Starting phenix.real_space_refine on Sun Jun 8 15:16:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtm_37836/06_2025/8wtm_37836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtm_37836/06_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_37836/06_2025/8wtm_37836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtm_37836/06_2025/8wtm_37836.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtm_37836/06_2025/8wtm_37836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtm_37836/06_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-5710/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: 9.55, per 1000 atoms: 0.99 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 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: 1.19 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: 2.87 Time building geometry restraints manager: 2.76 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: 1.850 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.450 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.29568 ( 494) hydrogen bonds : angle 9.18213 ( 1452) SS BOND : bond 0.00324 ( 2) SS BOND : angle 1.24976 ( 4) covalent geometry : bond 0.00820 ( 9888) covalent geometry : angle 0.91524 (13370) *********************** 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 : 1.030 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: 1.5314 time to fit residues: 259.4702 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 : 1.180 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.174381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104487 restraints weight = 9238.812| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.70 r_work: 0.2924 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1672 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= 0.123 Angle : 0.570 6.457 13374 Z= 0.304 Chirality : 0.041 0.138 1544 Planarity : 0.006 0.076 1668 Dihedral : 6.310 67.030 1366 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.23 % Allowed : 11.36 % Favored : 87.41 % 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: -1.07 (0.17), residues: 698 sheet: 0.88 (0.54), residues: 82 loop : -1.75 (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 B 562 TYR 0.013 0.002 TYR A 494 ARG 0.006 0.001 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.05124 ( 494) hydrogen bonds : angle 4.21570 ( 1452) SS BOND : bond 0.00034 ( 2) SS BOND : angle 1.12123 ( 4) covalent geometry : bond 0.00273 ( 9888) covalent geometry : angle 0.56933 (13370) *********************** 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 : 1.152 Fit side-chains REVERT: A 114 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7083 (tm-30) REVERT: A 237 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7471 (mtp180) REVERT: A 272 LYS cc_start: 0.7640 (ttpt) cc_final: 0.7211 (mtpp) REVERT: A 444 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7514 (ttm-80) REVERT: A 511 MET cc_start: 0.8760 (mtm) cc_final: 0.8031 (mmt) REVERT: A 528 HIS cc_start: 0.8526 (t-90) cc_final: 0.8319 (t-170) REVERT: A 598 ILE cc_start: 0.8453 (mt) cc_final: 0.8207 (tp) REVERT: B 114 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7048 (tm-30) REVERT: B 237 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7460 (mtp180) REVERT: B 272 LYS cc_start: 0.7605 (ttpt) cc_final: 0.7180 (mtpp) REVERT: B 338 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6213 (tm-30) REVERT: B 444 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7499 (ttm-80) REVERT: B 511 MET cc_start: 0.8761 (mtm) cc_final: 0.8030 (mmt) REVERT: B 528 HIS cc_start: 0.8532 (t-90) cc_final: 0.8324 (t-170) REVERT: B 598 ILE cc_start: 0.8452 (mt) cc_final: 0.8211 (tp) outliers start: 13 outliers final: 1 residues processed: 142 average time/residue: 1.2971 time to fit residues: 197.4952 Evaluate side-chains 113 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE 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 49 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 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 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 = 0.3891 r_free = 0.3891 target = 0.172885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105154 restraints weight = 9306.711| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.20 r_work: 0.2848 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9890 Z= 0.163 Angle : 0.584 8.159 13374 Z= 0.302 Chirality : 0.043 0.147 1544 Planarity : 0.005 