Starting phenix.real_space_refine on Fri Feb 14 03:13:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtp_37839/02_2025/8wtp_37839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtp_37839/02_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_37839/02_2025/8wtp_37839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtp_37839/02_2025/8wtp_37839.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtp_37839/02_2025/8wtp_37839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtp_37839/02_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-5592/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: 5.96, per 1000 atoms: 0.62 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: 2.29 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: 0.98 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: 2.57 Time building geometry restraints manager: 2.65 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: 1.080 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.290 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.350 ------------------------------------------------------------------------------- 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 9858 Z= 0.597 Angle : 1.034 12.850 13332 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 *********************** 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 : 1.105 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: 1.0453 time to fit residues: 160.3988 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 : 1.056 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122184 restraints weight = 9962.386| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.98 r_work: 0.3280 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- 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 9858 Z= 0.180 Angle : 0.591 6.451 13332 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 *********************** 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 : 1.143 Fit side-chains REVERT: A 164 LYS cc_start: 0.7469 (mmpt) cc_final: 0.7155 (tttt) REVERT: A 204 LYS cc_start: 0.7316 (mmmm) cc_final: 0.6826 (pttt) REVERT: A 223 ILE cc_start: 0.7689 (mt) cc_final: 0.7435 (mp) REVERT: A 288 ILE cc_start: 0.8018 (mt) cc_final: 0.7787 (mt) REVERT: A 301 ARG cc_start: 0.7227 (ttm110) cc_final: 0.6779 (ttp-110) REVERT: A 473 ASN cc_start: 0.8943 (m-40) cc_final: 0.8628 (m-40) REVERT: A 494 TYR cc_start: 0.8024 (t80) cc_final: 0.6288 (m-80) REVERT: A 528 HIS cc_start: 0.8085 (t-90) cc_final: 0.7568 (t70) REVERT: A 589 MET cc_start: 0.4511 (tpt) cc_final: 0.3594 (mmt) REVERT: A 680 MET cc_start: 0.7065 (mtt) cc_final: 0.6822 (mtm) REVERT: B 116 ARG cc_start: 0.7772 (mmm-85) cc_final: 0.7552 (mmm-85) REVERT: B 164 LYS cc_start: 0.7459 (mmpt) cc_final: 0.7131 (tttp) REVERT: B 179 MET cc_start: 0.7863 (mmp) cc_final: 0.7632 (mpm) REVERT: B 204 LYS cc_start: 0.7444 (tttp) cc_final: 0.7049 (mtpp) REVERT: B 249 ASP cc_start: 0.7417 (t0) cc_final: 0.6810 (t0) REVERT: B 456 THR cc_start: 0.8674 (p) cc_final: 0.8405 (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: 0.6271 (m-80) REVERT: B 528 HIS cc_start: 0.8086 (t-90) cc_final: 0.7556 (t70) REVERT: B 589 MET cc_start: 0.4444 (tpt) cc_final: 0.4068 (mmm) outliers start: 11 outliers final: 2 residues processed: 139 average time/residue: 0.9318 time to fit residues: 142.3221 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 : 1.163 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.186653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119011 restraints weight = 10080.798| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.99 r_work: 0.3258 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9858 Z= 0.278 Angle : 0.612 7.060 13332 Z= 0.317 Chirality : 0.043 0.161 1540 Planarity : 0.005 0.052 1662 Dihedral : 5.783 28.124 1326 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.56 % Allowed : 15.62 % Favored : 81.82 % 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: -2.90 (0.22), residues: 1212 helix: -1.82 (0.18), residues: 698 sheet: -1.03 (0.47), residues: 70 loop : -1.98 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 429 HIS 0.003 0.001 HIS A 587 PHE 0.013 0.001 PHE A 75 TYR 0.014 0.001 TYR A 630 ARG 0.003 0.000 ARG B 294 *********************** 