Starting phenix.real_space_refine on Fri Sep 19 10:28:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdr_45485/09_2025/9cdr_45485_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdr_45485/09_2025/9cdr_45485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cdr_45485/09_2025/9cdr_45485_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdr_45485/09_2025/9cdr_45485_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cdr_45485/09_2025/9cdr_45485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdr_45485/09_2025/9cdr_45485.map" } resolution = 3.91 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= -0.001 sd= 0.019 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 S 66 5.16 5 C 7990 2.51 5 N 2198 2.21 5 O 2348 1.98 5 H 12475 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s 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: 25079 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 12495 Classifications: {'peptide': 787} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 751} Chain: "B" Number of atoms: 12494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 12494 Classifications: {'peptide': 787} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 751} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.36, per 1000 atoms: 0.17 Number of scatterers: 25079 At special positions: 0 Unit cell: (88.7949, 103.325, 198.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 66 16.00 O 2348 8.00 N 2198 7.00 C 7990 6.00 H 12475 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 757.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 49.6% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.931A pdb=" N LEU A 26 " --> pdb=" O PHE A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.695A pdb=" N GLY A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 133 through 153 removed outlier: 3.891A pdb=" N LEU A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.563A pdb=" N ARG A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 Processing helix chain 'A' and resid 278 through 294 Processing helix chain 'A' and resid 352 through 380 removed outlier: 3.971A pdb=" N ARG A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 369 " --> pdb=" O HIS A 365 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 408 Processing helix chain 'A' and resid 422 through 429 Processing helix chain 'A' and resid 429 through 449 removed outlier: 4.447A pdb=" N TRP A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.784A pdb=" N LYS A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 539 through 563 removed outlier: 3.879A pdb=" N ASN A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 611 through 633 removed outlier: 3.617A pdb=" N GLY A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.816A pdb=" N GLN A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.853A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 740 through 756 removed outlier: 3.784A pdb=" N ILE A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 775 removed outlier: 3.520A pdb=" N LYS A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 Processing helix chain 'B' and resid 21 through 28 removed outlier: 3.724A pdb=" N ALA B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.774A pdb=" N VAL B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.611A pdb=" N TYR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 87 " --> pdb=" O HIS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 133 through 152 removed outlier: 3.765A pdb=" N ILE B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 201 through 212 Processing helix chain 'B' and resid 256 through 275 removed outlier: 3.693A pdb=" N SER B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 352 through 384 removed outlier: 3.530A pdb=" N LEU B 383 " --> pdb=" O HIS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 409 removed outlier: 3.587A pdb=" N ASN B 400 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 429 removed outlier: 3.685A pdb=" N ILE B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 449 removed outlier: 4.238A pdb=" N GLN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 485 removed outlier: 3.693A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 Processing helix chain 'B' and resid 539 through 563 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.680A pdb=" N ILE B 603 " --> pdb=" O PRO B 599 " (cutoff:3.500A) Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 611 through 632 Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 653 through 664 removed outlier: 4.068A pdb=" N VAL B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 670 No H-bonds generated for 'chain 'B' and resid 668 through 670' Processing helix chain 'B' and resid 686 through 699 removed outlier: 4.054A pdb=" N GLN B 693 " --> pdb=" O PHE B 689 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE B 694 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU B 695 " --> pdb=" O ARG B 691 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG