Starting phenix.real_space_refine on Fri Feb 14 03:12:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtm_37836/02_2025/8wtm_37836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtm_37836/02_2025/8wtm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtm_37836/02_2025/8wtm_37836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtm_37836/02_2025/8wtm_37836.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtm_37836/02_2025/8wtm_37836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtm_37836/02_2025/8wtm_37836.cif" } resolution = 2.65 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= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9680 Number of models: 1 Model: "" Number of chains: 2 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: "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} Restraints were copied for chains: B Time building chain proxies: 8.11, per 1000 atoms: 0.84 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 646 " - pdb=" SG CYS A 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: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.05 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: 2.60 Time building geometry restraints manager: 2.73 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: 440 35.75 - 53.63: 64 53.63 - 71.50: 14 71.50 - 89.38: 8 Dihedral angle restraints: 5881 sinusoidal: 2361 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 5878 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: 2.03 - 2.61: 63 2.61 - 3.18: 7566 3.18 - 3.75: 14582 3.75 - 4.33: 22007 4.33 - 4.90: 34778 Nonbonded interactions: 78996 Sorted by model distance: nonbonded pdb=" SG CYS B 646 " pdb=" SG CYS B 687 " model vdw 2.034 3.760 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 ... (remaining 78991 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: 1.760 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.310 Find NCS groups from input model: 0.330 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:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.450 ------------------------------------------------------------------------------- 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 9888 Z= 0.538 Angle : 0.915 11.417 13370 Z= 0.489 Chirality : 0.055 0.321 1544 Planarity : 0.007 0.066 1668 Dihedral : 13.621 89.378 3610 Min Nonbonded Distance : 2.034 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 (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: -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 TRP 0.009 0.002 TRP B 621 HIS 0.007 0.002 HIS A 248 PHE 0.015 0.002 PHE A 75 TYR 0.011 0.003 TYR A 630 ARG 0.006 0.001 ARG B 507 *********************** 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 : 1.047 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: 0.7275 (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: 0.7809 (ptp-170) cc_final: 0.7467 (ptp90) REVERT: B 342 ASP cc_start: 0.7380 (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: 1.5368 time to fit residues: 260.6356 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 : 1.080 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3919 r_free = 0.3919 target = 0.175174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104762 restraints weight = 9229.667| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.72 r_work: 0.2935 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9888 Z= 0.172 Angle : 0.562 6.211 13370 Z= 0.299 Chirality : 0.041 0.137 1544 Planarity : 0.006 0.073 1668 Dihedral : 6.276 66.168 1366 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.42 % Allowed : 10.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.22), residues: 1212 helix: -1.08 (0.17), residues: 698 sheet: 0.88 (0.54), residues: 82 loop : -1.74 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 572 HIS 0.003 0.001 HIS A 587 PHE 0.012 0.001 PHE A 562 TYR 0.014 0.002 TYR A 494 ARG 0.006 0.001 ARG B 649 *********************** 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 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.972 Fit side-chains REVERT: A 114 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7124 (tm-30) REVERT: A 237 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.7460 (mtp180) REVERT: A 272 LYS cc_start: 0.7631 (ttpt) cc_final: 0.7205 (mtpp) REVERT: A 307 ARG cc_start: 0.8018 (ptp-170) cc_final: 0.7811 (ptp-170) REVERT: A 444 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7508 (ttm-80) REVERT: A 511 MET cc_start: 0.8723 (mtm) cc_final: 0.7996 (mmt) REVERT: A 528 HIS cc_start: 0.8523 (t-90) cc_final: 0.8307 (t-170) REVERT: A 598 ILE cc_start: 0.8433 (mt) cc_final: 0.8199 (tp) REVERT: A 680 MET cc_start: 0.5967 (mtp) cc_final: 0.5580 (ptt) REVERT: B 114 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7107 (tm-30) REVERT: B 237 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7454 (mtp180) REVERT: B 272 LYS cc_start: 0.7613 (ttpt) cc_final: 0.7185 (mtpp) REVERT: B 307 ARG cc_start: 0.7974 (ptp-170) cc_final: 0.7765 (ptp-170) REVERT: B 444 ARG cc_start: 0.7806 (ttm170) cc_final: 0.7495 (ttm-80) REVERT: B 511 MET cc_start: 0.8717 (mtm) cc_final: 0.7994 (mmt) REVERT: B 528 HIS cc_start: 0.8544 (t-90) cc_final: 0.8343 (t-170) REVERT: B 598 ILE cc_start: 0.8434 (mt) cc_final: 0.8205 (tp) outliers start: 15 outliers final: 1 residues processed: 144 average time/residue: 1.2987 time to fit residues: 200.2153 Evaluate side-chains 111 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.5704 ------------------------------------------------------------------------------- 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 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.172806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.107392 restraints weight = 9300.346| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.21 r_work: 0.2872 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9888 Z= 0.260 Angle : 0.590 8.049 13370 Z= 0.306 Chirality : 0.044 0.149 1544 Planarity : 0.005 0.066 1668 Dihedral : 6.029 60.934 1364 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.03 % Allowed : 12.97 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1212 helix: 0.43 (0.19), residues: 686 sheet: 0.55 (0.53), residues: 94 loop : -1.54 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 621 HIS 0.004 0.001 HIS A 587 PHE 0.013 0.001 PHE B 562 TYR 0.014 0.002 TYR B 494 ARG 0.006 0.000 ARG B 301 *********************** 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 154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.032 Fit side-chains REVERT: A 114 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7179 (tm-30) REVERT: A 236 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 237 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7599 (mtp-110) REVERT: A 260 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8112 (p) REVERT: A 272 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7231 (mtpp) REVERT: A 307 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7735 (ptp-170) REVERT: A 428 PHE cc_start: 0.8024 (t80) cc_final: 0.7782 (t80) REVERT: A 511 MET cc_start: 0.8804 (mtm) cc_final: 0.8071 (mmt) REVERT: A 528 HIS cc_start: 0.8601 (t-90) cc_final: 0.8377 (t-170) REVERT: A 598 ILE cc_start: 0.8554 (mt) cc_final: 0.8297 (tp) REVERT: A 680 MET cc_start: 0.5973 (mtp) cc_final: 0.5584 (ptt) REVERT: B 114 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 236 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: B 237 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7630 (mtp-110) REVERT: B 260 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8111 (p) REVERT: B 272 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7226 (mtpp) REVERT: B 307 ARG cc_start: 0.7958 (ptp-170) cc_final: 0.7723 (ptp-170) REVERT: B 428 PHE cc_start: 0.8020 (t80) cc_final: 0.7809 (t80) REVERT: B 511 MET cc_start: 0.8778 (mtm) cc_final: 0.8056 (mmt) REVERT: B 528 HIS cc_start: 0.8580 (t-90) cc_final: 0.8380 (t-170) REVERT: B 598 ILE cc_start: 0.8553 (mt) cc_final: 0.8307 (tp) REVERT: B 680 MET cc_start: 0.5965 (mtp) cc_final: 0.5563 (ptt) outliers start: 32 outliers final: 15 residues processed: 143 average time/residue: 1.3848 time to fit residues: 211.0723 Evaluate side-chains 134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 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 60 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102580 restraints weight = 9212.168| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.04 r_work: 0.2847 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9888 Z= 0.310 Angle : 0.615 9.653 13370 Z= 0.316 Chirality : 0.046 0.152 1544 Planarity : 0.004 0.054 1668 Dihedral : 5.946 54.484 1364 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.98 % Allowed : 13.64 % Favored : 82.39 % 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: 0.04 (0.24), residues: 1212 helix: 0.83 (0.20), residues: 688 sheet: 0.58 (0.53), residues: 94 loop : -1.39 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 621 HIS 0.004 0.001 HIS A 587 PHE 0.014 0.002 PHE B 562 TYR 0.016 0.002 TYR B 601 ARG 0.006 0.000 ARG A 301 *********************** 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 172 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.160 Fit side-chains REVERT: A 114 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7122 (tm-30) REVERT: A 218 ASN cc_start: 0.7252 (p0) cc_final: 0.6770 (p0) REVERT: A 237 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7604 (mtp-110) REVERT: A 260 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 272 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7262 (mtpp) REVERT: A 307 ARG cc_start: 0.8009 (ptp-170) cc_final: 0.7788 (ptp-170) REVERT: A 511 MET cc_start: 0.8863 (mtm) cc_final: 0.8109 (mmt) REVERT: A 528 HIS cc_start: 0.8595 (t-90) cc_final: 0.8369 (t-170) REVERT: A 598 ILE cc_start: 0.8579 (mt) cc_final: 0.8307 (tp) REVERT: A 680 MET cc_start: 0.6074 (mtp) cc_final: 0.5666 (ptt) REVERT: B 114 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: B 218 ASN cc_start: 0.7234 (p0) cc_final: 0.6756 (p0) REVERT: B 237 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7619 (mtp180) REVERT: B 260 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8095 (p) REVERT: B 272 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7257 (mtpp) REVERT: B 307 ARG cc_start: 0.7991 (ptp-170) cc_final: 0.7772 (ptp-170) REVERT: B 511 MET cc_start: 0.8856 (mtm) cc_final: 0.8107 (mmt) REVERT: B 528 HIS cc_start: 0.8596 (t-90) cc_final: 0.8371 (t-170) REVERT: B 598 ILE cc_start: 0.8574 (mt) cc_final: 0.8304 (tp) REVERT: B 680 MET cc_start: 0.6074 (mtp) cc_final: 0.5664 (ptt) outliers start: 42 outliers final: 18 residues processed: 162 average time/residue: 1.3151 time to fit residues: 228.0304 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 : 1.055 ------------------------------------------------------------------------------- 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 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 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 50 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 0.0070 chunk 120 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.9202 ------------------------------------------------------------------------------- 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 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.174178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107038 restraints weight = 9168.843| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.19 r_work: 0.2890 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9888 Z= 0.177 Angle : 0.550 10.802 13370 Z= 0.279 Chirality : 0.042 0.132 1544 Planarity : 0.004 0.042 1668 Dihedral : 5.461 41.564 1364 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.88 % Allowed : 13.54 % Favored : 82.58 % 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: 0.58 (0.25), residues: 1212 helix: 1.34 (0.20), residues: 690 sheet: 0.74 (0.52), residues: 94 loop : -1.28 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 572 HIS 0.003 0.001 HIS A 587 PHE 0.009 0.001 PHE A 562 TYR 0.011 0.001 TYR B 630 ARG 0.007 0.000 ARG B 649 *********************** 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 162 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.103 Fit side-chains REVERT: A 114 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7043 (tm-30) REVERT: A 171 MET cc_start: 0.8559 (mtp) cc_final: 0.7942 (mmm) REVERT: A 236 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: A 237 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7589 (mtp180) REVERT: A 272 LYS cc_start: 0.7558 (ttpt) cc_final: 0.7153 (mtpp) REVERT: A 307 ARG cc_start: 0.7953 (ptp-170) cc_final: 0.7705 (ptp-170) REVERT: A 511 MET cc_start: 0.8719 (mtm) cc_final: 0.7958 (mmt) REVERT: A 642 ASP cc_start: 0.6931 (m-30) cc_final: 0.6730 (t0) REVERT: A 680 MET cc_start: 0.6030 (mtp) cc_final: 0.5641 (ptt) REVERT: B 114 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: B 171 MET cc_start: 0.8554 (mtp) cc_final: 0.7935 (mmm) REVERT: B 236 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: B 237 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7605 (mtp180) REVERT: B 272 LYS cc_start: 0.7552 (ttpt) cc_final: 0.7143 (mtpp) REVERT: B 307 ARG cc_start: 0.7950 (ptp-170) cc_final: 