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 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.146 Fit side-chains REVERT: A 164 LYS cc_start: 0.7397 (mmpt) cc_final: 0.7130 (tttt) REVERT: A 179 MET cc_start: 0.7802 (mmp) cc_final: 0.7488 (mpm) REVERT: A 198 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6847 (mp) REVERT: A 204 LYS cc_start: 0.7288 (mmmm) cc_final: 0.6792 (pttt) REVERT: A 223 ILE cc_start: 0.7724 (mt) cc_final: 0.7478 (mp) REVERT: A 473 ASN cc_start: 0.8949 (m-40) cc_final: 0.8617 (m-40) REVERT: A 494 TYR cc_start: 0.8205 (t80) cc_final: 0.6309 (m-80) REVERT: A 589 MET cc_start: 0.4525 (tpt) cc_final: 0.3546 (mmt) REVERT: A 666 MET cc_start: 0.6466 (pmm) cc_final: 0.6249 (pmm) REVERT: B 116 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7583 (mmm-85) REVERT: B 164 LYS cc_start: 0.7294 (mmpt) cc_final: 0.7037 (tttt) REVERT: B 179 MET cc_start: 0.7790 (mmp) cc_final: 0.7528 (mpm) REVERT: B 204 LYS cc_start: 0.7364 (tttp) cc_final: 0.6956 (pttt) REVERT: B 205 LEU cc_start: 0.7886 (mm) cc_final: 0.7501 (tp) REVERT: B 213 GLN cc_start: 0.7371 (tt0) cc_final: 0.7062 (tt0) REVERT: B 223 ILE cc_start: 0.7718 (mt) cc_final: 0.7472 (mp) REVERT: B 249 ASP cc_start: 0.7444 (t0) cc_final: 0.6862 (t0) REVERT: B 286 MET cc_start: 0.8910 (ptm) cc_final: 0.8563 (ptp) REVERT: B 473 ASN cc_start: 0.8946 (m-40) cc_final: 0.8600 (m-40) REVERT: B 494 TYR cc_start: 0.8181 (t80) cc_final: 0.6287 (m-80) REVERT: B 589 MET cc_start: 0.4565 (tpt) cc_final: 0.4042 (mmm) outliers start: 27 outliers final: 8 residues processed: 141 average time/residue: 0.8769 time to fit residues: 136.8053 Evaluate side-chains 116 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 198 LEU 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 288 ILE 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: 2.9990 chunk 111 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.188220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120575 restraints weight = 9861.871| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.97 r_work: 0.3278 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9858 Z= 0.225 Angle : 0.575 6.330 13332 Z= 0.297 Chirality : 0.042 0.154 1540 Planarity : 0.004 0.046 1662 Dihedral : 5.566 32.193 1326 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.84 % Allowed : 16.29 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.33 (0.23), residues: 1212 helix: -1.26 (0.19), residues: 702 sheet: -0.84 (0.47), residues: 70 loop : -1.93 (0.29), residues: 440 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 0.009 0.001 PHE B 562 TYR 0.012 0.001 TYR A 630 ARG 0.004 0.000 ARG B 237 *********************** 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 141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.055 Fit side-chains REVERT: A 164 LYS cc_start: 0.7271 (mmpt) cc_final: 0.7025 (tttt) REVERT: A 179 MET cc_start: 0.7758 (mmp) cc_final: 0.7515 (mpm) REVERT: A 223 ILE cc_start: 0.7801 (mt) cc_final: 0.7532 (mp) REVERT: A 473 ASN cc_start: 0.8948 (m-40) cc_final: 0.8617 (m-40) REVERT: A 494 TYR cc_start: 0.8120 (t80) cc_final: 0.6348 (m-80) REVERT: A 579 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8169 (p) REVERT: A 589 MET cc_start: 0.4585 (tpt) cc_final: 0.3611 (mmt) REVERT: A 666 MET cc_start: 0.6497 (pmm) cc_final: 0.6225 (pmm) REVERT: B 116 ARG cc_start: 0.7765 (mmm-85) cc_final: 0.7244 (mmm-85) REVERT: B 164 LYS cc_start: 0.7233 (mmpt) cc_final: 0.7026 (tmtp) REVERT: B 198 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6893 (mp) REVERT: B 204 LYS cc_start: 0.7348 (tttp) cc_final: 0.6929 (mtpp) REVERT: B 205 LEU cc_start: 0.7848 (mm) cc_final: 0.7521 (tp) REVERT: B 213 GLN cc_start: 0.7350 (tt0) cc_final: 0.6995 (tt0) REVERT: B 249 ASP cc_start: 0.7424 (t0) cc_final: 0.6844 (t0) REVERT: B 286 MET cc_start: 0.8875 (ptm) cc_final: 0.8459 (ptp) REVERT: B 301 ARG cc_start: 0.7236 (ttm110) cc_final: 0.6925 (ttm-80) REVERT: B 456 THR cc_start: 0.8718 (p) cc_final: 0.8402 (t) REVERT: B 473 ASN cc_start: 0.8941 (m-40) cc_final: 0.8611 (m-40) REVERT: B 494 TYR cc_start: 0.8152 (t80) cc_final: 0.6320 (m-80) REVERT: B 579 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8156 (p) REVERT: B 589 MET cc_start: 0.4608 (tpt) cc_final: 0.4039 (mmm) outliers start: 30 outliers final: 14 residues processed: 134 average time/residue: 0.8963 time to fit residues: 132.5150 Evaluate side-chains 126 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 680 MET Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 252 VAL 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 680 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 41 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 73 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 121 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.190824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123225 restraints weight = 9838.351| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.99 r_work: 0.3311 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9858 Z= 0.154 Angle : 0.542 6.154 13332 Z= 0.281 Chirality : 0.041 0.149 1540 Planarity : 0.004 0.042 1662 Dihedral : 5.254 31.793 1326 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.84 % Allowed : 17.71 % Favored : 79.45 % 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: -1.67 (0.24), residues: 1212 helix: -0.73 (0.20), residues: 712 sheet: -0.64 (0.49), residues: 70 loop : -1.61 (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 0.007 0.001 PHE B 571 TYR 0.010 0.001 TYR A 630 ARG 0.003 0.000 ARG A 239 *********************** 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 149 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.010 Fit side-chains REVERT: A 164 LYS cc_start: 0.7109 (mmpt) cc_final: 0.6867 (tttp) REVERT: A 179 MET cc_start: 0.7639 (mmp) cc_final: 0.7391 (mpm) REVERT: A 193 ARG cc_start: 0.7072 (mtp180) cc_final: 0.6222 (mmt90) REVERT: A 223 ILE cc_start: 0.7694 (mt) cc_final: 0.7430 (mp) REVERT: A 246 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7315 (pt) REVERT: A 301 ARG cc_start: 0.7281 (ttm110) cc_final: 0.7049 (mtp85) REVERT: A 489 MET cc_start: 0.8780 (mmp) cc_final: 0.8549 (mmm) REVERT: A 494 TYR cc_start: 0.8025 (t80) cc_final: 0.6317 (m-80) REVERT: A 579 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 589 MET cc_start: 0.4506 (tpt) cc_final: 0.3665 (mmt) REVERT: A 666 MET cc_start: 0.6583 (pmm) cc_final: 0.6292 (pmm) REVERT: B 116 ARG cc_start: 0.7769 (mmm-85) cc_final: 0.7243 (mmm-85) REVERT: B 193 ARG cc_start: 0.7113 (mtp180) cc_final: 0.6202 (mmt90) REVERT: B 204 LYS cc_start: 0.7418 (tttp) cc_final: 0.7052 (pttt) REVERT: B 205 LEU cc_start: 0.7845 (mm) cc_final: 0.7504 (tp) REVERT: B 249 ASP cc_start: 0.7227 (t0) cc_final: 0.6652 (t0) REVERT: B 286 MET cc_start: 0.8789 (ptm) cc_final: 0.8447 (ptp) REVERT: B 456 THR cc_start: 0.8618 (p) cc_final: 0.8317 (t) REVERT: B 473 ASN cc_start: 0.8945 (m-40) cc_final: 0.8744 (m-40) REVERT: B 494 TYR cc_start: 0.7994 (t80) cc_final: 0.6273 (m-80) REVERT: B 579 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8127 (p) REVERT: B 589 MET cc_start: 0.4537 (tpt) cc_final: 0.3991 (mmm) outliers start: 30 outliers final: 15 residues processed: 138 average time/residue: 0.9304 time to fit residues: 141.4137 Evaluate side-chains 129 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 339 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 690 THR 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 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: 0.0010 chunk 50 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 112 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 41 optimal weight: 0.0000 chunk 86 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.1790 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.194723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127296 restraints weight = 9882.967| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.01 r_work: 0.3342 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9858 Z= 0.115 Angle : 0.516 7.084 13332 Z= 0.265 Chirality : 0.040 0.140 1540 Planarity : 0.004 0.039 1662 Dihedral : 4.921 32.427 1326 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.75 % Allowed : 18.75 % Favored : 78.50 % 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: -1.15 (0.25), residues: 1212 helix: -0.22 (0.21), residues: 702 sheet: -0.27 (0.51), residues: 70 loop : -1.59 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 572 