Starting phenix.real_space_refine on Sun Aug 24 11:13:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jvi_36675/08_2025/8jvi_36675.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jvi_36675/08_2025/8jvi_36675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jvi_36675/08_2025/8jvi_36675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jvi_36675/08_2025/8jvi_36675.map" model { file = "/net/cci-nas-00/data/ceres_data/8jvi_36675/08_2025/8jvi_36675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jvi_36675/08_2025/8jvi_36675.cif" } resolution = 3.21 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= 0.109 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: 5 Type Number sf(0) Gaussians S 108 5.16 5 C 12748 2.51 5 N 3244 2.21 5 O 3436 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19548 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4859 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 584} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4837 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 18, 'TRANS': 581} Chain breaks: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'F9M': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'F9M': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, A Time building chain proxies: 5.94, per 1000 atoms: 0.30 Number of scatterers: 19548 At special positions: 0 Unit cell: (157.04, 159.12, 117.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 F 12 9.00 O 3436 8.00 N 3244 7.00 C 12748 6.00 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=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 814.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 68.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.141A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.571A pdb=" N ILE B 227 " --> pdb=" O MET B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.611A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 260 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.726A pdb=" N THR B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.403A pdb=" N MET B 449 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 removed outlier: 4.074A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 490 removed outlier: 3.679A pdb=" N TYR B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 534 removed outlier: 3.656A pdb=" N ASP B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 532 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 570 removed outlier: 3.862A pdb=" N TYR B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 removed outlier: 3.745A pdb=" N VAL B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 594 removed outlier: 4.119A pdb=" N ARG B 594 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 613 Processing helix chain 'B' and resid 613 through 634 Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.798A pdb=" N ILE B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 689 removed outlier: 3.617A pdb=" N SER B 687 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 725 removed outlier: 3.676A pdb=" N PHE B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 748 removed outlier: 3.712A pdb=" N LYS B 734 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 735 " --> pdb=" O HIS B 731 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'B' and resid 767 through 771 Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 168 through 176 removed outlier: 4.138A pdb=" N PHE C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.047A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 233 through 237 removed outlier: 4.100A pdb=" N ARG C 237 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.577A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.009A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.668A pdb=" N GLN C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.619A pdb=" N THR C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 335 through 356 removed outlier: 4.315A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 442 through 450 removed outlier: 3.640A pdb=" N ARG C 446 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU C 448 " --> pdb=" O ASN C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 removed outlier: 4.171A pdb=" N GLU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 490 Processing helix chain 'C' and resid 507 through 531 removed outlier: 3.633A pdb=" N ASP C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 534 No H-bonds generated for 'chain 'C' and resid 532 through 534' Processing helix chain 'C' and resid 546 through 570 removed outlier: 3.568A pdb=" N LEU C 551 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 590 removed outlier: 