Starting phenix.real_space_refine on Sun Jun 8 15:18:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtp_37839/06_2025/8wtp_37839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtp_37839/06_2025/8wtp_37839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtp_37839/06_2025/8wtp_37839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtp_37839/06_2025/8wtp_37839.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtp_37839/06_2025/8wtp_37839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtp_37839/06_2025/8wtp_37839.cif" } resolution = 2.82 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= -0.004 sd= 0.130 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 6274 2.51 5 N 1622 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9650 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: "B" Number of atoms: 4825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4825 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 3 Time building chain proxies: 6.43, per 1000 atoms: 0.67 Number of scatterers: 9650 At special positions: 0 Unit cell: (86.676, 92.268, 139.8, 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 1712 8.00 N 1622 7.00 C 6274 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: 2.68 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: 55 helices and 9 sheets defined 53.0% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 199 through 214 removed outlier: 3.608A pdb=" N LEU A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 removed outlier: 3.721A pdb=" N ARG A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.948A pdb=" N MET A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.629A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 4.134A pdb=" N ILE A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 4.258A pdb=" N GLU A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 removed outlier: 3.647A pdb=" N GLN A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 369 removed outlier: 4.076A 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 398 removed outlier: 3.551A pdb=" N SER A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.508A pdb=" N LEU A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 474 through 496 removed outlier: 3.710A pdb=" N GLN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE A 493 " --> pdb=" O MET A 489 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS A 496 " --> pdb=" O MET A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 521 through 550 removed outlier: 3.730A pdb=" N SER A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Proline residue: A 534 - end of helix removed outlier: 3.801A pdb=" N PHE A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 582 removed outlier: 3.694A pdb=" N PHE A 562 " --> pdb=" O MET A 558 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 578 " --> pdb=" O GLY A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 594 through 605 removed outlier: 3.537A pdb=" N ILE A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 628 through 640 removed outlier: 3.593A pdb=" N GLN A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 679 removed outlier: 3.506A pdb=" N LYS A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 668 " --> pdb=" O TYR A 664 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.572A pdb=" N LEU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 715 removed outlier: 3.533A pdb=" N THR A 712 " --> pdb=" O CYS A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 731 removed outlier: 3.582A pdb=" N PHE A 723 " --> pdb=" O PHE A 719 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 724 " --> pdb=" O ARG A 720 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 199 through 214 removed outlier: 3.540A pdb=" N LEU B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP B 212 " --> pdb=" O GLN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.652A pdb=" N ARG B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 279 removed outlier: 3.997A pdb=" N MET B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.692A pdb=" N LEU B 296 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 297 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 removed outlier: 3.626A pdb=" N PHE B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 4.091A pdb=" N ILE B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.173A pdb=" N GLU B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.676A pdb=" N GLN B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 369 removed outlier: 4.189A 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 398 Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.528A pdb=" N LEU B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 474 through 496 removed outlier: 3.717A pdb=" N GLN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE B 493 " --> pdb=" O MET B 489 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS B 496 " --> pdb=" O MET