Starting phenix.real_space_refine on Tue May 20 03:06:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jvi_36675/05_2025/8jvi_36675.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jvi_36675/05_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_36675/05_2025/8jvi_36675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jvi_36675/05_2025/8jvi_36675.map" model { file = "/net/cci-nas-00/data/ceres_data/8jvi_36675/05_2025/8jvi_36675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jvi_36675/05_2025/8jvi_36675.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "A" 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: "A" 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, C Time building chain proxies: 17.35, per 1000 atoms: 0.89 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: 4.73 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.85 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: 5.40 Time building geometry restraints manager: 5.43 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: 0.09 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.820 Set stop_for_unknowns flag: 0.010 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: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.080 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (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 TRP 0.014 0.002 TRP D 409 HIS 0.005 0.001 HIS C 309 PHE 0.028 0.001 PHE A 615 TYR 0.014 0.001 TYR A 628 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.16694 ( 1110) hydrogen bonds : angle 5.36784 ( 3168) covalent geometry : bond 0.01101 (20006) covalent geometry : angle 0.78248 (27120) *********************** 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 : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash 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: C 225 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7071 (pm20) REVERT: D 695 PHE cc_start: 0.7630 (t80) cc_final: 0.7329 (t80) outliers start: 19 outliers final: 10 residues processed: 324 average time/residue: 0.3060 time to fit residues: 152.0442 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 : 2.335 ------------------------------------------------------------------------------- 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 202 optimal weight: 0.8980 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 188 optimal weight: 0.0020 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- 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 297 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN C 401 HIS C 447 HIS C 528 ASN D 550 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN A 401 HIS A 447 HIS A 528 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.210295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151879 restraints weight = 24790.163| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.31 r_work: 0.3498 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20006 Z= 0.212 Angle : 0.668 8.561 27120 Z= 0.341 Chirality : 0.041 0.145 3090 Planarity : 0.005 0.081 3358 Dihedral : 7.207 57.706 2808 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.28 % Allowed : 7.95 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2384 helix: 0.86 (0.13), residues: 1444 sheet: -3.61 (0.50), residues: 92 loop : -1.17 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 785 HIS 0.006 0.001 HIS B 326 PHE 0.022 0.002 PHE A 624 TYR 0.020 0.002 TYR B 628 ARG 0.004 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 1110) hydrogen bonds : angle 4.37851 ( 3168) covalent geometry : bond 0.00501 (20006) covalent geometry : angle 0.66834 (27120) *********************** 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 315 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 2.045 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: 0.6364 (ttt) REVERT: C 225 GLU cc_start: 0.8291 (mt-10) cc_final: 0.6917 (pm20) REVERT: C 482 MET cc_start: 0.6897 (mmp) cc_final: 0.6690 (mmp) REVERT: C 685 MET cc_start: 0.7186 (tpp) cc_final: 0.6964 (tpp) REVERT: D 182 ASP cc_start: 0.7021 (m-30) cc_final: 0.6767 (m-30) REVERT: D 695 PHE cc_start: 0.7725 (t80) cc_final: 0.7315 (t80) REVERT: D 718 MET cc_start: 0.6588 (ppp) cc_final: 0.5978 (tpt) REVERT: A 225 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7033 (pm20) REVERT: A 449 MET cc_start: 0.8269 (mtp) cc_final: 0.7830 (mtp) outliers start: 27 outliers final: 18 residues processed: 299 average time/residue: 0.3170 time to fit residues: 143.9963 Evaluate side-chains 286 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 357 PHE Chi-restraints excluded: chain C residue 442 LYS 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 172 PHE Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 527 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 236 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 98 optimal weight: 0.4980 chunk 8 optimal weight: 0.0000 chunk 80 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 338 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.212832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.155125 restraints weight = 24692.410| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.33 r_work: 0.3558 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 0.046 20006 Z= 0.117 Angle : 0.572 10.232 27120 Z= 0.293 Chirality : 0.038 0.158 3090 Planarity : 0.004 0.059 3358 Dihedral : 6.115 39.708 2800 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.14 % Allowed : 10.60 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2384 helix: 1.01 (0.14), residues: 1442 sheet: -2.60 (0.56), residues: 68 loop : -1.30 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.004 