: A 452 MET cc_start: 0.8129 (tpt) cc_final: 0.7857 (mmp) REVERT: A 511 MET cc_start: 0.8671 (mtm) cc_final: 0.7795 (mmt) REVERT: A 554 GLU cc_start: 0.8489 (tp30) cc_final: 0.8191 (mm-30) REVERT: A 680 MET cc_start: 0.5941 (mtp) cc_final: 0.5530 (ptt) REVERT: B 114 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7020 (tm-30) REVERT: B 171 MET cc_start: 0.8506 (mtp) cc_final: 0.7875 (mmm) REVERT: B 272 LYS cc_start: 0.7517 (ttpt) cc_final: 0.7107 (mtpp) REVERT: B 307 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7710 (ptp-170) REVERT: B 389 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8191 (mmtm) REVERT: B 452 MET cc_start: 0.8116 (tpt) cc_final: 0.7841 (mmp) REVERT: B 511 MET cc_start: 0.8688 (mtm) cc_final: 0.7814 (mmt) REVERT: B 554 GLU cc_start: 0.8467 (tp30) cc_final: 0.8171 (mm-30) REVERT: B 680 MET cc_start: 0.5928 (mtp) cc_final: 0.5529 (ptt) outliers start: 20 outliers final: 18 residues processed: 132 average time/residue: 0.5005 time to fit residues: 70.7580 Evaluate side-chains 133 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS A 617 GLN B 81 ASN B 528 HIS B 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.171657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100142 restraints weight = 9283.720| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.15 r_work: 0.2832 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9890 Z= 0.176 Angle : 0.613 13.030 13374 Z= 0.308 Chirality : 0.045 0.148 1544 Planarity : 0.004 0.036 1668 Dihedral : 5.301 29.941 1364 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.08 % Allowed : 17.90 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1212 helix: 1.53 (0.20), residues: 692 sheet: 0.71 (0.49), residues: 94 loop : -1.01 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 649 TYR 0.027 0.002 TYR B 494 PHE 0.012 0.001 PHE B 562 TRP 0.006 0.001 TRP A 549 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 9888) covalent geometry : angle 0.61283 (13370) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.70600 ( 4) hydrogen bonds : bond 0.04896 ( 494) hydrogen bonds : angle 3.58491 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4217.31 seconds wall clock time: 72 minutes 19.59 seconds (4339.59 seconds total)