0.065 1668 Dihedral : 6.047 61.809 1364 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.22 % Allowed : 13.16 % Favored : 83.62 % 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: -0.42 (0.24), residues: 1212 helix: 0.42 (0.19), residues: 686 sheet: 0.57 (0.54), residues: 94 loop : -1.55 (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 0.013 0.002 TYR B 494 ARG 0.004 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.05266 ( 494) hydrogen bonds : angle 3.88413 ( 1452) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.80108 ( 4) covalent geometry : bond 0.00396 ( 9888) covalent geometry : angle 0.58342 (13370) *********************** 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 156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.065 Fit side-chains REVERT: A 114 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 236 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 237 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7633 (mtp-110) REVERT: A 260 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.8074 (p) REVERT: A 272 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7254 (mtpp) REVERT: A 428 PHE cc_start: 0.8024 (t80) cc_final: 0.7788 (t80) REVERT: A 511 MET cc_start: 0.8801 (mtm) cc_final: 0.8076 (mmt) REVERT: A 528 HIS cc_start: 0.8589 (t-90) cc_final: 0.8387 (t-170) REVERT: A 598 ILE cc_start: 0.8560 (mt) cc_final: 0.8319 (tp) REVERT: A 680 MET cc_start: 0.5970 (mtp) cc_final: 0.5568 (ptt) REVERT: B 114 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: B 236 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: B 237 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7644 (mtp-110) REVERT: B 260 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 272 LYS cc_start: 0.7656 (ttpt) cc_final: 0.7246 (mtpp) REVERT: B 428 PHE cc_start: 0.8024 (t80) cc_final: 0.7788 (t80) REVERT: B 511 MET cc_start: 0.8812 (mtm) cc_final: 0.8083 (mmt) REVERT: B 598 ILE cc_start: 0.8559 (mt) cc_final: 0.8318 (tp) REVERT: B 680 MET cc_start: 0.5967 (mtp) cc_final: 0.5550 (ptt) outliers start: 34 outliers final: 15 residues processed: 144 average time/residue: 1.3752 time to fit residues: 211.1520 Evaluate side-chains 139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 6 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.170239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.098684 restraints weight = 9237.647| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.13 r_work: 0.2808 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9890 Z= 0.227 Angle : 0.651 9.905 13374 Z= 0.333 Chirality : 0.047 0.158 1544 Planarity : 0.005 0.057 1668 Dihedral : 6.095 57.013 1364 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.26 % Allowed : 13.54 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1212 helix: 0.68 (0.19), residues: 696 sheet: 0.57 (0.53), residues: 94 loop : -1.65 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 621 HIS 0.005 0.002 HIS B 248 PHE 0.015 0.002 PHE B 562 TYR 0.021 0.002 TYR A 601 ARG 0.006 0.001 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.05798 ( 494) hydrogen bonds : angle 3.90228 ( 1452) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.71008 ( 4) covalent geometry : bond 0.00566 ( 9888) covalent geometry : angle 0.65144 (13370) *********************** 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 174 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 1.137 Fit side-chains REVERT: A 114 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 218 ASN cc_start: 0.7232 (p0) cc_final: 0.6587 (p0) REVERT: A 236 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: A 237 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7595 (mtp180) REVERT: A 260 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 272 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7252 (mtpp) REVERT: A 342 ASP cc_start: 0.7361 (t0) cc_final: 0.7053 (t0) REVERT: A 511 MET cc_start: 0.8883 (mtm) cc_final: 0.8015 (mmt) REVERT: A 528 HIS cc_start: 0.8597 (t-90) cc_final: 0.8362 (t-170) REVERT: A 598 ILE cc_start: 0.8550 (mt) cc_final: 0.8300 (tp) REVERT: B 114 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: B 218 ASN cc_start: 0.7233 (p0) cc_final: 0.6586 (p0) REVERT: B 236 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: B 237 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7612 (mtp180) REVERT: B 260 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.8084 (p) REVERT: B 272 LYS cc_start: 0.7689 (ttpt) cc_final: 0.7251 (mtpp) REVERT: B 342 ASP cc_start: 0.7383 (t0) cc_final: 0.7074 (t0) REVERT: B 511 MET cc_start: 0.8867 (mtm) cc_final: 0.8008 (mmt) REVERT: B 598 ILE cc_start: 0.8541 (mt) cc_final: 0.8294 (tp) outliers start: 45 outliers final: 18 residues processed: 161 average time/residue: 1.2540 time to fit residues: 216.3156 Evaluate side-chains 145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 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: 0.0060 chunk 120 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.175272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.105092 restraints weight = 9178.996| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.36 r_work: 0.2846 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9890 Z= 0.107 Angle : 0.534 11.502 13374 Z= 0.273 Chirality : 0.041 0.130 1544 Planarity : 0.004 0.042 1668 Dihedral : 5.432 42.431 1364 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.94 % Allowed : 15.81 % Favored : 81.25 % 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: 0.64 (0.25), residues: 1212 helix: 1.39 (0.20), residues: 690 sheet: 0.76 (0.52), residues: 94 loop : -1.27 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 572 HIS 0.003 0.001 HIS A 587 PHE 0.008 0.001 PHE A 75 TYR 0.009 0.001 TYR A 630 ARG 0.007 0.000 ARG A 649 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 494) hydrogen bonds : angle 3.51799 ( 1452) SS BOND : bond 0.00002 ( 2) SS BOND : angle 1.19389 ( 4) covalent geometry : bond 0.00241 ( 9888) covalent geometry : angle 0.53411 (13370) *********************** 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 156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.159 Fit side-chains REVERT: A 114 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7001 (tm-30) REVERT: A 171 MET cc_start: 0.8488 (mtp) cc_final: 0.7932 (mmm) REVERT: A 237 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7574 (mtp180) REVERT: A 272 LYS cc_start: 0.7556 (ttpt) cc_final: 0.7148 (mtpp) REVERT: A 307 ARG cc_start: 0.7938 (ptp-170) cc_final: 0.7727 (ptp-170) REVERT: A 452 MET cc_start: 0.8100 (tpt) cc_final: 0.7820 (mmp) REVERT: A 511 MET cc_start: 0.8675 (mtm) cc_final: 0.7939 (mmt) REVERT: A 554 GLU cc_start: 0.8496 (tp30) cc_final: 0.8169 (mm-30) REVERT: A 680 MET cc_start: 0.5993 (mtp) cc_final: 0.5610 (ptt) REVERT: B 114 GLU cc_start: 0.7811 (tm-30) cc_final: 0.6999 (tm-30) REVERT: B 141 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6706 (mtt180) REVERT: B 171 MET cc_start: 0.8483 (mtp) cc_final: 0.7950 (mmt) REVERT: B 237 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7600 (mtp180) REVERT: B 272 LYS cc_start: 0.7525 (ttpt) cc_final: 0.7120 (mtpp) REVERT: B 452 MET cc_start: 0.8101 (tpt) cc_final: 0.7819 (mmp) REVERT: B 511 MET cc_start: 0.8683 (mtm) cc_final: 0.7944 (mmt) REVERT: B 680 MET cc_start: 0.5998 (mtp) cc_final: 0.5602 (ptt) outliers start: 31 outliers final: 14 residues processed: 144 average time/residue: 1.3185 time to fit residues: 202.7469 Evaluate side-chains 127 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 264 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 141 ARG Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 502 VAL 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: 0.0270 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.170970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102691 restraints weight = 9318.701| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.10 r_work: 0.2821 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9890 Z= 0.194 Angle : 0.621 12.317 13374 Z= 0.314 Chirality : 0.046 0.151 1544 Planarity : 0.004 0.040 1668 Dihedral : 5.578 33.734 1364 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.79 % Allowed : 15.25 % 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 (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: 0.43 (0.25), residues: 1212 helix: 1.22 (0.20), residues: 698 sheet: 0.63 (0.51), residues: 94 loop : -1.38 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 621 HIS 0.004 0.002 HIS B 587 PHE 0.013 0.002 PHE A 562 TYR 0.017 0.002 TYR A 601 ARG 0.007 0.000 ARG A 649 Details of bonding type rmsd hydrogen bonds : bond 0.05222 ( 494) hydrogen bonds : angle 3.68937 ( 1452) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.79254 ( 4) covalent geometry : bond 0.00482 ( 9888) covalent geometry : angle 0.62093 (13370) *********************** 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: 