B 696 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 716 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.695A pdb=" N VAL B 732 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B 736 " --> pdb=" O VAL B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 755 removed outlier: 4.559A pdb=" N LEU B 744 " --> pdb=" O ARG B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 776 removed outlier: 3.845A pdb=" N LYS B 775 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE B 776 " --> pdb=" O MET B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.799A pdb=" N PHE A 44 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 99 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.789A pdb=" N SER A 254 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.789A pdb=" N SER A 254 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 314 removed outlier: 6.500A pdb=" N ARG A 305 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N HIS A 311 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA A 303 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 313 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 339 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 331 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE A 341 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA A 329 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN A 343 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP A 327 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS A 345 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 325 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 456 through 459 removed outlier: 5.125A pdb=" N ARG A 457 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 464 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 459 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE A 503 " --> pdb=" O GLN A 536 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.553A pdb=" N LEU A 640 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER A 641 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 583 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 580 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE A 574 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 582 " --> pdb=" O GLN A 572 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 566 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 780 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 168 removed outlier: 3.634A pdb=" N VAL B 167 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 223 through 224 removed outlier: 5.394A pdb=" N GLU B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 308 through 314 removed outlier: 6.502A pdb=" N LEU B 301 " --> pdb=" O TRP B 312 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER B 314 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL B 299 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 343 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 340 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 454 through 459 removed outlier: 7.006A pdb=" N GLN B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 490 through 492 removed outlier: 3.503A pdb=" N ILE B 490 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 566 through 569 removed outlier: 3.534A pdb=" N ARG B 588 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN B 643 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA B 587 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU B 640 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLU B 675 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 642 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU B 672 " --> pdb=" O GLY B 701 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER B 703 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 674 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B 702 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE B 725 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 704 " --> pdb=" O ILE B 725 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 727 " --> pdb=" O VAL B 704 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR B 723 " --> pdb=" O THR B 758 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 760 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE B 725 " --> pdb=" O VAL B 760 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU B 762 " --> pdb=" O ILE B 725 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE B 727 " --> pdb=" O GLU B 762 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 759 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLN B 782 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA B 761 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 781 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B 573 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN B 572 " --> pdb=" O TYR B 581 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1854 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: 