B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 521 through 550 removed outlier: 3.735A pdb=" N SER B 527 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Proline residue: B 534 - end of helix removed outlier: 3.800A pdb=" N PHE B 538 " --> pdb=" O PRO B 534 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE B 548 " --> pdb=" O ALA B 544 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP B 549 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 582 removed outlier: 3.700A pdb=" N PHE B 562 " --> pdb=" O MET B 558 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 578 " --> pdb=" O GLY B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 Processing helix chain 'B' and resid 594 through 605 removed outlier: 3.523A pdb=" N ILE B 598 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 628 through 640 removed outlier: 3.590A pdb=" N GLN B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 679 removed outlier: 3.943A pdb=" N LEU B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 678 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 699 removed outlier: 3.562A pdb=" N LEU B 695 " --> pdb=" O GLY B 691 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 715 removed outlier: 3.516A pdb=" N THR B 712 " --> pdb=" O CYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 731 removed outlier: 3.581A pdb=" N PHE B 723 " --> pdb=" O PHE B 719 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 724 " --> pdb=" O ARG B 720 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 111 removed outlier: 5.527A pdb=" N LEU A 78 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 170 removed outlier: 5.949A pdb=" N ALA A 168 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP A 256 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 170 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 312 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.504A pdb=" N THR A 689 " --> pdb=" O PHE A 647 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 111 removed outlier: 5.601A pdb=" N LEU B 78 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 167 through 170 removed outlier: 6.460A pdb=" N LEU B 302 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER B 313 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE B 304 " --> pdb=" O VAL B 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.482A pdb=" N THR B 689 " --> pdb=" O PHE B 647 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1110 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: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2516 1.33 - 1.45: 1808 1.45 - 1.57: 5462 1.57 - 1.69: 0 1.69 - 1.80: 72 Bond restraints: 9858 Sorted by residual: bond pdb=" CB VAL B 467 " pdb=" CG2 VAL B 467 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.21e+00 bond pdb=" CB VAL A 467 " pdb=" CG2 VAL A 467 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.05e+00 bond pdb=" CG1 ILE A 284 " pdb=" CD1 ILE A 284 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.61e+00 bond pdb=" CG1 ILE B 284 " pdb=" CD1 ILE B 284 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.34e+00 bond pdb=" CG LEU B 636 " pdb=" CD2 LEU B 636 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.20e+00 ... (remaining 9853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 12901 2.57 - 5.14: 370 5.14 - 7.71: 48 7.71 - 10.28: 12 10.28 - 12.85: 1 Bond angle restraints: 13332 Sorted by residual: angle pdb=" N GLU A 183 " pdb=" CA GLU A 183 " pdb=" C GLU A 183 " ideal model delta sigma weight residual 114.75 101.90 12.85 1.26e+00 6.30e-01 1.04e+02 angle pdb=" C GLU A 506 " pdb=" N ARG A 507 " pdb=" CA ARG A 507 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.35e+01 angle pdb=" N ARG A 230 " pdb=" CA ARG A 230 " pdb=" C ARG A 230 " ideal model delta sigma weight residual 110.42 117.11 -6.69 1.46e+00 4.69e-01 2.10e+01 angle pdb=" C THR B 337 " pdb=" N GLU B 338 " pdb=" CA GLU B 338 " ideal model delta sigma weight residual 122.46 130.10 -7.64 1.80e+00 3.09e-01 1.80e+01 angle pdb=" CA GLU B 236 " pdb=" CB GLU B 236 " pdb=" CG GLU B 236 " ideal model delta sigma weight residual 114.10 122.31 -8.21 2.00e+00 2.50e-01 1.68e+01 ... (remaining 13327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 5231 17.05 - 34.09: 507 34.09 - 51.14: 91 51.14 - 68.19: 12 68.19 - 85.23: 5 Dihedral angle restraints: 5846 sinusoidal: 2326 harmonic: 3520 Sorted by residual: dihedral pdb=" CA THR A 133 " pdb=" C THR A 133 " pdb=" N LEU A 134 " pdb=" CA LEU A 134 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ARG B 507 " pdb=" C ARG B 507 " pdb=" N TYR B 508 " pdb=" CA TYR B 508 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA GLN B 505 " pdb=" C GLN B 505 " pdb=" N GLU B 506 " pdb=" CA GLU B 506 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 5843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 930 0.048 - 0.095: 461 0.095 - 0.143: 120 0.143 - 0.191: 26 0.191 - 0.239: 3 