40 poor density : 120 time to evaluate : 1.197 Fit side-chains REVERT: A 114 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7090 (tm-30) REVERT: A 218 ASN cc_start: 0.7302 (p0) cc_final: 0.6631 (p0) REVERT: A 236 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: A 237 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7596 (mtp180) REVERT: A 272 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7289 (mtpp) REVERT: A 342 ASP cc_start: 0.7400 (t0) cc_final: 0.7120 (t0) REVERT: A 511 MET cc_start: 0.8820 (mtm) cc_final: 0.8094 (mmt) REVERT: A 680 MET cc_start: 0.6026 (mtp) cc_final: 0.5633 (ptt) REVERT: B 114 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7131 (tm-30) REVERT: B 218 ASN cc_start: 0.7314 (p0) cc_final: 0.6645 (p0) REVERT: B 236 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: B 237 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7608 (mtp180) REVERT: B 272 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7287 (mtpp) REVERT: B 342 ASP cc_start: 0.7576 (t0) cc_final: 0.7265 (t0) REVERT: B 511 MET cc_start: 0.8827 (mtm) cc_final: 0.8103 (mmt) REVERT: B 680 MET cc_start: 0.6006 (mtp) cc_final: 0.5610 (ptt) outliers start: 40 outliers final: 19 residues processed: 149 average time/residue: 1.2996 time to fit residues: 206.8650 Evaluate side-chains 138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 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: 0.0870 chunk 63 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- 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 = 0.173613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.105142 restraints weight = 9324.943| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.05 r_work: 0.2870 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9890 Z= 0.123 Angle : 0.564 12.802 13374 Z= 0.284 Chirality : 0.042 0.131 1544 Planarity : 0.004 0.035 1668 Dihedral : 5.352 28.811 1364 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.94 % Allowed : 16.19 % 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: 0.78 (0.25), residues: 1212 helix: 1.50 (0.20), residues: 696 sheet: 0.70 (0.50), residues: 94 loop : -1.21 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 572 HIS 0.006 0.001 HIS B 229 PHE 0.010 0.001 PHE A 75 TYR 0.011 0.001 TYR B 630 ARG 0.006 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 494) hydrogen bonds : angle 3.51154 ( 1452) SS BOND : bond 0.00025 ( 2) SS BOND : angle 0.77519 ( 4) covalent geometry : bond 0.00287 ( 9888) covalent geometry : angle 0.56344 (13370) *********************** 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 151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 1.204 Fit side-chains REVERT: A 114 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7007 (tm-30) REVERT: A 171 MET cc_start: 0.8499 (mtp) cc_final: 0.7922 (mmm) REVERT: A 236 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: A 272 LYS cc_start: 0.7540 (ttpt) cc_final: 0.7117 (mtpp) REVERT: A 511 MET cc_start: 0.8693 (mtm) cc_final: 0.7932 (mmt) REVERT: A 554 GLU cc_start: 0.8525 (tp30) cc_final: 0.8284 (mm-30) REVERT: A 680 MET cc_start: 0.5877 (mtp) cc_final: 0.5595 (ptt) REVERT: B 114 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: B 171 MET cc_start: 0.8502 (mtp) cc_final: 0.7918 (mmm) REVERT: B 236 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: B 272 LYS cc_start: 0.7543 (ttpt) cc_final: 0.7115 (mtpp) REVERT: B 511 MET cc_start: 0.8696 (mtm) cc_final: 0.7944 (mmt) REVERT: B 680 MET cc_start: 0.5976 (mtp) cc_final: 0.5628 (ptt) outliers start: 31 outliers final: 19 residues processed: 138 average time/residue: 1.3049 time to fit residues: 192.4309 Evaluate side-chains 134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 179 MET 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 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 179 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 236 GLU 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 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: 0.0970 chunk 121 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 0.0570 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.176673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110361 restraints weight = 9398.689| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.17 r_work: 0.2913 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9890 Z= 0.096 Angle : 0.523 12.346 13374 Z= 0.264 Chirality : 0.040 