6.27 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 12459 1.09 - 1.34: 4166 1.34 - 1.59: 8598 1.59 - 1.83: 116 1.83 - 2.08: 8 Bond restraints: 25347 Sorted by residual: bond pdb=" N ILE A 256 " pdb=" CA ILE A 256 " ideal model delta sigma weight residual 1.474 1.456 0.019 1.57e-02 4.06e+03 1.40e+00 bond pdb=" CA PHE A 198 " pdb=" CB PHE A 198 " ideal model delta sigma weight residual 1.525 1.534 -0.009 8.30e-03 1.45e+04 1.14e+00 bond pdb=" N VAL B 124 " pdb=" CA VAL B 124 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.02e+00 bond pdb=" C LEU B 449 " pdb=" N LYS B 450 " ideal model delta sigma weight residual 1.325 1.337 -0.012 1.25e-02 6.40e+03 9.89e-01 bond pdb=" CA PHE A 198 " pdb=" C PHE A 198 " ideal model delta sigma weight residual 1.534 1.525 0.009 9.50e-03 1.11e+04 9.71e-01 ... (remaining 25342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.13: 45860 7.13 - 14.25: 1 14.25 - 21.38: 0 21.38 - 28.50: 0 28.50 - 35.63: 3 Bond angle restraints: 45864 Sorted by residual: angle pdb=" N THR A 257 " pdb=" CA THR A 257 " pdb=" HA THR A 257 " ideal model delta sigma weight residual 110.00 74.37 35.63 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C THR A 257 " pdb=" CA THR A 257 " pdb=" HA THR A 257 " ideal model delta sigma weight residual 109.00 74.40 34.60 3.00e+00 1.11e-01 1.33e+02 angle pdb=" CB THR A 257 " pdb=" CA THR A 257 " pdb=" HA THR A 257 " ideal model delta sigma weight residual 109.00 76.00 33.00 3.00e+00 1.11e-01 1.21e+02 angle pdb=" N THR A 723 " pdb=" CA THR A 723 " pdb=" C THR A 723 " ideal model delta sigma weight residual 111.33 105.00 6.33 1.21e+00 6.83e-01 2.74e+01 angle pdb=" N GLU B 678 " pdb=" CA GLU B 678 " pdb=" C GLU B 678 " ideal model delta sigma weight residual 110.20 103.64 6.56 1.58e+00 4.01e-01 1.72e+01 ... (remaining 45859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10574 17.85 - 35.70: 907 35.70 - 53.55: 243 53.55 - 71.40: 77 71.40 - 89.25: 16 Dihedral angle restraints: 11817 sinusoidal: 6532 harmonic: 5285 Sorted by residual: dihedral pdb=" CA GLY B 227 " pdb=" C GLY B 227 " pdb=" N GLU B 228 " pdb=" CA GLU B 228 " ideal model delta harmonic sigma weight residual 180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA HIS B 648 " pdb=" C HIS B 648 " pdb=" N PHE B 649 " pdb=" CA PHE B 649 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA THR B 677 " pdb=" C THR B 677 " pdb=" N GLU B 678 " pdb=" CA GLU B 678 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 11814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1755 0.074 - 0.148: 173 0.148 - 0.222: 1 0.222 - 0.296: 0 0.296 - 0.370: 1 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CA THR A 257 " pdb=" N THR A 257 " pdb=" C THR A 257 " pdb=" CB THR A 257 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE A 583 " pdb=" N ILE A 583 " pdb=" C ILE A 583 " pdb=" CB ILE A 583 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 1927 not shown) Planarity restraints: 3774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 597 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 598 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 696 " 0.152 9.50e-02 1.11e+02 5.07e-02 2.82e+00 pdb=" NE ARG A 696 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 696 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 696 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 696 " 0.005 2.00e-02 2.50e+03 pdb="HH11 ARG A 696 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 696 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 696 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 696 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 539 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 540 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 540 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 540 " 0.021 5.00e-02 4.00e+02 ... (remaining 3771 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1118 2.16 - 2.77: 49419 2.77 - 3.38: 72429 3.38 - 3.99: 89538 3.99 - 4.60: 139250 Nonbonded interactions: 351754 Sorted by model distance: nonbonded pdb=" H THR A 257 " pdb=" HA THR A 257 " model vdw 1.546 1.816 nonbonded pdb=" OD1 ASN A 643 " pdb=" H SER A 645 " model vdw 1.571 2.450 nonbonded pdb=" HG1 THR A 766 " pdb=" OE1 GLN A 769 " model vdw 1.581 2.450 nonbonded pdb="HH21 ARG A 696 " pdb=" O VAL A 700 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASN B 512 " pdb=" H TYR B 515 " model vdw 1.590 2.450 ... (remaining 351749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 589 or (resid 590 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 591 through 902)) 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 group one per residue 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: 1.040 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: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.830 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 0.755 12874 Z= 0.157 Angle : 0.650 7.276 17464 Z= 0.434 Chirality : 0.041 0.370 1930 