3.567A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.559A pdb=" N ARG C 594 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY C 595 " --> pdb=" O PHE C 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 591 through 595' Processing helix chain 'C' and resid 596 through 614 removed outlier: 3.981A pdb=" N TYR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 633 Processing helix chain 'C' and resid 665 through 679 Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.671A pdb=" N SER C 687 " --> pdb=" O GLU C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 748 removed outlier: 4.523A pdb=" N PHE C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 709 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C 710 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET C 718 " --> pdb=" O LEU C 714 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY C 723 " --> pdb=" O GLY C 719 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN C 724 " --> pdb=" O GLU C 720 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LYS C 727 " --> pdb=" O GLY C 723 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU C 728 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 747 " --> pdb=" O ASP C 743 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing helix chain 'C' and resid 767 through 771 Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 168 through 176 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.141A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.572A pdb=" N ILE D 227 " --> pdb=" O MET D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.611A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.726A pdb=" N THR D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 445 through 450 removed outlier: 4.403A pdb=" N MET D 449 " --> pdb=" O ASN D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 4.074A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 490 removed outlier: 3.679A pdb=" N TYR D 490 " --> pdb=" O THR D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 534 removed outlier: 3.656A pdb=" N ASP D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 532 " --> pdb=" O ASN D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 570 removed outlier: 3.863A pdb=" N TYR D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 586 removed outlier: 3.745A pdb=" N VAL D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 594 removed outlier: 4.120A pdb=" N ARG D 594 " --> pdb=" O TYR D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 613 Processing helix chain 'D' and resid 613 through 634 Processing helix chain 'D' and resid 665 through 679 removed outlier: 3.798A pdb=" N ILE D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 689 removed outlier: 3.617A pdb=" N SER D 687 " --> pdb=" O GLU D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 725 removed outlier: 3.675A pdb=" N PHE D 695 " --> pdb=" O TYR D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 748 removed outlier: 3.712A pdb=" N LYS D 734 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 735 " --> pdb=" O HIS D 731 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D 736 " --> pdb=" O ILE D 732 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 Processing helix chain 'D' and resid 767 through 771 Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 168 through 176 removed outlier: 4.138A pdb=" N PHE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.047A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.100A pdb=" N ARG A 237 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.577A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.009A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.668A pdb=" N GLN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 297 through 306 removed outlier: 3.619A pdb=" N THR A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 335 through 356 removed outlier: 4.316A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.639A pdb=" N ARG A 446 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 448 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 4.171A pdb=" N GLU A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 490 Processing helix chain 'A' and resid 507 through 531 removed outlier: 3.633A pdb=" N ASP A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.568A pdb=" N LEU A 551 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.567A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.559A pdb=" N ARG A 594 " --> pdb=" O TYR A 591 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY A 595 " --> pdb=" O PHE A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 595' Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.981A pdb=" N