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CB ILE B 223 " pdb=" CA ILE B 223 " pdb=" CG1 ILE B 223 " pdb=" CG2 ILE B 223 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE A 223 " pdb=" CA ILE A 223 " pdb=" CG1 ILE A 223 " pdb=" CG2 ILE A 223 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE B 232 " pdb=" CA ILE B 232 " pdb=" CG1 ILE B 232 " pdb=" CG2 ILE B 232 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.31e-01 ... (remaining 1537 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 657 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO A 658 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 658 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 658 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 500 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO A 501 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 501 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 501 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 500 " -0.050 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO B 501 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " -0.042 5.00e-02 4.00e+02 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2876 2.81 - 3.33: 8327 3.33 - 3.85: 15772 3.85 - 4.38: 19950 4.38 - 4.90: 32937 Nonbonded interactions: 79862 Sorted by model distance: nonbonded pdb=" OG SER B 132 " pdb=" OD1 ASP B 256 " model vdw 2.283 3.040 nonbonded pdb=" CD2 LEU A 504 " pdb=" NH2 ARG A 507 " model vdw 2.286 3.540 nonbonded pdb=" CD2 LEU B 504 " pdb=" NH2 ARG B 507 " model vdw 2.289 3.540 nonbonded pdb=" O LYS B 389 " pdb=" OG SER B 393 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 582 " pdb=" OG SER A 582 " model vdw 2.298 3.040 ... (remaining 79857 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.090 Set scattering table: 0.130 Process input model: 26.980 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:14.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 0.009 0.089 9860 Z= 0.383 Angle : 1.034 12.850 13336 Z= 0.556 Chirality : 0.058 0.239 1540 Planarity : 0.008 0.080 1662 Dihedral : 13.825 85.232 3572 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % 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: -5.67 (0.17), residues: 1212 helix: -4.43 (0.09), residues: 674 sheet: -1.98 (0.46), residues: 80 loop : -2.65 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 429 HIS 0.005 0.002 HIS B 587 PHE 0.031 0.003 PHE A 715 TYR 0.016 0.003 TYR A 519 ARG 0.006 0.001 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.29685 ( 383) hydrogen bonds : angle 10.47714 ( 1110) SS BOND : bond 0.00335 ( 2) SS BOND : angle 1.61247 ( 4) covalent geometry : bond 0.00919 ( 9858) covalent geometry : angle 1.03412 (13332) *********************** 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 141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.107 Fit side-chains REVERT: A 164 LYS cc_start: 0.7483 (mmpt) cc_final: 0.7218 (tttp) REVERT: A 179 MET cc_start: 0.8024 (mmp) cc_final: 0.7423 (mpm) REVERT: A 223 ILE cc_start: 0.8085 (mt) cc_final: 0.7825 (mp) REVERT: A 473 ASN cc_start: 0.8665 (m110) cc_final: 0.8397 (m-40) REVERT: A 589 MET cc_start: 0.4718 (tpt) cc_final: 0.4335 (mpp) REVERT: B 116 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.6945 (ttm-80) REVERT: B 164 LYS cc_start: 0.7497 (mmpt) cc_final: 0.7235 (tttt) REVERT: B 179 MET cc_start: 0.8013 (mmp) cc_final: 0.7473 (mpm) REVERT: B 204 LYS cc_start: 0.7730 (tttp) cc_final: 0.7424 (mtpp) REVERT: B 223 ILE cc_start: 0.8048 (mt) cc_final: 0.7770 (mp) REVERT: B 249 ASP cc_start: 0.7455 (t0) cc_final: 0.7043 (t0) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 1.0488 time to fit residues: 161.0395 Evaluate side-chains 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 140 ASN A 154 ASN A 290 GLN A 473 ASN A 733 ASN B 81 ASN B 110 ASN B 140 ASN B 248 HIS B 289 HIS B 290 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.188858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122203 restraints weight = 9962.386| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.97 r_work: 0.3281 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9860 Z= 0.123 Angle : 0.591 6.451 13336 Z= 0.315 Chirality : 0.040 0.155 1540 Planarity : 0.006 0.061 1662 Dihedral : 6.119 33.274 1326 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.04 % Allowed : 13.83 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.93 (0.20), residues: 1212 helix: -2.77 (0.15), residues: 674 sheet: -1.62 (0.45), residues: 80 loop : -2.25 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.002 0.001 HIS A 587 PHE 0.009 0.001 PHE B 562 TYR 0.010 0.001 TYR A 630 ARG 0.003 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 383) hydrogen bonds : angle 5.19717 ( 1110) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.88851 ( 4) covalent geometry : bond 0.00282 ( 9858) covalent geometry : angle 0.59121 (13332) *********************** 