0.7703 (ptp-170) REVERT: B 511 MET cc_start: 0.8721 (mtm) cc_final: 0.7962 (mmt) REVERT: B 642 ASP cc_start: 0.6967 (m-30) cc_final: 0.6759 (t0) REVERT: B 680 MET cc_start: 0.6020 (mtp) cc_final: 0.5642 (ptt) outliers start: 41 outliers final: 18 residues processed: 151 average time/residue: 1.3292 time to fit residues: 214.6990 Evaluate side-chains 131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 236 GLU 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 165 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.170584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098824 restraints weight = 9330.307| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.17 r_work: 0.2804 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9888 Z= 0.338 Angle : 0.638 11.474 13370 Z= 0.323 Chirality : 0.047 0.155 1544 Planarity : 0.004 0.041 1668 Dihedral : 5.629 33.428 1364 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.41 % Allowed : 14.49 % Favored : 82.10 % 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 (0.24), residues: 1212 helix: 1.15 (0.20), residues: 698 sheet: 0.15 (0.53), residues: 78 loop : -1.33 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 621 HIS 0.004 0.001 HIS A 248 PHE 0.014 0.002 PHE A 562 TYR 0.019 0.002 TYR A 601 ARG 0.007 0.001 ARG A 649 *********************** 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 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 218 ASN cc_start: 0.7250 (p0) cc_final: 0.6753 (p0) REVERT: A 237 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7544 (mtp180) REVERT: A 272 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7242 (mtpp) REVERT: A 307 ARG cc_start: 0.7984 (ptp-170) cc_final: 0.7748 (ptp-170) REVERT: A 342 ASP cc_start: 0.7298 (t0) cc_final: 0.7019 (t0) REVERT: A 511 MET cc_start: 0.8827 (mtm) cc_final: 0.7979 (mmt) REVERT: A 642 ASP cc_start: 0.6935 (m-30) cc_final: 0.6729 (t0) REVERT: A 680 MET cc_start: 0.6037 (mtp) cc_final: 0.5615 (ptt) REVERT: B 114 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: B 218 ASN cc_start: 0.7244 (p0) cc_final: 0.6739 (p0) REVERT: B 237 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7564 (mtp180) REVERT: B 272 LYS cc_start: 0.7652 (ttpt) cc_final: 0.7242 (mtpp) REVERT: B 307 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7738 (ptp-170) REVERT: B 342 ASP cc_start: 0.7297 (t0) cc_final: 0.7018 (t0) REVERT: B 511 MET cc_start: 0.8819 (mtm) cc_final: 0.7975 (mmt) REVERT: B 680 MET cc_start: 0.6037 (mtp) cc_final: 0.5631 (ptt) outliers start: 36 outliers final: 22 residues processed: 143 average time/residue: 1.3731 time to fit residues: 209.9513 Evaluate side-chains 138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 264 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 454 LEU 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 718 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 35 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.173687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.105080 restraints weight = 9346.193| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.06 r_work: 0.2881 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9888 Z= 0.184 Angle : 0.563 12.344 13370 Z= 0.284 Chirality : 0.042 0.131 1544 Planarity : 0.004 0.035 1668 Dihedral : 5.344 28.923 1364 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.41 % Allowed : 15.15 % Favored : 81.44 % 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: 0.79 (0.25), residues: 1212 helix: 1.49 (0.20), residues: 696 sheet: 0.76 (0.51), residues: 94 loop : -1.19 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 572 HIS 0.003 0.001 HIS A 289 PHE 0.010 0.001 PHE A 562 TYR 0.010 0.001 TYR A 630 ARG 0.007 0.000 ARG B 301 *********************** 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 154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.031 Fit side-chains REVERT: A 114 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7014 (tm-30) REVERT: A 171 MET cc_start: 0.8497 (mtp) cc_final: 0.7914 (mmm) REVERT: A 236 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: A 272 LYS cc_start: 0.7537 (ttpt) cc_final: 0.7113 (mtpp) REVERT: A 307 ARG cc_start: 0.7937 (ptp-170) cc_final: 0.7680 (ptp-170) REVERT: A 511 MET cc_start: 0.8705 (mtm) cc_final: 0.7953 (mmt) REVERT: A 680 MET cc_start: 0.5889 (mtp) cc_final: 0.5590 (ptt) REVERT: B 114 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: B 171 MET