TYR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 633 Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 683 through 687 removed outlier: 3.672A pdb=" N SER A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 748 removed outlier: 4.546A pdb=" N PHE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 710 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A 724 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LYS A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'A' and resid 767 through 771 Processing sheet with id=AA1, first strand: chain 'B' and resid 405 through 410 removed outlier: 6.912A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.713A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 405 through 410 removed outlier: 6.912A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 410 removed outlier: 6.713A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3044 1.31 - 1.44: 5512 1.44 - 1.57: 11278 1.57 - 1.69: 4 1.69 - 1.82: 168 Bond restraints: 20006 Sorted by residual: bond pdb=" C35 F9M B1201 " pdb=" S02 F9M B1201 " ideal model delta sigma weight residual 1.739 1.508 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C35 F9M C1201 " pdb=" S02 F9M C1201 " ideal model delta sigma weight residual 1.739 1.508 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C35 F9M A1201 " pdb=" S02 F9M A1201 " ideal model delta sigma weight residual 1.739 1.509 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C35 F9M D1201 " pdb=" S02 F9M D1201 " ideal model delta sigma weight residual 1.739 1.509 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C34 F9M A1201 " pdb=" S01 F9M A1201 " ideal model delta sigma weight residual 1.727 1.511 0.216 2.00e-02 2.50e+03 1.17e+02 ... (remaining 20001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 26929 3.73 - 7.47: 181 7.47 - 11.20: 2 11.20 - 14.94: 0 14.94 - 18.67: 8 Bond angle restraints: 27120 Sorted by residual: angle pdb=" C32 F9M A1201 " pdb=" S01 F9M A1201 " pdb=" C34 F9M A1201 " ideal model delta sigma weight residual 89.16 107.83 -18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C32 F9M C1201 " pdb=" S01 F9M C1201 " pdb=" C34 F9M C1201 " ideal model delta sigma weight residual 89.16 107.82 -18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C32 F9M B1201 " pdb=" S01 F9M B1201 " pdb=" C34 F9M B1201 " ideal model delta sigma weight residual 89.16 107.41 -18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C32 F9M D1201 " pdb=" S01 F9M D1201 " pdb=" C34 F9M D1201 " ideal model delta sigma weight residual 89.16 107.41 -18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C35 F9M C1201 " pdb=" S02 F9M C1201 " pdb=" C37 F9M C1201 " ideal model delta sigma weight residual 89.81 107.82 -18.01 3.00e+00 1.11e-01 3.60e+01 ... (remaining 27115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.30: 10636 18.30 - 36.59: 1020 36.59 - 54.89: 176 54.89 - 73.19: 50 73.19 - 91.48: 18 Dihedral angle restraints: 11900 sinusoidal: 4856 harmonic: 7044 Sorted by residual: dihedral pdb=" C VAL C 469 " pdb=" N VAL C 469 " pdb=" CA VAL C 469 " pdb=" CB VAL C 469 " ideal model delta harmonic sigma weight residual -122.00 -133.15 11.15 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" C VAL A 469 " pdb=" N VAL A 469 " pdb=" CA VAL A 469 " pdb=" CB VAL A 469 " ideal model delta harmonic sigma weight residual -122.00 -133.12 11.12 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" CA PHE A 615 " pdb=" C PHE A 615 " pdb=" N ARG A 616 " pdb=" CA ARG A 616 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 11897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2655 0.058 - 0.116: 378 0.116 - 0.174: 31 0.174 - 0.232: 18 0.232 - 0.290: 8 Chirality restraints: 3090 Sorted by residual: chirality pdb=" CA VAL C 469 " pdb=" N VAL C 469 " pdb=" C VAL C 469 " pdb=" CB VAL C 469 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA VAL A 469 " pdb=" N VAL A 469 " pdb=" C VAL A 469 " pdb=" CB VAL A 469 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA PHE C 471 " pdb=" N PHE C 471 " pdb=" C PHE C 471 " pdb=" CB PHE C 471 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3087 not shown) Planarity restraints: 3358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 357 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 358 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 357 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 358 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO D 358 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 358 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 692 " -0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C PRO A 692 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO A 692 