Starting phenix.real_space_refine on Wed Sep 17 16:22:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtp_37839/09_2025/8wtp_37839.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtp_37839/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wtp_37839/09_2025/8wtp_37839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtp_37839/09_2025/8wtp_37839.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wtp_37839/09_2025/8wtp_37839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtp_37839/09_2025/8wtp_37839.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.38, per 1000 atoms: 0.25 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: 0.71 Conformation dependent library (CDL) restraints added in 380.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.36 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: 1.58 Time building geometry restraints manager: 1.00 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: 0.02 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.200 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.400 ------------------------------------------------------------------------------- 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 : 5.63 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG B 206 TYR 0.016 0.003 TYR A 519 PHE 0.031 0.003 PHE A 715 TRP 0.010 0.002 TRP A 429 HIS 0.005 0.002 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00919 ( 9858) covalent geometry : angle 1.03412 (13332) SS BOND : bond 0.00335 ( 2) SS BOND : angle 1.61247 ( 4) hydrogen bonds : bond 0.29685 ( 383) hydrogen bonds : angle 10.47714 ( 1110) *********************** 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 : 0.374 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: 0.4959 time to fit residues: 75.7610 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 : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.189302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122755 restraints weight = 9989.098| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.97 r_work: 0.3287 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1666 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= 0.119 Angle : 0.586 6.484 13336 Z= 0.312 Chirality : 0.040 0.154 1540 Planarity : 0.006 0.061 1662 Dihedral : 6.086 33.295 1326 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.04 % Allowed : 13.73 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.20), residues: 1212 helix: -2.77 (0.15), residues: 674 sheet: -1.60 (0.45), residues: 80 loop : -2.24 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 193 TYR 0.010 0.001 TYR A 630 PHE 0.008 0.001 PHE B 268 TRP 0.012 0.001 TRP B 572 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9858) covalent geometry : angle 0.58555 (13332) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.86458 ( 4) hydrogen bonds : bond 0.03562 ( 383) hydrogen bonds : angle 5.15225 ( 1110) *********************** 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 : 0.375 Fit side-chains REVERT: A 164 LYS cc_start: 0.7464 (mmpt) cc_final: 0.7156 (tttt) REVERT: A 204 LYS cc_start: 0.7315 (mmmm) cc_final: 0.6735 (ptmm) REVERT: A 223 ILE cc_start: 0.7684 (mt) cc_final: 0.7421 (mp) REVERT: A 288 ILE cc_start: 0.8011 (mt) cc_final: 0.7786 (mt) REVERT: A 301 ARG cc_start: 0.7226 (ttm110) cc_final: 0.6779 (ttp-110) REVERT: A 473 ASN cc_start: 0.8942 (m-40) cc_final: 0.8628 (m-40) REVERT: A 489 MET cc_start: 0.8831 (mmp) cc_final: 0.8606 (mmm) REVERT: A 494 TYR cc_start: 0.8042 (t80) cc_final: 0.6282 (m-80) REVERT: A 528 HIS cc_start: 0.8073 (t-90) cc_final: 0.7552 (t70) REVERT: A 589 MET cc_start: 0.4498 (tpt) cc_final: 0.3592 (mmt) REVERT: A 680 MET cc_start: 0.7055 (mtt) cc_final: 0.6817 (mtm) REVERT: B 116 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7556 (mmm-85) REVERT: B 164 LYS cc_start: 0.7436 (mmpt) cc_final: 0.7134 (tttp) REVERT: B 179 MET cc_start: 0.7836 (mmp) cc_final: 0.7601 (mpm) REVERT: B 204 LYS cc_start: 0.7443 (tttp) cc_final: 0.7053 (mtpp) REVERT: B 249 ASP cc_start: 0.7408 (t0) cc_final: 