Planarity : 0.005 0.068 2272 Dihedral : 14.874 89.250 4810 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.37 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.93 (0.22), residues: 1570 helix: 0.40 (0.20), residues: 673 sheet: -1.56 (0.30), residues: 287 loop : -1.16 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 774 TYR 0.017 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.010 0.001 TRP A 798 HIS 0.004 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00273 (12872) covalent geometry : angle 0.65032 (17464) hydrogen bonds : bond 0.11360 ( 637) hydrogen bonds : angle 6.23939 ( 1854) Misc. bond : bond 0.69369 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3093 time to fit residues: 72.6467 Evaluate side-chains 114 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 306 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 HIS ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.066915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049752 restraints weight = 257136.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.051696 restraints weight = 140436.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.052916 restraints weight = 92836.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.053756 restraints weight = 69397.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.054284 restraints weight = 56716.151| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 12874 Z= 0.137 Angle : 0.591 8.326 17464 Z= 0.311 Chirality : 0.042 0.372 1930 Planarity : 0.005 0.056 2272 Dihedral : 5.864 70.101 1714 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.62 % Favored : 93.18 % Rotamer: Outliers : 0.51 % Allowed : 13.40 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.83 (0.22), residues: 1570 helix: 0.54 (0.20), residues: 673 sheet: -1.51 (0.29), residues: 299 loop : -1.15 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 716 TYR 0.017 0.001 TYR A 526 PHE 0.023 0.001 PHE A 602 TRP 0.013 0.001 TRP B 327 HIS 0.005 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00293 (12872) covalent geometry : angle 0.59147 (17464) hydrogen bonds : bond 0.04047 ( 637) hydrogen bonds : angle 5.55965 ( 1854) Misc. bond : bond 0.16810 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.4699 (tpp) cc_final: 0.2076 (tpp) REVERT: A 281 GLU cc_start: 0.8963 (mp0) cc_final: 0.8616 (mp0) REVERT: A 357 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8896 (tp30) REVERT: A 453 GLN cc_start: 0.8721 (mt0) cc_final: 0.8297 (mm-40) REVERT: A 524 MET cc_start: 0.8922 (tmm) cc_final: 0.8606 (tmm) REVERT: B 456 CYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8181 (t) REVERT: B 682 MET cc_start: 0.6987 (mtm) cc_final: 0.6696 (mtp) outliers start: 7 outliers final: 5 residues processed: 122 average time/residue: 0.2891 time to fit residues: 50.1662 Evaluate side-chains 116 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 456 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.065032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.047530 restraints weight = 264749.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.049368 restraints weight = 144124.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.050606 restraints weight = 95849.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.051341 restraints weight = 72931.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.051786 restraints weight = 60882.682| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 12874 Z= 0.197 Angle : 0.599 7.369 17464 Z= 0.319 Chirality : 0.041 0.382 1930 Planarity : 0.004 0.046 2272 Dihedral : 5.791 66.666 1714 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.07 % Favored : 92.68 % Rotamer: Outliers : 0.66 % Allowed : 13.76 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.90 (0.22), residues: 1570 helix: 0.59 (0.20), residues: 666 sheet: -1.69 (0.28), residues: 319 loop : -1.18 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 696 TYR 0.018 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.012 0.001 TRP B 327 HIS 0.005 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00396 (12872) covalent geometry : angle 0.59918 (17464) hydrogen bonds : bond 0.03995 ( 637) hydrogen bonds : angle 5.47987 ( 1854) Misc. bond : bond 0.11415 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9107 (mp0) cc_final: 0.8664 (mp0) REVERT: A 453 GLN cc_start: 0.8749 (mt0) cc_final: 0.8241 (mm-40) REVERT: A 524 MET cc_start: 0.8914 (tmm) cc_final: 0.8563 (tmm) REVERT: B 456 CYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8238 (t) outliers start: 9 outliers final: 5 residues processed: 108 average time/residue: 0.2417 time to fit residues: 37.2498 Evaluate side-chains 106 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN A 634 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.064652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.047636 restraints weight = 266467.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049484 restraints weight = 141759.