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL A 693 " -0.021 2.00e-02 2.50e+03 ... (remaining 3355 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 90 2.48 - 3.09: 14120 3.09 - 3.69: 29639 3.69 - 4.30: 42181 4.30 - 4.90: 70521 Nonbonded interactions: 156551 Sorted by model distance: nonbonded pdb=" OH TYR C 490 " pdb=" CE1 PHE D 666 " model vdw 1.878 3.340 nonbonded pdb=" CE1 PHE B 666 " pdb=" OH TYR A 490 " model vdw 1.937 3.340 nonbonded pdb=" OH TYR C 490 " pdb=" CZ PHE D 666 " model vdw 1.999 3.340 nonbonded pdb=" CG1 VAL B 633 " pdb=" CE1 TYR A 490 " model vdw 2.121 3.760 nonbonded pdb=" OH TYR C 602 " pdb=" CE MET D 713 " model vdw 2.134 3.460 ... (remaining 156546 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.011 0.231 20006 Z= 0.561 Angle : 0.782 18.673 27120 Z= 0.399 Chirality : 0.044 0.290 3090 Planarity : 0.005 0.101 3358 Dihedral : 15.092 91.481 7356 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.90 % Allowed : 0.95 % Favored : 98.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.18), residues: 2384 helix: 1.04 (0.14), residues: 1426 sheet: -3.04 (0.58), residues: 68 loop : -1.38 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.014 0.001 TYR A 628 PHE 0.028 0.001 PHE A 615 TRP 0.014 0.002 TRP D 409 HIS 0.005 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.01101 (20006) covalent geometry : angle 0.78248 (27120) hydrogen bonds : bond 0.16694 ( 1110) hydrogen bonds : angle 5.36784 ( 3168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 310 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7543 (mm-40) REVERT: B 578 MET cc_start: 0.6712 (ttt) cc_final: 0.6512 (ttt) REVERT: B 739 THR cc_start: 0.8363 (m) cc_final: 0.8143 (m) REVERT: D 695 PHE cc_start: 0.7630 (t80) cc_final: 0.7330 (t80) REVERT: D 730 LYS cc_start: 0.8442 (tppt) cc_final: 0.7808 (ptpt) outliers start: 19 outliers final: 10 residues processed: 324 average time/residue: 0.1260 time to fit residues: 63.4306 Evaluate side-chains 272 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 262 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 694 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 GLN B 474 ASN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 338 ASN C 387 GLN C 401 HIS C 447 HIS C 528 ASN D 550 GLN A 297 GLN A 338 ASN A 387 GLN A 447 HIS A 528 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.215868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.159221 restraints weight = 24874.946| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.24 r_work: 0.3584 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20006 Z= 0.129 Angle : 0.597 8.397 27120 Z= 0.305 Chirality : 0.038 0.147 3090 Planarity : 0.004 0.078 3358 Dihedral : 7.355 61.655 2808 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.14 % Allowed : 6.81 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2384 helix: 1.04 (0.14), residues: 1444 sheet: -2.89 (0.56), residues: 72 loop : -1.24 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 779 TYR 0.021 0.001 TYR B 628 PHE 0.022 0.001 PHE A 624 TRP 0.013 0.001 TRP A 409 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00282 (20006) covalent geometry : angle 0.59735 (27120) hydrogen bonds : bond 0.03976 ( 1110) hydrogen bonds : angle 4.26240 ( 3168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 293 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 578 MET cc_start: 0.6577 (ttt) cc_final: 0.6328 (ttt) REVERT: C 224 ARG cc_start: 0.7715 (ttt180) cc_final: 0.6915 (mmp80) REVERT: C 225 GLU cc_start: 0.8185 (mt-10) cc_final: 0.6814 (pm20) REVERT: D 182 ASP cc_start: 0.6839 (m-30) cc_final: 0.6630 (m-30) REVERT: D 487 LEU cc_start: 0.7179 (mp) cc_final: 0.6964 (mt) REVERT: D 718 MET cc_start: 0.6451 (ppp) cc_final: 0.5985 (tpt) REVERT: A 224 ARG cc_start: 0.7781 (ttt180) cc_final: 0.6894 (mmp80) REVERT: A 225 GLU cc_start: 0.8192 (mt-10) cc_final: 0.6989 (pm20) REVERT: A 449 MET cc_start: 0.8062 (mtp) cc_final: 0.7665 (mtp) outliers start: 24 outliers final: 16 residues processed: 301 average time/residue: 0.1322 time to fit residues: 59.9423 Evaluate side-chains 289 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 273 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 233 optimal weight: 0.6980 chunk 176 optimal weight: 0.0170 chunk 219 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 401 HIS A 447 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.212899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154141 restraints weight = 25017.435| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.55 r_work: 0.3533 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20006 Z= 0.147 Angle : 0.593 10.185 27120 Z= 0.301 Chirality : 0.039 0.252 