cc_start: 0.8492 (mtp) cc_final: 0.7908 (mmm) REVERT: B 236 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: B 272 LYS cc_start: 0.7532 (ttpt) cc_final: 0.7113 (mtpp) REVERT: B 307 ARG cc_start: 0.7935 (ptp-170) cc_final: 0.7679 (ptp-170) REVERT: B 511 MET cc_start: 0.8710 (mtm) cc_final: 0.7963 (mmt) REVERT: B 642 ASP cc_start: 0.6958 (m-30) cc_final: 0.6754 (t0) REVERT: B 680 MET cc_start: 0.5881 (mtp) cc_final: 0.5604 (ptt) outliers start: 36 outliers final: 20 residues processed: 143 average time/residue: 1.3475 time to fit residues: 205.6089 Evaluate side-chains 134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.174787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108200 restraints weight = 9374.499| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.31 r_work: 0.2882 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9888 Z= 0.160 Angle : 0.550 13.158 13370 Z= 0.276 Chirality : 0.041 0.130 1544 Planarity : 0.004 0.034 1668 Dihedral : 5.111 27.938 1364 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.84 % Allowed : 16.29 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1212 helix: 1.68 (0.20), residues: 706 sheet: 0.85 (0.51), residues: 94 loop : -1.19 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 572 HIS 0.003 0.001 HIS A 289 PHE 0.009 0.001 PHE B 75 TYR 0.014 0.001 TYR A 494 ARG 0.007 0.000 ARG B 301 *********************** 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 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.060 Fit side-chains REVERT: A 114 GLU cc_start: 0.7789 (tm-30) cc_final: 0.6958 (tm-30) REVERT: A 171 MET cc_start: 0.8487 (mtp) cc_final: 0.7874 (mmm) REVERT: A 236 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 272 LYS cc_start: 0.7498 (ttpt) cc_final: 0.7094 (mtpp) REVERT: A 307 ARG cc_start: 0.7922 (ptp-170) cc_final: 0.7667 (ptp-170) REVERT: A 389 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8201 (mmtm) REVERT: A 511 MET cc_start: 0.8621 (mtm) cc_final: 0.7864 (mmt) REVERT: A 554 GLU cc_start: 0.8461 (tp30) cc_final: 0.8160 (mm-30) REVERT: A 680 MET cc_start: 0.5988 (mtp) cc_final: 0.5619 (ptt) REVERT: B 114 GLU cc_start: 0.7822 (tm-30) cc_final: 0.6977 (tm-30) REVERT: B 171 MET cc_start: 0.8481 (mtp) cc_final: 0.7882 (mmm) REVERT: B 236 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: B 272 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7078 (mtpp) REVERT: B 307 ARG cc_start: 0.7924 (ptp-170) cc_final: 0.7680 (ptp-170) REVERT: B 389 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8222 (mmtm) REVERT: B 511 MET cc_start: 0.8631 (mtm) cc_final: 0.7878 (mmt) REVERT: B 554 GLU cc_start: 0.8454 (tp30) cc_final: 0.8115 (mm-30) REVERT: B 680 MET cc_start: 0.5936 (mtp) cc_final: 0.5566 (ptt) outliers start: 30 outliers final: 16 residues processed: 144 average time/residue: 1.3225 time to fit residues: 203.5681 Evaluate side-chains 135 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 321 SER 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 182 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 69 optimal weight: 0.0270 chunk 120 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.175608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109083 restraints weight = 9237.650| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.20 r_work: 0.2892 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9888 Z= 0.148 Angle : 0.539 13.434 13370 Z= 0.271 Chirality : 0.041 0.129 1544 Planarity : 0.004 0.034 1668 Dihedral : 4.981 27.261 1364 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.27 % Allowed : 17.05 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1212 helix: 1.96 (0.21), residues: 694 sheet: 0.83 (0.50), residues: 94 loop : -1.10 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 572 HIS 0.003 0.001 HIS B 289 PHE 0.008 0.001 PHE B 75 TYR 0.022 0.001 TYR A 494 ARG 0.007 0.000 ARG B 301 *********************** 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 144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.034 Fit side-chains REVERT: A 114 GLU cc_start: 0.7776 (tm-30) cc_final: 0.6971 (tm-30) REVERT: A 171 MET cc_start: 0.8448 (mtp) cc_final: 0.7854 (mmm) REVERT: A 236 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: A 272 LYS cc_start: 0.7490 (ttpt) cc_final: 0.7091 (mtpp) REVERT: A 307 ARG cc_start: 0.7902 (ptp-170) cc_final: 0.7658 (ptp-170) REVERT: A 389 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8152 (mmtm) REVERT: A 511 MET cc_start: 0.8595 (mtm) cc_final: 0.7853 (mmt) REVERT: A 554 GLU cc_start: 0.8407 (tp30) cc_final: 0.8108 (mm-30) REVERT: A 680 MET cc_start: 0.6005 (mtp) cc_final: 0.5658 (ptt) REVERT: B 114 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7005 (tm-30) REVERT: B 236 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: B 272 LYS cc_start: 0.7474 (ttpt) cc_final: 0.7076 (mtpp) REVERT: B 307 ARG cc_start: 0.7923 (ptp-170) cc_final: 0.7679 (ptp-170) REVERT: B 389 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8191 (mmtm) REVERT: B 511 MET cc_start: 0.8608 (mtm) cc_final: 0.7842 (mmt) REVERT: B 554 GLU cc_start: 0.8431 (tp30) cc_final: 0.8127 (mm-30) REVERT: B 680 MET cc_start: 0.5957 (mtp) cc_final: 0.5635 (ptt) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 1.3636 time to fit residues: 195.1774 Evaluate side-chains 129 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 321 SER 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 182 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.172153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100930 restraints weight = 9342.694| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.19 r_work: 0.2833 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9888 Z= 0.253 Angle : 0.599 13.003 13370 Z= 0.302 Chirality : 0.044 0.145 1544 Planarity : 0.004 0.034 1668 Dihedral : 5.219 29.235 1364 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.18 % Allowed : 17.33 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1212 helix: 1.62 (0.20), residues: 700 sheet: 0.60 (0.51), residues: 96 loop : -0.97 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 549 HIS 0.004 0.001 HIS B 587 PHE 0.012 0.001 PHE B 75 TYR 0.025 0.002 TYR A 494 ARG 0.007 0.000 ARG B 301 ********************** 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 139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.133 Fit side-chains REVERT: A 114 GLU cc_start: 0.7865 (tm-30) cc_final: 0.6987 (tm-30) REVERT: A 171 MET cc_start: 0.8489 (mtp) cc_final: 0.7890 (mmm) REVERT: A 218 ASN cc_start: 0.7268 (p0) cc_final: 0.6521 (p0) REVERT: A 236 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: A 272 LYS cc_start: 0.7582 (ttpt) cc_final: 0.7180 (mtpp) REVERT: A 307 ARG cc_start: 0.7911 (ptp-170) cc_final: 0.7650 (ptp-170) REVERT: A 389 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8133 (mmtm) REVERT: A 511 MET cc_start: 0.8791 (mtm) cc_final: 0.8043 (mmt) REVERT: A 554 GLU cc_start: 0.8516 (tp30) cc_final: 0.8231 (mm-30) REVERT: A 680 MET cc_start: 0.5902 (mtp) cc_final: 0.5527 (ptt) REVERT: B 114 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: B 218 ASN cc_start: 0.7252 (p0) cc_final: 0.6567 (p0) REVERT: B 236 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: B 272 LYS cc_start: 0.7580 (ttpt) cc_final: 0.7177 (mtpp) REVERT: B 307 ARG cc_start: 0.7911 (ptp-170) cc_final: 0.7652 (ptp-170) REVERT: B 389 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8200 (mmtm) REVERT: B 511 MET cc_start: 0.8798 (mtm) cc_final: 0.8057 (mmt) REVERT: B 680 MET cc_start: 0.5814 (mtp) cc_final: 0.5487 (ptt) outliers start: 23 outliers final: 18 residues processed: 130 average time/residue: 1.3288 time to fit residues: 184.8511 Evaluate side-chains 134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 165 VAL Chi-restraints excluded: chain B residue 182 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 88 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 0.0050 overall best weight: 1.1598 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.173125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.101994 restraints weight = 9234.031| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.21 r_work: 0.2848 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9888 Z= 0.207 Angle : 0.576 13.273 13370 Z= 0.290 Chirality : 0.043 0.137 1544 Planarity : 0.004 0.034 1668 Dihedral : 5.218 28.709 1364 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.08 % Allowed : 17.80 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1212 helix: 1.69 (0.20), residues: 698 sheet: 0.62 (0.51), residues: 96 loop : -0.92 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 549 HIS 0.003 0.001 HIS B 587 PHE 0.010 0.001 PHE B 75 TYR 0.022 0.002 TYR A 494 ARG 0.008 0.000 ARG B 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8936.42 seconds wall clock time: 157 minutes 58.92 seconds (9478.92 seconds total)