HIS 0.002 0.000 HIS A 623 PHE 0.009 0.001 PHE A 571 TYR 0.006 0.001 TYR A 630 ARG 0.002 0.000 ARG B 237 *********************** 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 159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.111 Fit side-chains REVERT: A 245 ASP cc_start: 0.7900 (m-30) cc_final: 0.7645 (m-30) REVERT: A 246 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7280 (pt) REVERT: A 249 ASP cc_start: 0.7179 (t0) cc_final: 0.6489 (t0) REVERT: A 301 ARG cc_start: 0.7300 (ttm110) cc_final: 0.7059 (mtp85) REVERT: A 494 TYR cc_start: 0.7657 (t80) cc_final: 0.6324 (m-80) REVERT: A 541 LEU cc_start: 0.8443 (tp) cc_final: 0.8006 (mt) REVERT: A 589 MET cc_start: 0.4540 (tpt) cc_final: 0.3766 (mmt) REVERT: A 666 MET cc_start: 0.6591 (pmm) cc_final: 0.6283 (pmm) REVERT: B 116 ARG cc_start: 0.7709 (mmm-85) cc_final: 0.7331 (mmm-85) REVERT: B 213 GLN cc_start: 0.7131 (tt0) cc_final: 0.6879 (tt0) REVERT: B 246 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7342 (pt) REVERT: B 249 ASP cc_start: 0.7068 (t0) cc_final: 0.6440 (t0) REVERT: B 286 MET cc_start: 0.8691 (ptm) cc_final: 0.8348 (ptp) REVERT: B 301 ARG cc_start: 0.7246 (ttm110) cc_final: 0.6689 (ttp-110) REVERT: B 456 THR cc_start: 0.8608 (p) cc_final: 0.8291 (t) REVERT: B 473 ASN cc_start: 0.8998 (m-40) cc_final: 0.8716 (m-40) REVERT: B 494 TYR cc_start: 0.7662 (t80) cc_final: 0.6269 (m-80) REVERT: B 541 LEU cc_start: 0.8472 (tp) cc_final: 0.8026 (mt) REVERT: B 589 MET cc_start: 0.4432 (tpt) cc_final: 0.3993 (mmm) outliers start: 29 outliers final: 9 residues processed: 150 average time/residue: 0.9134 time to fit residues: 150.5644 Evaluate side-chains 126 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 311 VAL Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 402 VAL 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: 2.9990 chunk 12 optimal weight: 0.8980 chunk 73 optimal weight: 0.0170 chunk 8 optimal weight: 0.0570 chunk 76 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.195349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127055 restraints weight = 9863.964| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.23 r_work: 0.3407 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9858 Z= 0.147 Angle : 0.538 7.721 13332 Z= 0.274 Chirality : 0.041 0.146 1540 Planarity : 0.004 0.038 1662 Dihedral : 4.895 29.297 1326 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.65 % Allowed : 20.55 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1212 helix: -0.09 (0.21), residues: 700 sheet: -0.14 (0.51), residues: 70 loop : -1.51 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 429 HIS 0.002 0.000 HIS A 587 PHE 0.009 0.001 PHE B 571 TYR 0.010 0.001 TYR A 630 ARG 0.004 0.000 ARG A 193 *********************** 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 144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.100 Fit side-chains REVERT: A 200 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7244 (tttt) REVERT: A 236 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5722 (tm-30) REVERT: A 246 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.6835 (pt) REVERT: A 494 TYR cc_start: 0.7453 (t80) cc_final: 0.5818 (m-80) REVERT: A 541 LEU cc_start: 0.7868 (tp) cc_final: 0.7512 (mt) REVERT: A 579 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7694 (p) REVERT: A 589 MET cc_start: 0.4204 (tpt) cc_final: 0.3435 (mmt) REVERT: A 666 MET cc_start: 0.6893 (pmm) cc_final: 0.6521 (pmm) REVERT: B 116 ARG cc_start: 0.7363 (mmm-85) cc_final: 0.6380 (ttm-80) REVERT: B 213 GLN cc_start: 0.6494 (tt0) cc_final: 0.6242 (tt0) REVERT: B 246 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.6927 (pt) REVERT: B 249 ASP cc_start: 0.6976 (t0) cc_final: 0.6267 (t0) REVERT: B 286 MET cc_start: 0.8416 (ptm) cc_final: 0.7984 (ptp) REVERT: B 301 ARG cc_start: 0.6721 (ttm110) cc_final: 0.6167 (ttp-110) REVERT: B 473 ASN cc_start: 0.8847 (m-40) cc_final: 0.8541 (m-40) REVERT: B 494 TYR cc_start: 0.7378 (t80) cc_final: 0.5721 (m-80) REVERT: B 541 LEU cc_start: 0.7904 (tp) cc_final: 0.7543 (mt) REVERT: B 579 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7688 (p) REVERT: B 589 MET cc_start: 0.4004 (tpt) cc_final: 0.3612 (mmm) outliers start: 28 outliers final: 15 residues