3090 Planarity : 0.004 0.054 3358 Dihedral : 6.030 40.136 2800 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.18 % Allowed : 10.08 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2384 helix: 1.04 (0.13), residues: 1444 sheet: -2.70 (0.55), residues: 72 loop : -1.24 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 779 TYR 0.033 0.002 TYR D 628 PHE 0.022 0.001 PHE C 624 TRP 0.011 0.001 TRP A 733 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00341 (20006) covalent geometry : angle 0.59257 (27120) hydrogen bonds : bond 0.03843 ( 1110) hydrogen bonds : angle 4.12243 ( 3168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 273 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 683 LEU cc_start: 0.6599 (pp) cc_final: 0.5851 (mt) REVERT: C 224 ARG cc_start: 0.7626 (ttt180) cc_final: 0.6778 (mmp80) REVERT: D 182 ASP cc_start: 0.6951 (m-30) cc_final: 0.6708 (m-30) REVERT: D 213 LEU cc_start: 0.8547 (mp) cc_final: 0.7855 (mp) REVERT: D 578 MET cc_start: 0.6465 (ttp) cc_final: 0.6233 (mtp) REVERT: D 718 MET cc_start: 0.6538 (ppp) cc_final: 0.6051 (tpt) REVERT: A 224 ARG cc_start: 0.7672 (ttt180) cc_final: 0.6757 (mmp80) REVERT: A 449 MET cc_start: 0.8188 (mtp) cc_final: 0.7662 (mtp) outliers start: 25 outliers final: 20 residues processed: 286 average time/residue: 0.1293 time to fit residues: 56.7310 Evaluate side-chains 280 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 146 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 225 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 0.0370 chunk 94 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.214066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.155667 restraints weight = 24930.518| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.50 r_work: 0.3551 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20006 Z= 0.121 Angle : 0.563 10.323 27120 Z= 0.285 Chirality : 0.038 0.178 3090 Planarity : 0.004 0.041 3358 Dihedral : 5.699 38.567 2796 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.37 % Allowed : 11.87 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.18), residues: 2384 helix: 1.15 (0.13), residues: 1442 sheet: -2.28 (0.58), residues: 68 loop : -1.29 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 746 TYR 0.038 0.001 TYR D 628 PHE 0.026 0.001 PHE C 751 TRP 0.013 0.001 TRP A 733 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00275 (20006) covalent geometry : angle 0.56312 (27120) hydrogen bonds : bond 0.03483 ( 1110) hydrogen bonds : angle 3.97620 ( 3168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 284 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 224 ARG cc_start: 0.7576 (ttt180) cc_final: 0.6771 (mmp80) REVERT: C 449 MET cc_start: 0.8139 (mtp) cc_final: 0.7597 (mtp) REVERT: D 182 ASP cc_start: 0.6874 (m-30) cc_final: 0.6624 (m-30) REVERT: D 447 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7673 (m90) REVERT: D 736 GLN cc_start: 0.8184 (pm20) cc_final: 0.7771 (mp10) REVERT: A 224 ARG cc_start: 0.7640 (ttt180) cc_final: 0.6827 (mmp80) outliers start: 29 outliers final: 20 residues processed: 297 average time/residue: 0.1214 time to fit residues: 55.5881 Evaluate side-chains 289 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 128 optimal weight: 0.0370 chunk 57 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 30 optimal weight: 0.0050 chunk 23 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 overall best weight: 1.0474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 302 ASN C 447 HIS C 736 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 302 ASN A 447 HIS A 736 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.213134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159620 restraints weight = 24532.312| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.85 r_work: 0.3567 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20006 Z= 0.129 Angle : 0.575 11.129 27120 Z= 0.289 Chirality : 0.039 0.213 3090 Planarity : 0.004 0.040 3358 Dihedral : 5.576 38.637 2796 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.56 % Allowed : 12.87 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.25 (0.18), residues: 2384 helix: 1.16 (0.13), residues: 1442 sheet: -2.17 (0.61), residues: 68 loop : -1.30 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 746 TYR 0.017 0.001 TYR B 628 PHE 0.025 0.001 PHE B 172 TRP 0.020 0.001 TRP A 785 HIS 0.004 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00298 (20006) covalent geometry : angle 0.57479 (27120) hydrogen bonds : bond 0.03439 ( 1110) hydrogen bonds : angle 3.96887 ( 3168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 ARG cc_start: 0.7570 (ttm170) cc_final: 0.7243 (ttm-80) REVERT: C 224 ARG