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.050623 restraints weight = 93530.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.051409 restraints weight = 71104.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.051949 restraints weight = 58321.042| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 12874 Z= 0.156 Angle : 0.576 9.465 17464 Z= 0.301 Chirality : 0.041 0.380 1930 Planarity : 0.004 0.044 2272 Dihedral : 5.689 64.604 1714 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.01 % Favored : 92.80 % Rotamer: Outliers : 0.88 % Allowed : 13.47 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.75 (0.22), residues: 1570 helix: 0.70 (0.20), residues: 680 sheet: -1.60 (0.28), residues: 319 loop : -1.15 (0.28), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 131 TYR 0.017 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.015 0.001 TRP B 327 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00317 (12872) covalent geometry : angle 0.57567 (17464) hydrogen bonds : bond 0.03685 ( 637) hydrogen bonds : angle 5.31351 ( 1854) Misc. bond : bond 0.09154 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9172 (mp0) cc_final: 0.8679 (mp0) REVERT: A 413 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8051 (m) REVERT: A 524 MET cc_start: 0.8838 (tmm) cc_final: 0.8514 (tmm) REVERT: A 769 GLN cc_start: 0.9484 (OUTLIER) cc_final: 0.9205 (mt0) REVERT: B 456 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8111 (t) outliers start: 12 outliers final: 8 residues processed: 110 average time/residue: 0.2531 time to fit residues: 40.3107 Evaluate side-chains 110 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.064985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047810 restraints weight = 265478.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.049712 restraints weight = 142121.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.050948 restraints weight = 93664.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.051647 restraints weight = 70672.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.052150 restraints weight = 57999.008| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 12874 Z= 0.118 Angle : 0.556 6.746 17464 Z= 0.287 Chirality : 0.041 0.377 1930 Planarity : 0.004 0.044 2272 Dihedral : 5.595 64.705 1714 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.88 % Favored : 92.93 % Rotamer: Outliers : 1.02 % Allowed : 13.62 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.54 (0.22), residues: 1570 helix: 0.93 (0.20), residues: 681 sheet: -1.50 (0.29), residues: 308 loop : -1.14 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.016 0.001 TYR A 526 PHE 0.020 0.001 PHE A 602 TRP 0.012 0.001 TRP B 327 HIS 0.003 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00251 (12872) covalent geometry : angle 0.55552 (17464) hydrogen bonds : bond 0.03446 ( 637) hydrogen bonds : angle 5.14140 ( 1854) Misc. bond : bond 0.07586 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9232 (mp0) cc_final: 0.8763 (mp0) REVERT: A 413 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8011 (m) REVERT: A 524 MET cc_start: 0.8846 (tmm) cc_final: 0.8544 (tmm) REVERT: A 769 GLN cc_start: 0.9490 (OUTLIER) cc_final: 0.9202 (mt0) REVERT: B 456 CYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8109 (t) REVERT: B 542 MET cc_start: 0.9304 (mtp) cc_final: 0.8961 (mtp) outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 0.2670 time to fit residues: 43.3609 Evaluate side-chains 113 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 671 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.064341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.047024 restraints weight = 266088.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.048882 restraints weight = 143487.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.050102 restraints weight = 95150.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.050786 restraints weight = 72003.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.051288 restraints weight = 59593.890| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 12874 Z= 0.138 Angle : 0.553 6.815 17464 Z= 0.286 Chirality : 0.041 0.382 1930 Planarity : 0.004 0.042 2272 Dihedral : 5.515 63.666 1714 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.13 % Favored : 92.68 % Rotamer: Outliers : 1.10 % Allowed : 13.98 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.48 (0.22), residues: 1570 helix: 1.04 (0.20), residues: 682 sheet: -1.46 (0.28), residues: 323 loop : -1.18 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.016 0.001 TYR A 526 PHE 0.020 0.001 PHE A 602 TRP 0.011 0.001 TRP B 327 HIS 0.003 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00282 (12872) covalent geometry : angle 0.55250 (17464) hydrogen bonds : bond 0.03438 ( 637) hydrogen bonds : angle 5.07266 ( 1854) Misc. bond : bond 0.07028 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9261 (mp0) cc_final: 0.8759 (mp0) REVERT: A 413 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.8020 (m) REVERT: A 524 MET cc_start: 0.8860 (tmm) cc_final: 0.8531 (tmm) REVERT: A 769 GLN cc_start: 0.9490 (OUTLIER) cc_final: 0.9206 (mt0) REVERT: B 456 CYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8407 (t) outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 0.2782 time to fit residues: 45.4297 Evaluate side-chains 111 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 153 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.0010 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.064353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.047387 restraints weight = 263662.