processed: 134 average time/residue: 0.9874 time to fit residues: 144.7491 Evaluate side-chains 129 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 252 VAL 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 540 SER Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 310 THR 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 680 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.190677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121790 restraints weight = 10081.069| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.25 r_work: 0.3354 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9858 Z= 0.284 Angle : 0.596 7.951 13332 Z= 0.305 Chirality : 0.044 0.156 1540 Planarity : 0.004 0.036 1662 Dihedral : 5.257 29.364 1326 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.84 % Allowed : 20.45 % Favored : 76.70 % 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: -1.15 (0.25), residues: 1212 helix: -0.33 (0.20), residues: 712 sheet: -0.13 (0.51), residues: 70 loop : -1.44 (0.31), residues: 430 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 0.012 0.001 PHE B 562 TYR 0.013 0.002 TYR B 630 ARG 0.005 0.000 ARG A 239 *********************** 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 146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.934 Fit side-chains REVERT: A 200 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7248 (tttt) REVERT: A 494 TYR cc_start: 0.7867 (t80) cc_final: 0.5738 (m-80) REVERT: A 541 LEU cc_start: 0.7904 (tp) cc_final: 0.7554 (mt) REVERT: A 579 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7683 (p) REVERT: A 589 MET cc_start: 0.4216 (tpt) cc_final: 0.3281 (mmt) REVERT: B 116 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.6745 (mmm-85) REVERT: B 204 LYS cc_start: 0.7211 (tttp) cc_final: 0.6777 (mtpp) REVERT: B 205 LEU cc_start: 0.7742 (mm) cc_final: 0.7456 (tp) REVERT: B 249 ASP cc_start: 0.7161 (t0) cc_final: 0.6534 (t0) REVERT: B 301 ARG cc_start: 0.6728 (ttm110) cc_final: 0.6306 (ttp-110) REVERT: B 439 SER cc_start: 0.7578 (OUTLIER) cc_final: 0.7016 (m) REVERT: B 473 ASN cc_start: 0.8881 (m-40) cc_final: 0.8535 (m-40) REVERT: B 494 TYR cc_start: 0.7809 (t80) cc_final: 0.5722 (m-80) REVERT: B 541 LEU cc_start: 0.7888 (tp) cc_final: 0.7557 (mt) REVERT: B 579 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7707 (p) REVERT: B 589 MET cc_start: 0.4061 (tpt) cc_final: 0.3537 (mmm) outliers start: 30 outliers final: 17 residues processed: 138 average time/residue: 0.8622 time to fit residues: 131.3933 Evaluate side-chains 131 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 252 VAL 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 540 SER Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 339 PHE Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 680 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.190395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122224 restraints weight = 9958.602| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.22 r_work: 0.3357 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9858 Z= 0.277 Angle : 0.598 7.963 13332 Z= 0.306 Chirality : 0.044 0.154 1540 Planarity : 0.004 0.037 1662 Dihedral : 5.315 29.171 1326 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.56 % Allowed : 21.69 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1212 helix: -0.37 (0.20), residues: 706 sheet: -0.16 (0.52), residues: 70 loop : -1.48 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 429 HIS 0.003 0.001 HIS A 587 PHE 0.011 0.001 PHE B 562 TYR 0.012 0.002 TYR B 630 ARG 0.006 0.000 ARG B 444 *********************** 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 134 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.094 Fit side-chains REVERT: A 200 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7234 (ttmt) REVERT: A 439 SER cc_start: 0.7381 (OUTLIER) cc_final: 0.6824 (m) REVERT: A 494 TYR cc_start: 0.7862 (t80) cc_final: 0.5779 (m-80) REVERT: A 541 LEU cc_start: 0.7908 (tp) cc_final: 0.7569 (mt) REVERT: A 579 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.7768 (p) REVERT: A 589 MET cc_start: 0.4123 (tpt) cc_final: 0.3238 (mmt) REVERT: B 116 ARG cc_start: 0.7431 (mmm-85) cc_final: 0.7011 (mmm-85) REVERT: B 204 LYS cc_start: 