cc_start: 0.7618 (ttt180) cc_final: 0.6838 (mmp80) REVERT: C 225 GLU cc_start: 0.8067 (mt-10) cc_final: 0.6764 (pm20) REVERT: D 182 ASP cc_start: 0.6807 (m-30) cc_final: 0.6536 (m-30) REVERT: D 447 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7569 (m90) REVERT: D 736 GLN cc_start: 0.8226 (pm20) cc_final: 0.7774 (mp10) REVERT: A 224 ARG cc_start: 0.7690 (ttt180) cc_final: 0.6897 (mmp80) outliers start: 33 outliers final: 23 residues processed: 295 average time/residue: 0.1409 time to fit residues: 63.8010 Evaluate side-chains 293 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 269 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 28 optimal weight: 0.2980 chunk 97 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 447 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.213139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157549 restraints weight = 24570.860| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.02 r_work: 0.3553 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20006 Z= 0.125 Angle : 0.567 11.320 27120 Z= 0.286 Chirality : 0.038 0.222 3090 Planarity : 0.003 0.044 3358 Dihedral : 5.491 38.658 2796 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.66 % Allowed : 13.77 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.18), residues: 2384 helix: 1.18 (0.13), residues: 1442 sheet: -2.14 (0.60), residues: 68 loop : -1.25 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 746 TYR 0.021 0.001 TYR D 628 PHE 0.027 0.001 PHE C 751 TRP 0.012 0.001 TRP C 733 HIS 0.007 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00288 (20006) covalent geometry : angle 0.56658 (27120) hydrogen bonds : bond 0.03367 ( 1110) hydrogen bonds : angle 3.94576 ( 3168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 276 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 ARG cc_start: 0.7558 (ttm170) cc_final: 0.7219 (ttm-80) REVERT: B 699 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 224 ARG cc_start: 0.7623 (ttt180) cc_final: 0.6840 (mmp80) REVERT: C 225 GLU cc_start: 0.8061 (mt-10) cc_final: 0.6751 (pm20) REVERT: C 732 ILE cc_start: 0.8087 (mp) cc_final: 0.7869 (tp) REVERT: D 182 ASP cc_start: 0.6833 (m-30) cc_final: 0.6534 (m-30) REVERT: D 447 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7587 (m90) REVERT: D 578 MET cc_start: 0.6489 (ttp) cc_final: 0.6234 (ttt) REVERT: D 605 MET cc_start: 0.7596 (mmm) cc_final: 0.7381 (mmm) REVERT: D 736 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: A 224 ARG cc_start: 0.7633 (ttt180) cc_final: 0.6844 (mmp80) outliers start: 35 outliers final: 26 residues processed: 294 average time/residue: 0.1302 time to fit residues: 58.6024 Evaluate side-chains 299 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 447 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.213189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.157912 restraints weight = 24546.983| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.02 r_work: 0.3551 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20006 Z= 0.126 Angle : 0.580 11.623 27120 Z= 0.290 Chirality : 0.039 0.230 3090 Planarity : 0.004 0.094 3358 Dihedral : 5.439 38.336 2796 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 1.89 % Allowed : 14.43 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.18), residues: 2384 helix: 1.18 (0.13), residues: 1438 sheet: -1.94 (0.62), residues: 68 loop : -1.22 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 746 TYR 0.033 0.001 TYR A 439 PHE 0.020 0.001 PHE B 669 TRP 0.019 0.001 TRP A 785 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00291 (20006) covalent geometry : angle 0.58000 (27120) hydrogen bonds : bond 0.03355 ( 1110) hydrogen bonds : angle 3.95614 ( 3168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 699 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8124 (mp) REVERT: B 736 GLN cc_start: 0.8182 (pt0) cc_final: 0.7646 (mp10) REVERT: C 224 ARG cc_start: 0.7646 (ttt180) cc_final: 0.6848 (mmp80) REVERT: C 225 GLU cc_start: 0.8050 (mt-10) cc_final: 0.6754 (pm20) REVERT: C 437 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8617 (tt) REVERT: C 449 MET cc_start: 0.8286 (mtp) cc_final: 0.7931 (mtp) REVERT: D 182 ASP cc_start: 0.6865 (m-30) cc_final: 0.6575 (m-30) REVERT: D 447 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7601 (m90) REVERT: D 605 MET cc_start: 0.7680 (mmm) cc_final: 0.7300 (mmm) REVERT: D 736 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: A 224 ARG cc_start: 0.7658 (ttt180) cc_final: 0.6869 (mmp80) REVERT: A 628 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6717 (t80) outliers start: 40 outliers final: 29 residues processed: 297 average time/residue: 0.1426 time to fit residues: 