0.6799 (t0) REVERT: B 456 THR cc_start: 0.8680 (p) cc_final: 0.8422 (t) REVERT: B 473 ASN cc_start: 0.8931 (m110) cc_final: 0.8626 (m-40) REVERT: B 494 TYR cc_start: 0.7991 (t80) cc_final: 0.6257 (m-80) REVERT: B 528 HIS cc_start: 0.8077 (t-90) cc_final: 0.7546 (t70) REVERT: B 589 MET cc_start: 0.4430 (tpt) cc_final: 0.4041 (mmm) outliers start: 11 outliers final: 2 residues processed: 139 average time/residue: 0.4710 time to fit residues: 71.5135 Evaluate side-chains 122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 114 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 108 optimal weight: 0.0040 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.187702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120184 restraints weight = 9971.564| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.98 r_work: 0.3251 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1872 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 : 0.593 6.976 13336 Z= 0.308 Chirality : 0.042 0.158 1540 Planarity : 0.004 0.054 1662 Dihedral : 5.712 28.854 1326 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.46 % Allowed : 15.44 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.22), residues: 1212 helix: -1.78 (0.18), residues: 694 sheet: -0.99 (0.47), residues: 70 loop : -1.94 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 239 TYR 0.013 0.001 TYR A 630 PHE 0.011 0.001 PHE A 562 TRP 0.009 0.001 TRP B 429 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9858) covalent geometry : angle 0.59264 (13332) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.73766 ( 4) hydrogen bonds : bond 0.03517 ( 383) hydrogen bonds : angle 4.63531 ( 1110) *********************** 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 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.368 Fit side-chains REVERT: A 164 LYS cc_start: 0.7383 (mmpt) cc_final: 0.7107 (tttt) REVERT: A 179 MET cc_start: 0.7786 (mmp) cc_final: 0.7540 (mpm) REVERT: A 204 LYS cc_start: 0.7318 (mmmm) cc_final: 0.6798 (pttt) REVERT: A 223 ILE cc_start: 0.7679 (mt) cc_final: 0.7427 (mp) REVERT: A 473 ASN cc_start: 0.8948 (m-40) cc_final: 0.8737 (m-40) REVERT: A 494 TYR cc_start: 0.8146 (t80) cc_final: 0.6333 (m-80) REVERT: A 589 MET cc_start: 0.4579 (tpt) cc_final: 0.3591 (mmt) REVERT: A 666 MET cc_start: 0.6462 (pmm) cc_final: 0.6250 (pmm) REVERT: B 116 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7568 (mmm-85) REVERT: B 164 LYS cc_start: 0.7284 (mmpt) cc_final: 0.7026 (tttp) REVERT: B 179 MET cc_start: 0.7849 (mmp) cc_final: 0.7610 (mpm) REVERT: B 204 LYS cc_start: 0.7402 (tttp) cc_final: 0.6966 (mtpp) REVERT: B 205 LEU cc_start: 0.7863 (mm) cc_final: 0.7510 (tp) REVERT: B 223 ILE cc_start: 0.7690 (mt) cc_final: 0.7434 (mp) REVERT: B 249 ASP cc_start: 0.7445 (t0) cc_final: 0.6852 (t0) REVERT: B 286 MET cc_start: 0.8937 (ptm) cc_final: 0.8603 (ptp) REVERT: B 301 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6808 (ttm-80) REVERT: B 456 THR cc_start: 0.8727 (p) cc_final: 0.8437 (t) REVERT: B 473 ASN cc_start: 0.8939 (m-40) cc_final: 0.8589 (m-40) REVERT: B 494 TYR cc_start: 0.8166 (t80) cc_final: 0.6357 (m-80) REVERT: B 589 MET cc_start: 0.4578 (tpt) cc_final: 0.4095 (mmm) outliers start: 26 outliers final: 7 residues processed: 144 average time/residue: 0.4508 time to fit residues: 71.1905 Evaluate side-chains 119 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 97 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 68 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.190256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122657 restraints weight = 9999.008| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.00 r_work: 0.3282 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9860 Z= 0.110 Angle : 0.546 6.150 13336 Z= 0.283 Chirality : 0.041 0.150 1540 Planarity : 0.004 0.051 1662 Dihedral : 5.411 32.982 1326 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.56 % Allowed : 15.72 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.23), residues: 1212 helix: -1.18 (0.19), residues: 