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 143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.083 Fit side-chains REVERT: A 164 LYS cc_start: 0.7470 (mmpt) cc_final: 0.7160 (tttt) REVERT: A 204 LYS cc_start: 0.7322 (mmmm) cc_final: 0.6835 (pttt) REVERT: A 223 ILE cc_start: 0.7694 (mt) cc_final: 0.7440 (mp) REVERT: A 288 ILE cc_start: 0.8016 (mt) cc_final: 0.7785 (mt) REVERT: A 301 ARG cc_start: 0.7225 (ttm110) cc_final: 0.6777 (ttp-110) REVERT: A 473 ASN cc_start: 0.8942 (m-40) cc_final: 0.8628 (m-40) REVERT: A 494 TYR cc_start: 0.8023 (t80) cc_final: 0.6290 (m-80) REVERT: A 528 HIS cc_start: 0.8085 (t-90) cc_final: 0.7569 (t70) REVERT: A 589 MET cc_start: 0.4506 (tpt) cc_final: 0.3591 (mmt) REVERT: A 680 MET cc_start: 0.7065 (mtt) cc_final: 0.6820 (mtm) REVERT: B 116 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7555 (mmm-85) REVERT: B 164 LYS cc_start: 0.7462 (mmpt) cc_final: 0.7135 (tttp) REVERT: B 179 MET cc_start: 0.7867 (mmp) cc_final: 0.7634 (mpm) REVERT: B 204 LYS cc_start: 0.7449 (tttp) cc_final: 0.7055 (mtpp) REVERT: B 249 ASP cc_start: 0.7418 (t0) cc_final: 0.6811 (t0) REVERT: B 456 THR cc_start: 0.8671 (p) cc_final: 0.8404 (t) REVERT: B 473 ASN cc_start: 0.8931 (m110) cc_final: 0.8653 (m-40) REVERT: B 494 TYR cc_start: 0.8018 (t80) cc_final: 0.6273 (m-80) REVERT: B 528 HIS cc_start: 0.8087 (t-90) cc_final: 0.7558 (t70) REVERT: B 589 MET cc_start: 0.4438 (tpt) cc_final: 0.4065 (mmm) outliers start: 11 outliers final: 2 residues processed: 139 average time/residue: 0.9032 time to fit residues: 138.2475 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 : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 388 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 248 HIS A 289 HIS B 213 GLN B 473 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.188394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120769 restraints weight = 10042.177| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.00 r_work: 0.3256 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9860 Z= 0.142 Angle : 0.580 6.935 13336 Z= 0.301 Chirality : 0.041 0.157 1540 Planarity : 0.004 0.052 1662 Dihedral : 5.643 29.173 1326 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.37 % Allowed : 15.62 % Favored : 82.01 % 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: -2.80 (0.22), residues: 1212 helix: -1.75 (0.18), residues: 702 sheet: -0.83 (0.47), residues: 68 loop : -1.95 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 572 HIS 0.002 0.001 HIS A 587 PHE 0.011 0.001 PHE A 75 TYR 0.012 0.001 TYR A 630 ARG 0.002 0.000 ARG B 294 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 383) hydrogen bonds : angle 4.56544 ( 1110) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.71632 ( 4) covalent geometry : bond 0.00338 ( 9858) covalent geometry : angle 0.57977 (13332) *********************** 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 149 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.065 Fit side-chains REVERT: A 116 ARG cc_start: 0.6934 (ttm110) cc_final: 0.6686 (ttm110) REVERT: A 164 LYS cc_start: 0.7401 (mmpt) cc_final: 0.7125 (tttt) REVERT: A 179 MET cc_start: 0.7745 (mmp) cc_final: 0.7484 (mpm) REVERT: A 204 LYS cc_start: 0.7317 (mmmm) cc_final: 0.6797 (pttt) REVERT: A 223 ILE cc_start: 0.7669 (mt) cc_final: 0.7417 (mp) REVERT: A 301 ARG cc_start: 0.7337 (ttm110) cc_final: 0.6734 (ttp-110) REVERT: A 473 ASN cc_start: 0.8950 (m-40) cc_final: 0.8593 (m-40) REVERT: A 494 TYR cc_start: 0.8100 (t80) cc_final: 0.6291 (m-80) REVERT: A 589 MET cc_start: 0.4515 (tpt) cc_final: 0.3549 (mmt) REVERT: A 666 MET cc_start: 0.6421 (pmm) cc_final: 0.6203 (pmm) REVERT: B 116 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7559 (mmm-85) REVERT: B 164 LYS cc_start: 0.7260 (mmpt) cc_final: 0.7021 (tttp) REVERT: B 179 MET cc_start: 0.7808 (mmp) cc_final: 0.7574 (mpm) REVERT: B 204 LYS cc_start: 0.7386 (tttp) cc_final: 0.6955 (mtpp) REVERT: B 205 LEU cc_start: 0.7855 (mm) cc_final: 0.7504 (tp) REVERT: B 217 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7977 (tpp-160) REVERT: B 223 ILE cc_start: 0.7724 (mt) cc_final: 0.7482 (mp) REVERT: B 249 ASP cc_start: 0.7429 (t0) cc_final: 0.6832 (t0) REVERT: B 286 MET cc_start: 0.8922 (ptm) cc_final: 0.8584 (ptp) REVERT: B 456 THR cc_start: 0.8718 (p) cc_final: 0.8437 (t) REVERT: B 473 ASN cc_start: 0.8942 (m-40) cc_final: 0.8594 (m-40) REVERT: B 494 TYR cc_start: 0.8126 (t80) cc_final: 0.6348 (m-80) REVERT: B 589 MET cc_start: 0.4563 (tpt) cc_final: 0.3996 (mmm) outliers start: 25 outliers final: 7 residues processed: 143 average time/residue: 0.8740 time to fit residues: 137.7686 Evaluate side-chains 120 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 388 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.187536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119653 restraints weight = 9880.562| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.99 r_work: 