64.3342 Evaluate side-chains 300 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 746 ARG Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 111 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 94 optimal weight: 0.0470 chunk 161 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 447 HIS D 528 ASN D 550 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 447 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.208995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152616 restraints weight = 24579.814| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.04 r_work: 0.3487 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20006 Z= 0.201 Angle : 0.645 11.565 27120 Z= 0.326 Chirality : 0.041 0.254 3090 Planarity : 0.004 0.039 3358 Dihedral : 5.634 40.205 2796 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.27 % Allowed : 15.09 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2384 helix: 1.02 (0.13), residues: 1434 sheet: -2.53 (0.58), residues: 78 loop : -1.20 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 206 TYR 0.024 0.002 TYR A 602 PHE 0.029 0.002 PHE C 751 TRP 0.010 0.001 TRP C 733 HIS 0.010 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00481 (20006) covalent geometry : angle 0.64482 (27120) hydrogen bonds : bond 0.03754 ( 1110) hydrogen bonds : angle 4.11812 ( 3168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 285 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 699 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 730 LYS cc_start: 0.8609 (tppt) cc_final: 0.7876 (ptpt) REVERT: B 736 GLN cc_start: 0.8328 (pt0) cc_final: 0.7747 (mp10) REVERT: C 224 ARG cc_start: 0.7719 (ttt180) cc_final: 0.6869 (mmp80) REVERT: C 225 GLU cc_start: 0.8150 (mt-10) cc_final: 0.6803 (pm20) REVERT: C 347 ASP cc_start: 0.8489 (m-30) cc_final: 0.8103 (m-30) REVERT: C 437 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8648 (tt) REVERT: C 669 PHE cc_start: 0.8701 (t80) cc_final: 0.8491 (t80) REVERT: D 182 ASP cc_start: 0.6934 (m-30) cc_final: 0.6614 (m-30) REVERT: D 206 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.6922 (tpp-160) REVERT: D 447 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7598 (m90) REVERT: D 730 LYS cc_start: 0.8622 (tppt) cc_final: 0.7951 (ptpt) REVERT: D 736 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: A 224 ARG cc_start: 0.7649 (ttt180) cc_final: 0.6737 (mmp80) REVERT: A 225 GLU cc_start: 0.8185 (mt-10) cc_final: 0.6872 (pm20) REVERT: A 347 ASP cc_start: 0.8446 (m-30) cc_final: 0.8065 (m-30) REVERT: A 437 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8693 (tt) outliers start: 48 outliers final: 33 residues processed: 310 average time/residue: 0.1316 time to fit residues: 62.9189 Evaluate side-chains 309 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 628 TYR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 746 ARG Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 169 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 218 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.212827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159333 restraints weight = 24368.980| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.83 r_work: 0.3569 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20006 Z= 0.118 Angle : 0.617 19.287 27120 Z= 0.304 Chirality : 0.039 0.223 3090 Planarity : 0.003 0.039 3358 Dihedral : 5.527 39.116 2796 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.61 % Allowed : 15.94 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.18), residues: 2384 helix: 1.11 (0.13), residues: 1436 sheet: -1.86 (0.65), residues: 68 loop : -1.19 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 746 TYR 0.028 0.001 TYR D 628 PHE 0.025 0.001 PHE B 669 TRP 0.017 0.001 TRP C 733 HIS 0.003 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00264 (20006) covalent geometry : angle 0.61690 (27120) hydrogen bonds : bond 0.03343 ( 1110) hydrogen bonds : angle 4.04981 ( 3168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 699 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8170 (mp) REVERT: B 730 LYS cc_start: 0.8633 (tppt) cc_final: 0.7999 (ptpt) REVERT: B 736 GLN cc_start: 0.8270 (pt0) cc_final: 0.7698 (mp10) REVERT: C 224 ARG cc_start: 0.7687 (ttt180) cc_final: 0.6870 (mmp80) REVERT: C 225 GLU cc_start: 0.8062 (mt-10) cc_final: 0.6788 (pm20) REVERT: C 437 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8603 (tt) REVERT: C 669 PHE cc_start: 0.8669 (t80) cc_final: 0.8455 (t80) REVERT: C 732 ILE cc_start: 0.8130 (mp) cc_final: 0.7904 (tp) REVERT: D 182 ASP cc_start: 0.6866 (m-30) cc_final: 0.6560 (m-30) REVERT: D 206 ARG cc_start: 0.7722 (tpp-160) cc_final: 0.7469 (tpp-160) REVERT: D 