712 sheet: -0.70 (0.48), residues: 70 loop : -1.81 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.010 0.001 TYR A 630 PHE 0.007 0.001 PHE A 75 TRP 0.009 0.001 TRP A 572 HIS 0.002 0.001 HIS A 623 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9858) covalent geometry : angle 0.54644 (13332) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.66503 ( 4) hydrogen bonds : bond 0.02811 ( 383) hydrogen bonds : angle 4.29371 ( 1110) *********************** 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 145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.462 Fit side-chains REVERT: A 164 LYS cc_start: 0.7253 (mmpt) cc_final: 0.7012 (tttt) REVERT: A 193 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6230 (mmt90) REVERT: A 223 ILE cc_start: 0.7746 (mt) cc_final: 0.7513 (mp) REVERT: A 301 ARG cc_start: 0.7314 (ttm110) cc_final: 0.7077 (mtp85) REVERT: A 473 ASN cc_start: 0.8939 (m-40) cc_final: 0.8592 (m-40) REVERT: A 494 TYR cc_start: 0.8030 (t80) cc_final: 0.6276 (m-80) REVERT: A 579 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8167 (p) REVERT: A 589 MET cc_start: 0.4542 (tpt) cc_final: 0.3649 (mmt) REVERT: A 666 MET cc_start: 0.6457 (pmm) cc_final: 0.6180 (pmm) REVERT: B 116 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.7261 (mmm-85) REVERT: B 164 LYS cc_start: 0.7099 (mmpt) cc_final: 0.6873 (tttp) REVERT: B 204 LYS cc_start: 0.7459 (tttp) cc_final: 0.7032 (mtpp) REVERT: B 205 LEU cc_start: 0.7838 (mm) cc_final: 0.7521 (tp) REVERT: B 249 ASP cc_start: 0.7313 (t0) cc_final: 0.6725 (t0) REVERT: B 286 MET cc_start: 0.8851 (ptm) cc_final: 0.8430 (ptp) REVERT: B 301 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6834 (ttp-110) REVERT: B 456 THR cc_start: 0.8618 (p) cc_final: 0.8332 (t) REVERT: B 494 TYR cc_start: 0.8040 (t80) cc_final: 0.6288 (m-80) REVERT: B 579 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8147 (p) REVERT: B 589 MET cc_start: 0.4626 (tpt) cc_final: 0.4054 (mmm) outliers start: 27 outliers final: 11 residues processed: 138 average time/residue: 0.4539 time to fit residues: 68.8357 Evaluate side-chains 125 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 456 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 680 MET 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 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 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 102 optimal weight: 0.0050 chunk 81 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.191816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124240 restraints weight = 9926.948| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.01 r_work: 0.3322 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9860 Z= 0.095 Angle : 0.527 6.251 13336 Z= 0.272 Chirality : 0.040 0.148 1540 Planarity : 0.004 0.044 1662 Dihedral : 5.115 30.783 1326 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.46 % Allowed : 17.71 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.24), residues: 1212 helix: -0.63 (0.20), residues: 712 sheet: -0.44 (0.49), residues: 70 loop : -1.61 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 239 TYR 0.009 0.001 TYR B 630 PHE 0.007 0.001 PHE A 571 TRP 0.010 0.001 TRP B 572 HIS 0.002 0.000 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9858) covalent geometry : angle 0.52666 (13332) SS BOND : bond 0.00128 ( 2) SS BOND : angle 1.02425 ( 4) hydrogen bonds : bond 0.02559 ( 383) hydrogen bonds : angle 4.04569 ( 1110) *********************** 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 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.409 Fit side-chains REVERT: A 179 MET cc_start: 0.7588 (mmp) cc_final: 0.7359 (mpm) REVERT: A 193 ARG cc_start: 0.6978 (mtp180) cc_final: 0.6755 (mtm-85) REVERT: A 223 ILE cc_start: 0.7713 (mt) cc_final: 0.7459 (mp) REVERT: A 269 MET cc_start: 0.6242 (tpp) cc_final: 0.6023 (tpp) REVERT: A 301 ARG cc_start: 0.7289 (ttm110) cc_final: 0.7051 (mtp85) REVERT: A 473 ASN cc_start: 0.8931 (m-40) cc_final: 0.8719 (m-40) REVERT: A 494 TYR cc_start: 0.7857 (t80) cc_final: 0.6214 (m-80) REVERT: A 541 LEU cc_start: 0.8540 (tp) cc_final: 0.8097 (mt) REVERT: A 579 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 589 MET cc_start: 0.4424 (tpt) cc_final: 0.3599 (mmt) REVERT: A 666 MET cc_start: 0.6526 (pmm) cc_final: 0.6233 (pmm) REVERT: B 116 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7253 (mmm-85) REVERT: B 193 ARG cc_start: 0.7052 (mtp180) cc_final: 0.6195 (mmt90) REVERT: B 205 LEU cc_start: 0.7911 (mm) cc_final: 0.7613 (tp) REVERT: B 249 ASP cc_start: 0.7195 (t0) cc_final: 0.6611 (t0) REVERT: B 286 MET cc_start: 0.8791 (ptm) cc_final: 0.8396 (ptp) REVERT: B 456 THR cc_start: 0.8565 (p) cc_final: 0.8284 (t) REVERT: B 494 TYR cc_start: 0.7864 (t80) cc_final: 0.6219 (m-80) REVERT: B 541 LEU cc_start: 0.8564 (tp) cc_final: 0.8097 (mt) REVERT: B 579 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8153 (p) REVERT: B 589 MET cc_start: 0.4470 (tpt) cc_final: 0.3931 (mmm) outliers start: 26 outliers final: 10 residues processed: 131 average time/residue: 0.4485 time to fit residues: 64.5509 Evaluate side-chains 120 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 456 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 680 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.190577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122663 restraints weight = 9949.916| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.00 r_work: 0.3259 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9860 Z= 0.120 Angle : 0.547 6.116 13336 Z= 0.281 Chirality : 0.041 0.150 1540 Planarity : 0.004 0.041 1662 Dihedral : 5.127 31.009 1326 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.46 % Allowed : 19.60 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.25), residues: 1212 helix: -0.39 (0.21), residues: 706 sheet: -0.29 (0.49), residues: 70 loop : -1.54 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 239 TYR 0.011 0.001 TYR A 630 PHE 0.008 0.001 PHE B 562 TRP 0.009 0.001 TRP B 429 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9858) covalent geometry : angle 0.54719 (13332) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.93412 ( 4) hydrogen bonds : bond 0.02731 ( 383) hydrogen bonds : angle 4.03834 ( 1110) *********************** 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 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.393 Fit side-chains REVERT: A 179 MET cc_start: 0.7766 (mmp) cc_final: 0.7503 (mpm) REVERT: A 223 ILE cc_start: 0.7741 (mt) cc_final: 0.7490 (mp) REVERT: A 246 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7296 (pt) REVERT: A 301 ARG cc_start: 0.7264 (ttm110) cc_final: 0.7054 (mtp85) REVERT: A 473 ASN cc_start: 0.8990 (m-40) cc_final: 0.8769 (m-40) REVERT: A 494 TYR cc_start: 0.7981 (t80) cc_final: 0.6308 (m-80) REVERT: A 541 LEU cc_start: 0.8389 (tp) cc_final: 0.8005 (mt) REVERT: A 579 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 589 MET cc_start: 0.4412 (tpt) cc_final: 0.3579 (mmt) REVERT: A 666 MET cc_start: 0.6619 (pmm) cc_final: 0.6307 (pmm) REVERT: B 116 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7380 (mmm-85) REVERT: B 193 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6823 (mtm-85) REVERT: B 205 LEU cc_start: 0.7940 (mm) cc_final: 0.7640 (tp) REVERT: B 249 ASP cc_start: 0.7302 (t0) cc_final: 0.6710 (t0) REVERT: B 286 MET cc_start: 0.8797 (ptm) cc_final: 0.8362 (ptp) REVERT: B 301 ARG cc_start: 0.7230 (ttm110) cc_final: 0.6855 (ttp-110) REVERT: B 367 MET cc_start: 0.6979 (mmm) cc_final: 0.6755 (ptm) REVERT: B 456 THR cc_start: 0.8688 (p) cc_final: 0.8375 (t) REVERT: B 494 TYR cc_start: 0.7956 (t80) cc_final: 0.6291 (m-80) REVERT: B 541 LEU cc_start: 0.8381 (tp) cc_final: 0.7990 (mt) REVERT: B 579 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8155 (p) REVERT: B 589 MET cc_start: 0.4439 (tpt) cc_final: 0.3893 (mmm) outliers start: 26 outliers final: 14 residues processed: 133 average time/residue: 0.4588 time to fit residues: 66.8709 Evaluate side-chains 124 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 246 ILE 