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.049220 restraints weight = 141627.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.050376 restraints weight = 93820.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.051161 restraints weight = 70717.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.051630 restraints weight = 58383.140| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 12874 Z= 0.133 Angle : 0.554 7.531 17464 Z= 0.287 Chirality : 0.041 0.383 1930 Planarity : 0.004 0.041 2272 Dihedral : 5.475 63.022 1714 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.94 % Favored : 92.80 % Rotamer: Outliers : 1.02 % Allowed : 14.71 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.42 (0.22), residues: 1570 helix: 1.13 (0.20), residues: 677 sheet: -1.54 (0.28), residues: 319 loop : -1.13 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.016 0.001 TYR A 526 PHE 0.020 0.001 PHE A 602 TRP 0.017 0.001 TRP B 327 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00277 (12872) covalent geometry : angle 0.55423 (17464) hydrogen bonds : bond 0.03433 ( 637) hydrogen bonds : angle 5.01485 ( 1854) Misc. bond : bond 0.06856 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.5220 (mmm) cc_final: 0.2670 (tpp) REVERT: A 281 GLU cc_start: 0.9284 (mp0) cc_final: 0.8754 (mp0) REVERT: A 413 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7975 (m) REVERT: A 524 MET cc_start: 0.8854 (tmm) cc_final: 0.8514 (tmm) REVERT: A 769 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.9209 (mt0) REVERT: B 456 CYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8439 (t) REVERT: B 772 MET cc_start: 0.8712 (ttp) cc_final: 0.8180 (ttt) outliers start: 14 outliers final: 10 residues processed: 110 average time/residue: 0.2498 time to fit residues: 40.2450 Evaluate side-chains 110 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.063163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.046103 restraints weight = 266379.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.047861 restraints weight = 143865.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.049023 restraints weight = 95776.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.049731 restraints weight = 72787.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.050196 restraints weight = 60209.056| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12874 Z= 0.176 Angle : 0.576 7.710 17464 Z= 0.301 Chirality : 0.041 0.390 1930 Planarity : 0.004 0.039 2272 Dihedral : 5.487 61.334 1714 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.52 % Favored : 92.23 % Rotamer: Outliers : 0.88 % Allowed : 15.15 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.51 (0.22), residues: 1570 helix: 1.00 (0.20), residues: 684 sheet: -1.51 (0.28), residues: 320 loop : -1.16 (0.29), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 774 TYR 0.016 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.014 0.001 TRP B 327 HIS 0.004 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00355 (12872) covalent geometry : angle 0.57559 (17464) hydrogen bonds : bond 0.03579 ( 637) hydrogen bonds : angle 5.07387 ( 1854) Misc. bond : bond 0.07002 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.5751 (mmm) cc_final: 0.3308 (tpp) REVERT: A 281 GLU cc_start: 0.9301 (mp0) cc_final: 0.8778 (mp0) REVERT: A 413 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7847 (m) REVERT: A 524 MET cc_start: 0.8862 (tmm) cc_final: 0.8467 (tmm) REVERT: A 769 GLN cc_start: 0.9502 (OUTLIER) cc_final: 0.9216 (mt0) REVERT: B 456 CYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8398 (t) REVERT: B 772 MET cc_start: 0.8837 (ttp) cc_final: 0.8343 (ttt) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.2499 time to fit residues: 39.0251 Evaluate side-chains 108 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 129 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.063950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.047005 restraints weight = 267507.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.048803 restraints weight = 141982.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.050042 restraints weight = 93450.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.050787 restraints weight = 70106.