0.3269 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9860 Z= 0.165 Angle : 0.587 6.357 13336 Z= 0.303 Chirality : 0.043 0.157 1540 Planarity : 0.004 0.047 1662 Dihedral : 5.576 32.013 1326 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.31 % Allowed : 15.62 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.40 (0.23), residues: 1212 helix: -1.30 (0.19), residues: 710 sheet: -0.84 (0.47), residues: 70 loop : -1.98 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 429 HIS 0.003 0.001 HIS B 248 PHE 0.011 0.001 PHE B 562 TYR 0.013 0.001 TYR A 630 ARG 0.005 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 383) hydrogen bonds : angle 4.43139 ( 1110) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.80609 ( 4) covalent geometry : bond 0.00397 ( 9858) covalent geometry : angle 0.58694 (13332) *********************** 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 144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.133 Fit side-chains REVERT: A 164 LYS cc_start: 0.7283 (mmpt) cc_final: 0.7035 (tttt) REVERT: A 179 MET cc_start: 0.7793 (mmp) cc_final: 0.7562 (mpm) REVERT: A 223 ILE cc_start: 0.7809 (mt) cc_final: 0.7552 (mp) REVERT: A 473 ASN cc_start: 0.8983 (m-40) cc_final: 0.8647 (m-40) REVERT: A 494 TYR cc_start: 0.8165 (t80) cc_final: 0.6325 (m-80) REVERT: A 579 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8190 (p) REVERT: A 589 MET cc_start: 0.4607 (tpt) cc_final: 0.3605 (mmt) REVERT: A 666 MET cc_start: 0.6478 (pmm) cc_final: 0.6203 (pmm) REVERT: B 116 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7233 (mmm-85) REVERT: B 164 LYS cc_start: 0.7230 (mmpt) cc_final: 0.7030 (tmtp) REVERT: B 204 LYS cc_start: 0.7369 (tttp) cc_final: 0.6948 (mtpp) REVERT: B 205 LEU cc_start: 0.7841 (mm) cc_final: 0.7515 (tp) REVERT: B 249 ASP cc_start: 0.7448 (t0) cc_final: 0.6860 (t0) REVERT: B 286 MET cc_start: 0.8880 (ptm) cc_final: 0.8485 (ptp) REVERT: B 301 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6998 (ttm-80) REVERT: B 456 THR cc_start: 0.8703 (p) cc_final: 0.8413 (t) REVERT: B 473 ASN cc_start: 0.8982 (m-40) cc_final: 0.8648 (m-40) REVERT: B 494 TYR cc_start: 0.8181 (t80) cc_final: 0.6318 (m-80) REVERT: B 579 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8173 (p) REVERT: B 589 MET cc_start: 0.4621 (tpt) cc_final: 0.4045 (mmm) outliers start: 35 outliers final: 17 residues processed: 133 average time/residue: 0.8398 time to fit residues: 123.5594 Evaluate side-chains 127 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 680 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 41 optimal weight: 0.0000 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.189308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121526 restraints weight = 9859.055| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.98 r_work: 0.3271 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9860 Z= 0.125 Angle : 0.555 6.305 13336 Z= 0.288 Chirality : 0.041 0.151 1540 Planarity : 0.004 0.043 1662 Dihedral : 5.341 29.794 1326 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.94 % Allowed : 16.76 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.75 (0.24), residues: 1212 helix: -0.82 (0.20), residues: 712 sheet: -0.65 (0.49), residues: 70 loop : -1.62 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 572 HIS 0.002 0.001 HIS A 587 PHE 0.008 0.001 PHE A 75 TYR 0.011 0.001 TYR A 630 ARG 0.002 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 383) hydrogen bonds : angle 4.22156 ( 1110) SS BOND : bond 0.00026 ( 2) SS BOND : angle 1.10473 ( 4) covalent geometry : bond 0.00296 ( 9858) covalent geometry : angle 0.55470 (13332) *********************** 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 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.217 Fit side-chains REVERT: A 164 LYS cc_start: 0.7097 (mmpt) cc_final: 0.6875 (tttp) REVERT: A 179 MET cc_start: 0.7781 (mmp) cc_final: 0.7508 (mpm) REVERT: A 193 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6303 (mmt90) REVERT: A 223 ILE cc_start: 0.7693 (mt) cc_final: 0.7416 (mp) REVERT: A 473 ASN cc_start: 0.8912 (m-40) cc_final: 0.8620 (m-40) REVERT: A 494 TYR cc_start: 0.8058 (t80) cc_final: 0.6300 (m-80) REVERT: A 579 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8182 (p) REVERT: A 589 MET cc_start: 0.4552 (tpt) cc_final: 0.3655 (mmt) REVERT: A 666 MET cc_start: 0.6566 (pmm) cc_final: 0.6271 (pmm) REVERT: B 116 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7235 (mmm-85) REVERT: B 204 LYS cc_start: 0.7348 (tttp) cc_final: 0.6992 (pttt) REVERT: B 205 LEU cc_start: 0.7866 (mm) cc_final: 0.7522 (tp) REVERT: B 249 ASP cc_start: 0.7305 (t0) cc_final: 0.6718 (t0) REVERT: B 286 MET cc_start: 0.8792 (ptm) cc_final: 0.8379 (ptp) REVERT: B 301 ARG cc_start: 0.7268 (ttm110) cc_final: 0.6973 (ttm-80) REVERT: B 456 THR cc_start: 0.8631 (p) cc_final: 0.8361 (t) REVERT: B 473 ASN cc_start: 0.8982 (m-40) cc_final: 0.8645 (m-40) REVERT: B 494 TYR cc_start: 0.8060 (t80) cc_final: 0.6294 (m-80) REVERT: B 579 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8151 (p) REVERT: B 589 MET cc_start: 0.4541 (tpt) cc_final: 0.3999 (mmm) outliers start: 31 outliers final: 18 residues processed: 137 average time/residue: 0.8435 time to fit residues: 128.0247 Evaluate side-chains 130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 690 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 41 optimal weight: 0.0020 chunk 86 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.187685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119648 restraints weight = 9961.492| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.99 r_work: 0.3245 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9860 Z= 0.157 Angle : 0.580 6.400 13336 Z= 0.299 Chirality : 0.043 0.154 1540 Planarity : 0.004 0.039 1662 Dihedral : 5.363 30.674 1326 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.31 % Allowed : 17.90 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.54 (0.24), residues: 1212 helix: -0.65 (0.20), residues: 720 sheet: -0.58 (0.50), residues: 70 loop : -1.54 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 572 HIS 0.003 0.001 HIS A 587 PHE 0.010 0.001 PHE B 562 TYR 0.012 0.001 TYR A 630 ARG 0.004 0.000 ARG A 239 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 383) hydrogen bonds : angle 4.21292 ( 1110) SS BOND : bond 0.00229 ( 2) SS BOND : angle 1.07923 ( 4) covalent geometry : bond 0.00379 ( 9858) covalent geometry : angle 0.57986 (13332) *********************** 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 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.091 Fit side-chains REVERT: A 164 LYS cc_start: 0.6999 (mmpt) cc_final: 0.6771 (tttp) REVERT: A 179 MET cc_start: 0.7797 (mmp) cc_final: 0.7566 (mpm) REVERT: A 193 ARG cc_start: 0.7114 (mtp180) cc_final: 0.6850 (mtm-85) REVERT: A 223 ILE cc_start: 0.7749 (mt) cc_final: 0.7502 (mp) REVERT: A 246 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7311 (pt) REVERT: A 269 MET cc_start: 0.6176 (tpp) cc_final: 0.5945 (tpp) REVERT: A 473 ASN cc_start: 0.8964 (m-40) cc_final: 0.8655 (m-40) REVERT: A 494 TYR cc_start: 0.8152 (t80) cc_final: 0.6308 (m-80) REVERT: A 541 LEU cc_start: 0.8551 (tp) cc_final: 0.8077 (mt) REVERT: A 579 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8192 (p) REVERT: A 589 MET cc_start: 0.4598 (tpt) cc_final: 0.3662 (mmt) REVERT: B 116 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7254 (mmm-85) REVERT: B 204 LYS cc_start: 0.7326 (tttp) cc_final: 0.6961 (pttt) REVERT: B 205 LEU cc_start: 0.7899 (mm) cc_final: 0.7554 (tp) REVERT: B 249 ASP cc_start: 0.7389 (t0) cc_final: 0.6803 (t0) REVERT: B 301 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6987 (ttm-80) REVERT: B 367 MET cc_start: 0.6981 (mmm) cc_final: 0.6756 (ptm) REVERT: B 456 THR cc_start: 0.8723 (p) cc_final: 0.8433 (t) REVERT: B 489 MET cc_start: 0.8773 (mmp) cc_final: 0.8516 (mmm) REVERT: B 494 TYR cc_start: 0.8156 (t80) cc_final: 0.6276 (m-80) REVERT: B 541 LEU cc_start: 0.8570 (tp) cc_final: 0.8091 (mt) REVERT: B 579 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 589 MET cc_start: 0.4471 (tpt) cc_final: 0.3917 (mmm) outliers start: 35 outliers final: 21 residues processed: 136 average time/residue: 0.9188 time to fit residues: 137.9121 Evaluate side-chains 132 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 690 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN B 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.184874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117016 restraints weight = 10005.573| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.00 r_work: 0.3233 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9860 Z= 0.224 Angle : 0.635 6.685 13336 Z= 0.326 Chirality : 0.045 0.159 1540 Planarity : 0.004 0.038 1662 Dihedral : 5.616 28.375 1326 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.17 % Allowed : 17.14 % Favored : 78.69 % 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: -1.61 (0.24), residues: 1212 helix: -0.68 (0.20), residues: 710 sheet: -0.55 (0.50), residues: 68 loop : -1.63 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 429 HIS 0.003 0.001 HIS A 587 PHE 0.013 0.002 PHE B 562 TYR 0.013 0.002 TYR A 630 ARG 0.007 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 383) hydrogen bonds : angle 4.38256 ( 1110) SS BOND : bond 0.00343 ( 2) SS BOND : angle 1.18358 ( 4) covalent geometry : bond 0.00545 ( 9858) covalent geometry : angle 0.63495 (13332) *********************** 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 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 1.226 Fit side-chains REVERT: A 164 LYS cc_start: 0.6995 (mmpt) cc_final: 0.6732 (tttp) REVERT: A 179 MET cc_start: 0.7736 (mmp) cc_final: 0.7395 (mpm) REVERT: A 223 ILE cc_start: 0.7793 (mt) cc_final: 0.7528 (mp) REVERT: A 473 ASN cc_start: 0.8974 (m-40) cc_final: 0.8647 (m-40) REVERT: A 494 TYR cc_start: 0.8285 (t80) cc_final: 0.6196 (m-80) REVERT: A 541 LEU cc_start: 0.8423 (tp) cc_final: 0.8100 (mt) REVERT: A 589 MET cc_start: 0.4647 (tpt) cc_final: 0.3627 (mmt) REVERT: B 116 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7373 (mmm-85) REVERT: B 216 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.5991 (pp) REVERT: B 223 ILE cc_start: 0.7799 (mt) cc_final: 0.7542 (mp) REVERT: B 249 ASP cc_start: 0.7580 (t0) cc_final: 0.7009 (t0) REVERT: B 301 ARG cc_start: 0.7309 (ttm110) cc_final: 0.6947 (ttm-80) REVERT: B 494 TYR cc_start: 0.8258 (t80) cc_final: 0.6194 (m-80) REVERT: B 541 LEU cc_start: 0.8424 (tp) cc_final: 0.8097 (mt) REVERT: B 589 MET cc_start: 0.4406 (tpt) cc_final: 0.3766 (mmm) outliers start: 44 outliers final: 27 residues processed: 143 average time/residue: 0.8302 time to fit residues: 131.8182 Evaluate side-chains 136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 690 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.188254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120306 restraints weight = 10062.323| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.00 r_work: 0.3254 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9860 Z= 0.130 Angle : 0.573 8.039 13336 Z= 0.294 Chirality : 0.042 0.150 1540 Planarity : 0.004 0.039 1662 Dihedral : 5.345 31.742 1326 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.84 % Allowed : 19.60 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.26 (0.25), residues: 1212 helix: -0.35 (0.20), residues: 708 sheet: -0.60 (0.50), residues: 70 loop : -1.52 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 572 HIS 0.002 0.001 HIS A 587 PHE 0.007 0.001 PHE A 75 TYR 0.011 0.001 TYR A 630 ARG 0.006 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 383) hydrogen bonds : angle 4.13991 ( 1110) SS BOND : bond 0.00178 ( 2) SS BOND : angle 1.22133 ( 4) covalent geometry : bond 0.00312 ( 9858) covalent geometry : angle 0.57255 (13332) *********************** 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 141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.166 Fit side-chains REVERT: A 164 LYS cc_start: 0.6860 (mmpt) cc_final: 0.6589 (tmtp) REVERT: A 179 MET cc_start: 0.7704 (mmp) cc_final: 0.7459 (mpm) REVERT: A 193 ARG cc_start: 0.7093 (mtp180) cc_final: 0.6326 (mmt90) REVERT: A 223 ILE cc_start: 0.7827 (mt) cc_final: 0.7543 (mp) REVERT: A 494 TYR cc_start: 0.8038 (t80) cc_final: 0.6295 (m-80) REVERT: A 541 LEU cc_start: 0.8329 (tp) cc_final: 0.7990 (mt) REVERT: A 579 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8191 (p) REVERT: A 589 MET cc_start: 0.4460 (tpt) cc_final: 0.3610 (mmt) REVERT: B 116 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7368 (mmm-85) REVERT: B 204 LYS cc_start: 0.7288 (tttp) cc_final: 0.6897 (mtpp) REVERT: B 216 ILE cc_start: 0.6366 (OUTLIER) cc_final: 0.5939 (pp) REVERT: B 249 ASP cc_start: 0.7347 (t0) cc_final: 0.6772 (t0) REVERT: B 286 MET cc_start: 0.8773 (ptm) cc_final: 0.8369 (ptp) REVERT: B 301 ARG cc_start: 0.7308 (ttm110) cc_final: 0.7003 (ttp-110) REVERT: B 367 MET cc_start: 0.7083 (mtp) cc_final: 0.6764 (mmm) REVERT: B 456 THR cc_start: 0.8706 (p) cc_final: 0.8392 (t) REVERT: B 494 TYR cc_start: 0.8034 (t80) cc_final: 0.6300 (m-80) REVERT: B 541 LEU cc_start: 0.8336 (tp) cc_final: 0.7993 (mt) REVERT: B 579 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8158 (p) REVERT: B 589 MET cc_start: 0.4556 (tpt) cc_final: 0.4048 (mmm) outliers start: 30 outliers final: 20 residues processed: 130 average time/residue: 0.8699 time to fit residues: 125.0161 Evaluate side-chains 130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 690 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 0.0370 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.192882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124514 restraints weight = 9941.920| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.23 r_work: 0.3355 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9860 Z= 0.113 Angle : 0.558 8.557 13336 Z= 0.285 Chirality : 0.041 0.148 1540 Planarity : 0.004 0.039 1662 Dihedral : 5.184 30.042 1326 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.18 % Allowed : 20.17 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.06 (0.25), residues: 1212 helix: -0.14 (0.21), residues: 706 sheet: -0.43 (0.51), residues: 70 loop : -1.56 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 572 HIS 0.002 0.001 HIS A 587 PHE 0.008 0.001 PHE A 571 TYR 0.012 0.001 TYR A 630 ARG 0.005 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.02666 ( 383) hydrogen bonds : angle 3.99188 ( 1110) SS BOND : bond 0.00107 ( 2) SS BOND : angle 1.20839 ( 4) covalent geometry : bond 0.00266 ( 9858) covalent geometry : angle 0.55775 (13332) *********************** 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 135 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.443 