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 579 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 233 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.189946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121181 restraints weight = 9902.866| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.06 r_work: 0.3275 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9860 Z= 0.149 Angle : 0.571 6.260 13336 Z= 0.294 Chirality : 0.042 0.154 1540 Planarity : 0.004 0.039 1662 Dihedral : 5.206 28.917 1326 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.65 % Allowed : 19.60 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.25), residues: 1212 helix: -0.31 (0.20), residues: 712 sheet: -0.28 (0.49), residues: 70 loop : -1.51 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 193 TYR 0.012 0.001 TYR A 630 PHE 0.010 0.001 PHE A 562 TRP 0.009 0.001 TRP B 429 HIS 0.002 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9858) covalent geometry : angle 0.57089 (13332) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.94509 ( 4) hydrogen bonds : bond 0.02963 ( 383) hydrogen bonds : angle 4.07541 ( 1110) *********************** 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 139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.388 Fit side-chains REVERT: A 179 MET cc_start: 0.7709 (mmp) cc_final: 0.7390 (mpm) REVERT: A 223 ILE cc_start: 0.7678 (mt) cc_final: 0.7426 (mp) REVERT: A 439 SER cc_start: 0.7879 (OUTLIER) cc_final: 0.7323 (m) REVERT: A 473 ASN cc_start: 0.8985 (m-40) cc_final: 0.8661 (m-40) REVERT: A 494 TYR cc_start: 0.8075 (t80) cc_final: 0.6268 (m-80) REVERT: A 541 LEU cc_start: 0.8271 (tp) cc_final: 0.7944 (mt) REVERT: A 579 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8152 (p) REVERT: A 589 MET cc_start: 0.4427 (tpt) cc_final: 0.3541 (mmt) REVERT: B 116 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7325 (mmm-85) REVERT: B 193 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6279 (mmt90) REVERT: B 204 LYS cc_start: 0.7376 (tttp) cc_final: 0.6920 (mtpp) REVERT: B 205 LEU cc_start: 0.7942 (mm) cc_final: 0.7633 (tp) REVERT: B 233 SER cc_start: 0.7473 (m) cc_final: 0.7052 (p) REVERT: B 249 ASP cc_start: 0.7340 (t0) cc_final: 0.6732 (t0) REVERT: B 301 ARG cc_start: 0.7245 (ttm110) cc_final: 0.6830 (ttp-110) REVERT: B 456 THR cc_start: 0.8699 (p) cc_final: 0.8369 (t) REVERT: B 494 TYR cc_start: 0.8031 (t80) cc_final: 0.6225 (m-80) REVERT: B 541 LEU cc_start: 0.8288 (tp) cc_final: 0.7954 (mt) REVERT: B 579 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8121 (p) REVERT: B 589 MET cc_start: 0.4478 (tpt) cc_final: 0.3954 (mmm) outliers start: 28 outliers final: 13 residues processed: 132 average time/residue: 0.4612 time to fit residues: 66.7470 Evaluate side-chains 125 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 252 VAL 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 456 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 114 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 154 ASN B 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121674 restraints weight = 9979.712| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.22 r_work: 0.3376 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9860 Z= 0.181 Angle : 0.593 6.412 13336 Z= 0.305 Chirality : 0.044 0.156 1540 Planarity : 0.004 0.038 1662 Dihedral : 5.369 30.136 1326 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.75 % Allowed : 20.17 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.25), residues: 1212 helix: -0.32 (0.20), residues: 706 sheet: -0.11 (0.50), residues: 68 loop : -1.52 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 239 TYR 0.012 0.001 TYR B 630 PHE 0.012 0.001 PHE A 562 TRP 0.009 0.001 TRP B 429 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 9858) covalent geometry : angle 0.59278 (13332) SS BOND : bond 0.00279 ( 2) SS BOND : angle 1.21706 ( 4) hydrogen bonds : bond 0.03146 ( 383) hydrogen bonds : angle 4.16943 ( 1110) *********************** 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 