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.051328 restraints weight = 57565.946| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12874 Z= 0.109 Angle : 0.555 8.714 17464 Z= 0.283 Chirality : 0.041 0.380 1930 Planarity : 0.004 0.039 2272 Dihedral : 5.424 62.481 1714 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.56 % Favored : 93.18 % Rotamer: Outliers : 0.95 % Allowed : 15.52 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.34 (0.22), residues: 1570 helix: 1.18 (0.20), residues: 689 sheet: -1.49 (0.28), residues: 317 loop : -1.11 (0.29), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 716 TYR 0.015 0.001 TYR A 526 PHE 0.019 0.001 PHE A 602 TRP 0.013 0.001 TRP B 327 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00241 (12872) covalent geometry : angle 0.55476 (17464) hydrogen bonds : bond 0.03292 ( 637) hydrogen bonds : angle 4.89889 ( 1854) Misc. bond : bond 0.06260 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: -0.1355 (ptt) cc_final: -0.2556 (ptt) REVERT: A 31 MET cc_start: 0.5385 (mmm) cc_final: 0.2741 (tpp) REVERT: A 281 GLU cc_start: 0.9334 (mp0) cc_final: 0.8908 (mp0) REVERT: A 413 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7952 (m) REVERT: A 524 MET cc_start: 0.8919 (tmm) cc_final: 0.8609 (tmm) REVERT: A 769 GLN cc_start: 0.9519 (OUTLIER) cc_final: 0.9210 (mt0) REVERT: B 456 CYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8394 (t) REVERT: B 772 MET cc_start: 0.8811 (ttp) cc_final: 0.8300 (ttt) outliers start: 13 outliers final: 9 residues processed: 106 average time/residue: 0.2643 time to fit residues: 40.6112 Evaluate side-chains 107 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.063892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.046897 restraints weight = 268040.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.048700 restraints weight = 143205.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.049908 restraints weight = 94854.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.050708 restraints weight = 71745.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.051111 restraints weight = 59256.708| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12874 Z= 0.116 Angle : 0.560 9.891 17464 Z= 0.285 Chirality : 0.041 0.383 1930 Planarity : 0.004 0.039 2272 Dihedral : 5.356 62.264 1714 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.75 % Favored : 93.06 % Rotamer: Outliers : 1.02 % Allowed : 15.52 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.29 (0.22), residues: 1570 helix: 1.21 (0.20), residues: 695 sheet: -1.42 (0.29), residues: 309 loop : -1.14 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.015 0.001 TYR A 526 PHE 0.019 0.001 PHE A 602 TRP 0.011 0.001 TRP B 327 HIS 0.003 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00250 (12872) covalent geometry : angle 0.55980 (17464) hydrogen bonds : bond 0.03231 ( 637) hydrogen bonds : angle 4.86189 ( 1854) Misc. bond : bond 0.05724 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: -0.1352 (ptt) cc_final: -0.2544 (ptt) REVERT: A 31 MET cc_start: 0.5382 (mmm) cc_final: 0.2741 (tpp) REVERT: A 281 GLU cc_start: 0.9319 (mp0) cc_final: 0.8892 (mp0) REVERT: A 413 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7928 (m) REVERT: A 524 MET cc_start: 0.8946 (tmm) cc_final: 0.8630 (tmm) REVERT: A 769 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.9211 (mt0) REVERT: B 456 CYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8377 (t) REVERT: B 772 MET cc_start: 0.8808 (ttp) cc_final: 0.8281 (ttt) outliers start: 14 outliers final: 10 residues processed: 110 average time/residue: 0.2330 time to fit residues: 36.8912 Evaluate side-chains 107 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.063340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046283 restraints weight = 265831.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.048081 restraints weight = 142741.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.049268 restraints weight = 94879.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.049958 restraints weight = 72209.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.050441 restraints weight = 59583.410| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12874 Z= 0.141 Angle : 0.589 14.929 17464 Z= 0.301 Chirality : 0.041 0.386 1930 Planarity : 0.004 0.039 2272 Dihedral : 5.350 61.581 1714 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.01 % Favored : 92.80 % Rotamer: Outliers : 0.95 % Allowed : 16.03 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.33 (0.22), residues: 1570 helix: 1.19 (0.20), residues: 691 sheet: -1.45 (0.29), residues: 316 loop : -1.15 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.019 0.001 TYR A 80 PHE 0.020 0.001 PHE A 602 TRP 0.008 0.001 TRP A 231 HIS 0.003 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00295 (12872) covalent geometry : angle 0.58941 (17464) hydrogen bonds : bond 0.03369 ( 637) hydrogen bonds : angle 4.89925 ( 1854) Misc. bond : bond 0.06288 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4694.49 seconds wall clock time: 80 minutes 36.20 seconds (4836.20 seconds total)