Fit side-chains REVERT: A 164 LYS cc_start: 0.6483 (mmpt) cc_final: 0.6247 (tmtp) REVERT: A 223 ILE cc_start: 0.7324 (mt) cc_final: 0.7094 (mp) REVERT: A 301 ARG cc_start: 0.6712 (ttm110) cc_final: 0.6432 (ttm-80) REVERT: A 494 TYR cc_start: 0.7705 (t80) cc_final: 0.5839 (m-80) REVERT: A 541 LEU cc_start: 0.7863 (tp) cc_final: 0.7510 (mt) REVERT: A 589 MET cc_start: 0.4152 (tpt) cc_final: 0.3321 (mmt) REVERT: B 116 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.6991 (mmm-85) REVERT: B 204 LYS cc_start: 0.7022 (tttp) cc_final: 0.6634 (mtpp) REVERT: B 216 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5460 (pp) REVERT: B 249 ASP cc_start: 0.7018 (t0) cc_final: 0.6366 (t0) REVERT: B 367 MET cc_start: 0.7029 (mtp) cc_final: 0.6629 (mmm) REVERT: B 494 TYR cc_start: 0.7644 (t80) cc_final: 0.5791 (m-80) REVERT: B 541 LEU cc_start: 0.7874 (tp) cc_final: 0.7516 (mt) REVERT: B 589 MET cc_start: 0.4025 (tpt) cc_final: 0.3552 (mmm) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 1.3013 time to fit residues: 183.3426 Evaluate side-chains 126 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 690 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.2980 chunk 94 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.194090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125382 restraints weight = 9951.889| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.24 r_work: 0.3368 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9860 Z= 0.105 Angle : 0.552 9.048 13336 Z= 0.280 Chirality : 0.041 0.146 1540 Planarity : 0.004 0.039 1662 Dihedral : 5.090 31.477 1326 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.99 % Allowed : 20.45 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1212 helix: 0.03 (0.21), residues: 706 sheet: -0.33 (0.51), residues: 70 loop : -1.47 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 572 HIS 0.002 0.001 HIS A 587 PHE 0.009 0.001 PHE A 571 TYR 0.010 0.001 TYR A 630 ARG 0.005 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.02554 ( 383) hydrogen bonds : angle 3.92335 ( 1110) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.06240 ( 4) covalent geometry : bond 0.00245 ( 9858) covalent geometry : angle 0.55149 (13332) ********************** 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 133 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.136 Fit side-chains REVERT: A 164 LYS cc_start: 0.6477 (mmpt) cc_final: 0.6260 (tmtp) REVERT: A 179 MET cc_start: 0.7204 (mmp) cc_final: 0.6957 (mpm) REVERT: A 223 ILE cc_start: 0.7428 (mt) cc_final: 0.7177 (mp) REVERT: A 246 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.6907 (pt) REVERT: A 301 ARG cc_start: 0.6725 (ttm110) cc_final: 0.6461 (ttm-80) REVERT: A 310 THR cc_start: 0.8489 (p) cc_final: 0.8221 (p) REVERT: A 494 TYR cc_start: 0.7590 (t80) cc_final: 0.5719 (m-80) REVERT: A 541 LEU cc_start: 0.7768 (tp) cc_final: 0.7450 (mt) REVERT: A 558 MET cc_start: 0.8102 (mmm) cc_final: 0.7861 (mmm) REVERT: A 589 MET cc_start: 0.4066 (tpt) cc_final: 0.3273 (mmt) REVERT: B 116 ARG cc_start: 0.7401 (mmm-85) cc_final: 0.6719 (mmm-85) REVERT: B 204 LYS cc_start: 0.7065 (tttp) cc_final: 0.6749 (mtpt) REVERT: B 216 ILE cc_start: 0.5885 (OUTLIER) cc_final: 0.5448 (pp) REVERT: B 249 ASP cc_start: 0.6962 (t0) cc_final: 0.6287 (t0) REVERT: B 286 MET cc_start: 0.8401 (ptm) cc_final: 0.8160 (ptp) REVERT: B 301 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6183 (ttp-110) REVERT: B 367 MET cc_start: 0.7011 (mtp) cc_final: 0.6606 (mmm) REVERT: B 494 TYR cc_start: 0.7559 (t80) cc_final: 0.5695 (m-80) REVERT: B 541 LEU cc_start: 0.7776 (tp) cc_final: 0.7453 (mt) REVERT: B 589 MET cc_start: 0.4025 (tpt) cc_final: 0.3601 (mmm) outliers start: 21 outliers final: 11 residues processed: 125 average time/residue: 0.9504 time to fit residues: 130.3551 Evaluate side-chains 118 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123748 restraints weight = 10000.074| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.25 r_work: 0.3404 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9860 Z= 0.139 Angle : 0.577 7.841 13336 Z= 0.292 Chirality : 0.043 0.151 1540 Planarity : 0.004 0.038 1662 Dihedral : 5.165 29.305 1326 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.80 % Allowed : 20.83 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1212 helix: -0.07 (0.21), residues: 706 sheet: -0.35 (0.51), residues: 70 loop : -1.41 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 429 HIS 0.002 0.001 HIS A 587 PHE 0.009 0.001 PHE A 571 TYR 0.011 0.001 TYR B 630 ARG 0.005 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 383) hydrogen bonds : angle 3.99969 ( 1110) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.26656 ( 4) covalent geometry : bond 0.00335 ( 9858) covalent geometry : angle 0.57622 (13332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7964.80 seconds wall clock time: 138 minutes 9.23 seconds (8289.23 seconds total)