144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.404 Fit side-chains REVERT: A 179 MET cc_start: 0.7480 (mmp) cc_final: 0.7168 (mpm) REVERT: A 223 ILE cc_start: 0.7465 (mt) cc_final: 0.7205 (mp) REVERT: A 439 SER cc_start: 0.7471 (OUTLIER) cc_final: 0.6927 (m) REVERT: A 473 ASN cc_start: 0.8887 (m-40) cc_final: 0.8568 (m-40) REVERT: A 494 TYR cc_start: 0.7873 (t80) cc_final: 0.5868 (m-80) REVERT: A 541 LEU cc_start: 0.7884 (tp) cc_final: 0.7567 (mt) REVERT: A 589 MET cc_start: 0.4098 (tpt) cc_final: 0.3209 (mmt) REVERT: B 116 ARG cc_start: 0.7463 (mmm-85) cc_final: 0.7044 (mmm-85) REVERT: B 204 LYS cc_start: 0.7139 (tttp) cc_final: 0.6679 (mtpp) REVERT: B 205 LEU cc_start: 0.7779 (mm) cc_final: 0.7500 (tp) REVERT: B 249 ASP cc_start: 0.7230 (t0) cc_final: 0.6580 (t0) REVERT: B 286 MET cc_start: 0.8530 (ptm) cc_final: 0.8254 (ptp) REVERT: B 301 ARG cc_start: 0.6819 (ttm110) cc_final: 0.6360 (ttp-110) REVERT: B 367 MET cc_start: 0.7193 (mtp) cc_final: 0.6833 (mmm) REVERT: B 494 TYR cc_start: 0.7832 (t80) cc_final: 0.5836 (m-80) REVERT: B 541 LEU cc_start: 0.7889 (tp) cc_final: 0.7571 (mt) REVERT: B 589 MET cc_start: 0.4046 (tpt) cc_final: 0.3514 (mmm) outliers start: 29 outliers final: 19 residues processed: 137 average time/residue: 0.4265 time to fit residues: 64.4521 Evaluate side-chains 128 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 439 SER 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 115 THR 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 680 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.190066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122041 restraints weight = 9969.739| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.21 r_work: 0.3354 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9860 Z= 0.174 Angle : 0.596 6.280 13336 Z= 0.305 Chirality : 0.044 0.152 1540 Planarity : 0.004 0.038 1662 Dihedral : 5.376 29.976 1326 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.25), residues: 1212 helix: -0.26 (0.20), residues: 706 sheet: -0.30 (0.50), residues: 70 loop : -1.54 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 193 TYR 0.012 0.001 TYR A 630 PHE 0.011 0.001 PHE A 562 TRP 0.009 0.001 TRP B 429 HIS 0.003 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9858) covalent geometry : angle 0.59565 (13332) SS BOND : bond 0.00184 ( 2) SS BOND : angle 1.44097 ( 4) hydrogen bonds : bond 0.03082 ( 383) hydrogen bonds : angle 4.14812 ( 1110) *********************** 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 136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.348 Fit side-chains REVERT: A 179 MET cc_start: 0.7436 (mmp) cc_final: 0.7114 (mpm) REVERT: A 223 ILE cc_start: 0.7448 (mt) cc_final: 0.7186 (mp) REVERT: A 439 SER cc_start: 0.7420 (OUTLIER) cc_final: 0.6885 (m) REVERT: A 473 ASN cc_start: 0.8877 (m-40) cc_final: 0.8547 (m-40) REVERT: A 494 TYR cc_start: 0.7809 (t80) cc_final: 0.5802 (m-80) REVERT: A 541 LEU cc_start: 0.7917 (tp) cc_final: 0.7565 (mt) REVERT: A 579 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7748 (p) REVERT: A 589 MET cc_start: 0.4078 (tpt) cc_final: 0.3198 (mmt) REVERT: B 116 ARG cc_start: 0.7438 (mmm-85) cc_final: 0.7003 (mmm-85) REVERT: B 204 LYS cc_start: 0.7175 (tttp) cc_final: 0.6706 (mtpp) REVERT: B 249 ASP cc_start: 0.7257 (t0) cc_final: 0.6608 (t0) REVERT: B 286 MET cc_start: 0.8530 (ptm) cc_final: 0.8236 (ptp) REVERT: B 301 ARG cc_start: 0.6822 (ttm110) cc_final: 0.6381 (ttp-110) REVERT: B 367 MET cc_start: 0.7244 (mtp) cc_final: 0.6788 (mmm) REVERT: B 494 TYR cc_start: 0.7736 (t80) cc_final: 0.5696 (m-80) REVERT: B 541 LEU cc_start: 0.7840 (tp) cc_final: 0.7491 (mt) REVERT: B 579 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.7739 (p) REVERT: B 589 MET cc_start: 0.4084 (tpt) cc_final: 0.3572 (mmm) outliers start: 28 outliers final: 16 residues processed: 129 average time/residue: 0.4198 time to fit residues: 59.7552 Evaluate side-chains 126 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 310 THR 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 