447 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.7592 (m90) REVERT: D 730 LYS cc_start: 0.8624 (tppt) cc_final: 0.7975 (ptpt) REVERT: D 736 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: A 224 ARG cc_start: 0.7665 (ttt180) cc_final: 0.6743 (mmp80) REVERT: A 225 GLU cc_start: 0.8100 (mt-10) cc_final: 0.6881 (pm20) REVERT: A 437 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8608 (tt) outliers start: 34 outliers final: 26 residues processed: 291 average time/residue: 0.1380 time to fit residues: 61.2439 Evaluate side-chains 301 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 628 TYR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 746 ARG Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 170 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 202 optimal weight: 0.7980 chunk 217 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS D 550 GLN ** D 712 ASN ** 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 = 0.4309 r_free = 0.4309 target = 0.209808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154975 restraints weight = 24555.639| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.90 r_work: 0.3518 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20006 Z= 0.176 Angle : 0.653 17.948 27120 Z= 0.323 Chirality : 0.041 0.194 3090 Planarity : 0.004 0.039 3358 Dihedral : 5.554 39.188 2796 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.56 % Allowed : 16.23 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.14 (0.18), residues: 2384 helix: 1.02 (0.13), residues: 1436 sheet: -2.91 (0.56), residues: 88 loop : -1.10 (0.24), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 746 TYR 0.037 0.001 TYR D 628 PHE 0.031 0.001 PHE C 751 TRP 0.019 0.002 TRP A 785 HIS 0.005 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00418 (20006) covalent geometry : angle 0.65252 (27120) hydrogen bonds : bond 0.03621 ( 1110) hydrogen bonds : angle 4.12847 ( 3168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 699 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 732 ILE cc_start: 0.7416 (mm) cc_final: 0.7116 (mm) REVERT: B 736 GLN cc_start: 0.8323 (pt0) cc_final: 0.7743 (mp10) REVERT: C 224 ARG cc_start: 0.7744 (ttt180) cc_final: 0.6906 (mmp-170) REVERT: C 225 GLU cc_start: 0.8093 (mt-10) cc_final: 0.6753 (pm20) REVERT: C 299 HIS cc_start: 0.8105 (m-70) cc_final: 0.7837 (m-70) REVERT: C 347 ASP cc_start: 0.8436 (m-30) cc_final: 0.8051 (m-30) REVERT: C 437 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8654 (tt) REVERT: D 182 ASP cc_start: 0.6890 (m-30) cc_final: 0.6552 (m-30) REVERT: D 206 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.6926 (tpp-160) REVERT: D 447 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7602 (m90) REVERT: D 683 LEU cc_start: 0.6582 (pp) cc_final: 0.5882 (mt) REVERT: D 736 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: D 761 MET cc_start: 0.8102 (mmm) cc_final: 0.7872 (mmm) REVERT: A 224 ARG cc_start: 0.7689 (ttt180) cc_final: 0.6834 (mmp80) REVERT: A 347 ASP cc_start: 0.8418 (m-30) cc_final: 0.8029 (m-30) REVERT: A 437 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8620 (tt) outliers start: 33 outliers final: 27 residues processed: 284 average time/residue: 0.1435 time to fit residues: 62.6546 Evaluate side-chains 292 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 628 TYR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 746 ARG Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 181 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 236 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** 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 = 0.4331 r_free = 0.4331 target = 0.212194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156146 restraints weight = 24528.516| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.04 r_work: 0.3543 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20006 Z= 0.127 Angle : 0.634 17.761 27120 Z= 0.312 Chirality : 0.039 0.190 3090 Planarity : 0.003 0.039 3358 Dihedral : 5.485 38.371 2796 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.56 % Allowed : 16.75 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.24 (0.18), residues: 2384 helix: 1.08 (0.13), residues: 1436 sheet: -1.85 (0.64), residues: 68 loop : -1.18 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 779 TYR 0.040 0.001 TYR D 628 PHE 0.026 0.001 PHE B 669 TRP 0.017 0.001 TRP C 733 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00291 (20006) covalent geometry : angle 0.63389 (27120) hydrogen bonds : bond 0.03396 ( 1110) hydrogen bonds : angle 4.06817 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5756.42 seconds wall clock time: 99 minutes 6.43 seconds (5946.43 seconds total)