0.127 1544 Planarity : 0.004 0.033 1668 Dihedral : 5.012 28.724 1364 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.84 % Allowed : 16.95 % Favored : 80.21 % 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: 1.14 (0.26), residues: 1212 helix: 1.88 (0.21), residues: 700 sheet: 0.75 (0.50), residues: 94 loop : -1.24 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 572 HIS 0.004 0.001 HIS B 229 PHE 0.008 0.001 PHE A 75 TYR 0.016 0.001 TYR B 494 ARG 0.008 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 494) hydrogen bonds : angle 3.31974 ( 1452) SS BOND : bond 0.00015 ( 2) SS BOND : angle 0.65527 ( 4) covalent geometry : bond 0.00209 ( 9888) covalent geometry : angle 0.52332 (13370) *********************** 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 154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 3.020 Fit side-chains REVERT: A 114 GLU cc_start: 0.7786 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 171 MET cc_start: 0.8413 (mtp) cc_final: 0.7883 (mmm) REVERT: A 236 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: A 272 LYS cc_start: 0.7496 (ttpt) cc_final: 0.7084 (mtpp) REVERT: A 389 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8228 (mmtm) REVERT: A 452 MET cc_start: 0.8041 (tpt) cc_final: 0.7734 (mmp) REVERT: A 554 GLU cc_start: 0.8452 (tp30) cc_final: 0.8146 (mm-30) REVERT: A 680 MET cc_start: 0.6007 (mtp) cc_final: 0.5662 (ptt) REVERT: B 114 GLU cc_start: 0.7791 (tm-30) cc_final: 0.6981 (tm-30) REVERT: B 171 MET cc_start: 0.8415 (mtp) cc_final: 0.7880 (mmm) REVERT: B 236 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 272 LYS cc_start: 0.7491 (ttpt) cc_final: 0.7079 (mtpp) REVERT: B 389 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8235 (mmtm) REVERT: B 452 MET cc_start: 0.8032 (tpt) cc_final: 0.7722 (mmp) REVERT: B 554 GLU cc_start: 0.8455 (tp30) cc_final: 0.8149 (mm-30) REVERT: B 680 MET cc_start: 0.5973 (mtp) cc_final: 0.5622 (ptt) outliers start: 30 outliers final: 13 residues processed: 144 average time/residue: 1.9189 time to fit residues: 297.1206 Evaluate side-chains 131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 182 VAL Chi-restraints excluded: chain B residue 236 GLU 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: 0.9980 chunk 64 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 105 optimal weight: 0.8980 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.175671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.108928 restraints weight = 9289.035| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.26 r_work: 0.2921 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9890 Z= 0.104 Angle : 0.533 11.121 13374 Z= 0.270 Chirality : 0.041 0.129 1544 Planarity : 0.004 0.034 1668 Dihedral : 4.941 27.233 1364 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.70 % Allowed : 18.47 % Favored : 79.83 % 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: 1.34 (0.26), residues: 1212 helix: 2.03 (0.21), residues: 694 sheet: 0.77 (0.50), residues: 94 loop : -1.07 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 572 HIS 0.004 0.001 HIS A 229 PHE 0.008 0.001 PHE A 75 TYR 0.017 0.001 TYR B 494 ARG 0.007 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 494) hydrogen bonds : angle 3.33542 ( 1452) SS BOND : bond 0.00033 ( 2) SS BOND : angle 0.67997 ( 4) covalent geometry : bond 0.00230 ( 9888) covalent geometry : angle 0.53298 (13370) *********************** 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 143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.051 Fit side-chains REVERT: A 114 GLU cc_start: 0.7764 (tm-30) cc_final: 0.6969 (tm-30) REVERT: A 171 MET cc_start: 0.8474 (mtp) cc_final: 0.8263 (mmm) REVERT: A 236 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: A 272 LYS cc_start: 0.7497 (ttpt) cc_final: 0.7089 (mtpp) REVERT: A 389 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8213 (mmtm) REVERT: A 452 MET cc_start: 0.8097 (tpt) cc_final: 0.7780 (mmp) REVERT: A 511 MET cc_start: 0.8460 (mtp) cc_final: 0.7560 (mmt) REVERT: A 554 GLU cc_start: 0.8429 (tp30) cc_final: 0.8139 (mm-30) REVERT: A 680 MET cc_start: 0.6003 (mtp) cc_final: 0.5653 (ptt) REVERT: B 114 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 171 MET cc_start: 0.8499 (mtp) cc_final: 0.8276 (mmm) REVERT: B 236 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: B 272 LYS cc_start: 0.7482 (ttpt) cc_final: 0.7074 (mtpp) REVERT: B 389 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8219 (mmtm) REVERT: B 452 MET cc_start: 0.8071 (tpt) cc_final: 0.7752 (mmp) REVERT: B 511 MET cc_start: 0.8472 (mtp) cc_final: 0.7574 (mmt) REVERT: B 554 GLU cc_start: 0.8428 (tp30) cc_final: 0.8139 (mm-30) REVERT: B 680 MET cc_start: 0.5981 (mtp) cc_final: 0.5612 (ptt) outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 1.3428 time to fit residues: 191.9287 Evaluate side-chains 131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain B residue 236 GLU 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: 2.