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 163 LEU Chi-restraints excluded: chain B residue 233 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.0270 chunk 95 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.194041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125606 restraints weight = 9862.939| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.23 r_work: 0.3422 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2772 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= 0.104 Angle : 0.545 7.212 13336 Z= 0.279 Chirality : 0.041 0.144 1540 Planarity : 0.004 0.039 1662 Dihedral : 5.117 31.220 1326 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.80 % Allowed : 21.78 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.25), residues: 1212 helix: 0.11 (0.21), residues: 694 sheet: -0.12 (0.50), residues: 70 loop : -1.58 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 193 TYR 0.009 0.001 TYR A 630 PHE 0.008 0.001 PHE A 571 TRP 0.009 0.001 TRP A 572 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9858) covalent geometry : angle 0.54442 (13332) SS BOND : bond 0.00110 ( 2) SS BOND : angle 1.27090 ( 4) hydrogen bonds : bond 0.02538 ( 383) hydrogen bonds : angle 3.92777 ( 1110) ********************** 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 129 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.398 Fit side-chains REVERT: A 179 MET cc_start: 0.7316 (mmp) cc_final: 0.7069 (mpm) REVERT: A 223 ILE cc_start: 0.7459 (mt) cc_final: 0.7184 (mp) REVERT: A 439 SER cc_start: 0.7311 (OUTLIER) cc_final: 0.6787 (m) REVERT: A 494 TYR cc_start: 0.7575 (t80) cc_final: 0.5744 (m-80) REVERT: A 541 LEU cc_start: 0.7800 (tp) cc_final: 0.7484 (mt) REVERT: A 579 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7742 (p) REVERT: A 589 MET cc_start: 0.4171 (tpt) cc_final: 0.3384 (mmt) REVERT: B 116 ARG cc_start: 0.7489 (mmm-85) cc_final: 0.7052 (mmm-85) REVERT: B 204 LYS cc_start: 0.7242 (tttp) cc_final: 0.6796 (mtpp) REVERT: B 249 ASP cc_start: 0.7013 (t0) cc_final: 0.6353 (t0) REVERT: B 286 MET cc_start: 0.8446 (ptm) cc_final: 0.8145 (ptp) REVERT: B 301 ARG cc_start: 0.6826 (ttm110) cc_final: 0.6348 (ttp-110) REVERT: B 494 TYR cc_start: 0.7543 (t80) cc_final: 0.5715 (m-80) REVERT: B 541 LEU cc_start: 0.7783 (tp) cc_final: 0.7475 (mt) REVERT: B 579 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7730 (p) REVERT: B 589 MET cc_start: 0.4064 (tpt) cc_final: 0.3542 (mmm) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 0.4419 time to fit residues: 60.3698 Evaluate side-chains 120 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 310 THR Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 439 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 B residue 163 LEU 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 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 92 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.192704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123944 restraints weight = 9922.217| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.24 r_work: 0.3371 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2748 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= 0.134 Angle : 0.568 8.277 13336 Z= 0.289 Chirality : 0.042 0.150 1540 Planarity : 0.004 0.039 1662 Dihedral : 5.162 29.954 1326 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.70 % Allowed : 21.78 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.25), residues: 1212 helix: 0.13 (0.21), residues: 694 sheet: -0.13 (0.51), residues: 70 loop : -1.55 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 193 TYR 0.012 0.001 TYR B 630 PHE 0.008 0.001 PHE A 562 TRP 0.009 0.001 TRP B 429 HIS 0.002 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9858) covalent geometry : angle 0.56763 (13332) SS BOND : bond 0.00140 ( 2) SS BOND : angle 1.19616 ( 4) hydrogen bonds : bond 0.02791 ( 383) hydrogen bonds : angle 3.96778 ( 1110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3871.83 seconds wall clock time: 66 minutes 46.33 seconds (4006.33 seconds total)