0.7176 (tttp) cc_final: 0.6716 (mtpp) REVERT: B 205 LEU cc_start: 0.7766 (mm) cc_final: 0.7487 (tp) REVERT: B 249 ASP cc_start: 0.7224 (t0) cc_final: 0.6576 (t0) REVERT: B 301 ARG cc_start: 0.6819 (ttm110) cc_final: 0.6399 (ttp-110) REVERT: B 439 SER cc_start: 0.7604 (OUTLIER) cc_final: 0.7039 (m) REVERT: B 473 ASN cc_start: 0.8886 (m-40) cc_final: 0.8552 (m-40) REVERT: B 494 TYR cc_start: 0.7808 (t80) cc_final: 0.5805 (m-80) REVERT: B 541 LEU cc_start: 0.7914 (tp) cc_final: 0.7558 (mt) REVERT: B 579 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.7755 (p) REVERT: B 589 MET cc_start: 0.4083 (tpt) cc_final: 0.3570 (mmm) outliers start: 27 outliers final: 14 residues processed: 126 average time/residue: 0.8819 time to fit residues: 123.4440 Evaluate side-chains 125 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 339 PHE Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 680 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 117 optimal weight: 0.0000 chunk 52 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.192793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124055 restraints weight = 9949.347| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.24 r_work: 0.3409 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9858 Z= 0.191 Angle : 0.567 7.913 13332 Z= 0.290 Chirality : 0.042 0.149 1540 Planarity : 0.004 0.037 1662 Dihedral : 5.180 31.286 1326 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.37 % Allowed : 21.78 % Favored : 75.85 % 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: -0.96 (0.25), residues: 1212 helix: -0.11 (0.21), residues: 700 sheet: -0.08 (0.52), residues: 70 loop : -1.45 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 429 HIS 0.002 0.001 HIS A 587 PHE 0.008 0.001 PHE A 571 TYR 0.011 0.001 TYR B 630 ARG 0.006 0.000 ARG B 444 ********************** 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 130 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.004 Fit side-chains REVERT: A 439 SER cc_start: 0.7358 (OUTLIER) cc_final: 0.6807 (m) REVERT: A 494 TYR cc_start: 0.7698 (t80) cc_final: 0.5696 (m-80) REVERT: A 541 LEU cc_start: 0.7899 (tp) cc_final: 0.7550 (mt) REVERT: A 579 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7756 (p) REVERT: A 589 MET cc_start: 0.4107 (tpt) cc_final: 0.3282 (mmt) REVERT: B 116 ARG cc_start: 0.7477 (mmm-85) cc_final: 0.6802 (mmm-85) REVERT: B 204 LYS cc_start: 0.7209 (tttp) cc_final: 0.6759 (mtpp) REVERT: B 249 ASP cc_start: 0.7105 (t0) cc_final: 0.6457 (t0) REVERT: B 301 ARG cc_start: 0.6788 (ttm110) cc_final: 0.6377 (ttp-110) REVERT: B 439 SER cc_start: 0.7597 (OUTLIER) cc_final: 0.7026 (m) REVERT: B 473 ASN cc_start: 0.8881 (m-40) cc_final: 0.8530 (m-40) REVERT: B 494 TYR cc_start: 0.7688 (t80) cc_final: 0.5712 (m-80) REVERT: B 541 LEU cc_start: 0.7903 (tp) cc_final: 0.7545 (mt) REVERT: B 579 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7747 (p) REVERT: B 589 MET cc_start: 0.4096 (tpt) cc_final: 0.3550 (mmm) outliers start: 25 outliers final: 14 residues processed: 125 average time/residue: 0.8913 time to fit residues: 123.1282 Evaluate side-chains 119 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 680 MET 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 339 PHE Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 680 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN B 528 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.189268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.120890 restraints weight = 10082.360| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.24 r_work: 0.3369 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9858 Z= 0.335 Angle : 0.637 7.981 13332 Z= 0.324 Chirality : 0.046 0.159 1540 Planarity : 0.004 0.037 1662 Dihedral : 5.464 28.127 1326 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.99 % Allowed : 22.44 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.24), residues: 1212 helix: -0.36 (0.20), residues: 706 sheet: -0.11 (0.51), residues: 68 loop : -1.43 (0.30), residues: 438 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 B 630 ARG 0.005 0.000 ARG B 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6946.26 seconds wall clock time: 123 minutes 11.91 seconds (7391.91 seconds total)