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.173589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107280 restraints weight = 9378.862| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.15 r_work: 0.2873 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9890 Z= 0.126 Angle : 0.556 11.262 13374 Z= 0.282 Chirality : 0.042 0.137 1544 Planarity : 0.004 0.033 1668 Dihedral : 5.018 28.094 1364 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % 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: 1.19 (0.25), residues: 1212 helix: 1.95 (0.20), residues: 690 sheet: 0.40 (0.53), residues: 78 loop : -1.03 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 572 HIS 0.005 0.001 HIS B 229 PHE 0.010 0.001 PHE A 75 TYR 0.017 0.002 TYR B 494 ARG 0.007 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 494) hydrogen bonds : angle 3.43180 ( 1452) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.68272 ( 4) covalent geometry : bond 0.00295 ( 9888) covalent geometry : angle 0.55593 (13370) ********************** 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: 22 poor density : 118 time to evaluate : 1.162 Fit side-chains REVERT: A 114 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7022 (tm-30) REVERT: A 171 MET cc_start: 0.8517 (mtp) cc_final: 0.7902 (mmm) REVERT: A 236 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: A 272 LYS cc_start: 0.7592 (ttpt) cc_final: 0.7163 (mtpp) REVERT: A 389 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8210 (mmtm) REVERT: A 511 MET cc_start: 0.8525 (mtp) cc_final: 0.7728 (mmt) REVERT: A 554 GLU cc_start: 0.8462 (tp30) cc_final: 0.8175 (mm-30) REVERT: A 680 MET cc_start: 0.5966 (mtp) cc_final: 0.5656 (ptt) REVERT: B 114 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7005 (tm-30) REVERT: B 171 MET cc_start: 0.8529 (mtp) cc_final: 0.7904 (mmm) REVERT: B 236 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: B 272 LYS cc_start: 0.7565 (ttpt) cc_final: 0.7153 (mtpp) REVERT: B 389 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8227 (mmtm) REVERT: B 511 MET cc_start: 0.8541 (mtp) cc_final: 0.7744 (mmt) REVERT: B 554 GLU cc_start: 0.8463 (tp30) cc_final: 0.8176 (mm-30) REVERT: B 680 MET cc_start: 0.5942 (mtp) cc_final: 0.5621 (ptt) outliers start: 22 outliers final: 15 residues processed: 132 average time/residue: 1.3107 time to fit residues: 184.9627 Evaluate side-chains 132 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 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 88 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 0.0870 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 96 optimal weight: 0.0470 overall best weight: 0.8456 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.173952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109884 restraints weight = 9276.124| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.21 r_work: 0.2899 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2642 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= 0.115 Angle : 0.543 11.611 13374 Z= 0.276 Chirality : 0.041 0.130 1544 Planarity : 0.004 0.034 1668 Dihedral : 4.989 27.648 1364 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.99 % Allowed : 17.80 % Favored : 80.21 % 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: 1.30 (0.26), residues: 1212 helix: 1.98 (0.20), residues: 694 sheet: 0.77 (0.50), residues: 94 loop : -1.04 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 572 HIS 0.005 0.001 HIS A 229 PHE 0.009 0.001 PHE A 75 TYR 0.016 0.002 TYR A 494 ARG 0.007 0.000 ARG B 301 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 494) hydrogen bonds : angle 3.38341 ( 1452) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.70028 ( 4) covalent geometry : bond 0.00264 ( 9888) covalent geometry : angle 0.54321 (13370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9269.35 seconds wall clock time: 159 minutes 54.82 seconds (9594.82 seconds total)