0.001 HIS C 252 PHE 0.022 0.001 PHE C 624 TYR 0.031 0.001 TYR D 628 ARG 0.014 0.000 ARG B 746 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 1110) hydrogen bonds : angle 4.13913 ( 3168) covalent geometry : bond 0.00257 (20006) covalent geometry : angle 0.57227 (27120) *********************** 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 306 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 578 MET cc_start: 0.6483 (ttt) cc_final: 0.6280 (ttt) REVERT: B 683 LEU cc_start: 0.6427 (pp) cc_final: 0.5704 (mt) REVERT: B 743 ASP cc_start: 0.8303 (m-30) cc_final: 0.8061 (m-30) REVERT: C 224 ARG cc_start: 0.7700 (ttt180) cc_final: 0.6744 (mmp80) REVERT: C 225 GLU cc_start: 0.8164 (mt-10) cc_final: 0.6795 (pm20) REVERT: C 685 MET cc_start: 0.7138 (tpp) cc_final: 0.6919 (tpp) REVERT: D 182 ASP cc_start: 0.6913 (m-30) cc_final: 0.6661 (m-30) REVERT: D 718 MET cc_start: 0.6550 (ppp) cc_final: 0.6070 (tpt) REVERT: A 224 ARG cc_start: 0.7638 (ttt180) cc_final: 0.6765 (mmp80) REVERT: A 225 GLU cc_start: 0.8164 (mt-10) cc_final: 0.6852 (pm20) outliers start: 24 outliers final: 16 residues processed: 291 average time/residue: 0.3087 time to fit residues: 136.8243 Evaluate side-chains 279 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 2.140 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain C residue 345 MET 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 194 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 345 MET 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 129 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 45 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 137 optimal weight: 0.0070 overall best weight: 1.5780 ------------------------------------------------------------------------------- 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 338 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 = 0.4316 r_free = 0.4316 target = 0.210521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150709 restraints weight = 24687.901| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.47 r_work: 0.3508 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20006 Z= 0.166 Angle : 0.601 10.244 27120 Z= 0.305 Chirality : 0.039 0.174 3090 Planarity : 0.004 0.044 3358 Dihedral : 5.770 39.782 2796 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.75 % Allowed : 11.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2384 helix: 1.01 (0.13), residues: 1428 sheet: -3.31 (0.51), residues: 88 loop : -1.23 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 785 HIS 0.005 0.001 HIS A 252 PHE 0.024 0.002 PHE A 751 TYR 0.032 0.001 TYR D 628 ARG 0.004 0.000 ARG B 746 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 1110) hydrogen bonds : angle 4.13723 ( 3168) covalent geometry : bond 0.00392 (20006) covalent geometry : angle 0.60068 (27120) *********************** 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 314 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 578 MET cc_start: 0.6575 (ttt) cc_final: 0.6328 (ttt) REVERT: C 224 ARG cc_start: 0.7649 (ttt180) cc_final: 0.6815 (mmp80) REVERT: C 225 GLU cc_start: 0.8188 (mt-10) cc_final: 0.6799 (pm20) REVERT: D 182 ASP cc_start: 0.7002 (m-30) cc_final: 0.6749 (m-30) REVERT: D 447 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7573 (m90) REVERT: D 736 GLN cc_start: 0.8251 (pm20) cc_final: 0.7818 (mp10) REVERT: A 224 ARG cc_start: 0.7682 (ttt180) cc_final: 0.6774 (mmp80) REVERT: A 225 GLU cc_start: 0.8187 (mt-10) cc_final: 0.6894 (pm20) outliers start: 37 outliers final: 23 residues processed: 294 average time/residue: 0.3075 time to fit residues: 139.6311 Evaluate side-chains 285 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 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 476 VAL Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 710 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 130 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 229 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 219 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 736 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.211327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153868 restraints weight = 24730.440| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.23 r_work: 0.3509 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20006 Z= 0.140 Angle : 0.588 10.681 27120 Z= 0.297 Chirality : 0.039 0.209 3090 Planarity : 0.004 0.040 3358 Dihedral : 5.672 39.887 2796 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.42 % Allowed : 13.81 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.18), residues: 2384 helix: 1.04 (0.13), residues: 1432 sheet: -2.59 (0.57), residues: 78 loop : -1.26 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.005 0.001 HIS C 252 PHE 0.019 0.001 PHE C 624 TYR 0.022 0.001 TYR A 702 ARG 0.003 0.000 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 1110) hydrogen bonds : angle 4.02881 ( 3168) covalent geometry : bond 0.00329 (20006) covalent geometry : angle 0.58827 (27120) *********************** 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 299 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 ARG cc_start: 0.7279 (tpp80) cc_final: 0.6874 (tpp80) REVERT: B 578 MET cc_start: 0.6675 (ttt) cc_final: 0.6430 (ttt) REVERT: B 736 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: C 224 ARG cc_start: 0.7663 (ttt180) cc_final: 0.6852 (mmp80) REVERT: C 225 GLU cc_start: 0.8109 (mt-10) cc_final: 0.6746 (pm20) REVERT: C 628 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.7071 (t80) REVERT: D 182 ASP cc_start: 0.6906 (m-30) cc_final: 0.6618 (m-30) REVERT: D 447 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7600 (m90) REVERT: D 736 GLN cc_start: 0.8293 (pm20) cc_final: 0.7821 (mp10) REVERT: A 224 ARG cc_start: 0.7666 (ttt180) cc_final: 0.6782 (mmp80) REVERT: A 225 GLU cc_start: 0.8159 (mt-10) cc_final: 0.6872 (pm20) outliers start: 30 outliers final: 19 residues processed: 283 average time/residue: 0.3015 time to fit residues: 132.1113 Evaluate side-chains 283 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 261 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 736 GLN 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 209 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 628 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 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 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 184 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 226 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 387 GLN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN D 387 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.211212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156517 restraints weight = 24527.513| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.95 r_work: 0.3528 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2270 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= 0.135 Angle : 0.579 11.119 27120 Z= 0.293 Chirality : 0.039 0.223 3090 Planarity : 0.003 0.040 3358 Dihedral : 5.551 39.311 2796 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.99 % Allowed : 14.19 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2384 helix: 1.06 (0.13), residues: 1436 sheet: -2.55 (0.57), residues: 78 loop : -1.19 (0.23), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 785 HIS 0.004 0.001 HIS C 252 PHE 0.018 0.001 PHE C 624 TYR 0.026 0.001 TYR D 628 ARG 0.003 0.000 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 1110) hydrogen bonds : angle 3.98801 ( 3168) covalent geometry : bond 0.00313 (20006) covalent geometry : angle 0.57887 (27120) *********************** 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 313 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 ARG cc_start: 0.7266 (tpp80) cc_final: 0.6849 (tpp80) REVERT: B 578 MET cc_start: 0.6748 (ttt) cc_final: 0.6481 (ttt) REVERT: B 699 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 730 LYS cc_start: 0.8552 (tppt) cc_final: 0.7858 (ptpt) REVERT: B 736 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: B 761 MET cc_start: 0.8185 (mmm) cc_final: 0.7803 (mmm) REVERT: C 224 ARG cc_start: 0.7658 (ttt180) cc_final: 0.6842 (mmp80) REVERT: C 225 GLU cc_start: 0.8083 (mt-10) cc_final: 0.6715 (pm20) REVERT: C 449 MET cc_start: 0.8320 (mtp) cc_final: 0.8115 (mtp) REVERT: C 732 ILE cc_start: 0.8112 (mp) cc_final: 0.7889 (tp) REVERT: D 182 ASP cc_start: 0.6864 (m-30) cc_final: 0.6557 (m-30) REVERT: D 447 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7587 (m90) REVERT: D 578 MET cc_start: 0.6582 (ttp) cc_final: 0.6363 (ttt) REVERT: D 730 LYS cc_start: 0.8652 (tppt) cc_final: 0.7946 (ptpt) REVERT: D 736 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: A 224 ARG cc_start: 0.7667 (ttt180) cc_final: 0.6853 (mmp80) REVERT: A 225 GLU cc_start: 0.8119 (mt-10) cc_final: 0.6838 (pm20) REVERT: A 732 ILE cc_start: 0.8149 (mp) cc_final: 0.7943 (tp) outliers start: 42 outliers final: 29 residues processed: 292 average time/residue: 0.3363 time to fit residues: 151.1508 Evaluate side-chains 297 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 2.067 ------------------------------------------------------------------------------- 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 736 GLN 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 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 487 LEU 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 D residue 247 GLU Chi-restraints excluded: chain D residue 250 CYS 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 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 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 Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 746 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 39 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 123 optimal weight: 0.0970 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 D 387 GLN ** D 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.212000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157150 restraints weight = 24537.549| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.91 r_work: 0.3551 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20006 Z= 0.125 Angle : 0.582 11.575 27120 Z= 0.291 Chirality : 0.039 0.227 3090 Planarity : 0.003 0.039 3358 Dihedral : 5.492 38.754 2796 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.94 % Allowed : 15.37 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2384 helix: 1.10 (0.13), residues: 1438 sheet: -2.08 (0.61), residues: 68 loop : -1.20 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 733 HIS 0.004 0.001 HIS C 252 PHE 0.020 0.001 PHE D 669 TYR 0.040 0.001 TYR C 628 ARG 0.003 0.000 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 1110) hydrogen bonds : angle 3.97614 ( 3168) covalent geometry : bond 0.00288 (20006) covalent geometry : angle 0.58176 (27120) *********************** 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 323 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6837 (tpp80) REVERT: B 578 MET cc_start: 0.6749 (ttt) cc_final: 0.6548 (ttt) REVERT: B 699 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 730 LYS cc_start: 0.8554 (tppt) cc_final: 0.7875 (ptpt) REVERT: B 736 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: B 761 MET cc_start: 0.8166 (mmm) cc_final: 0.7794 (mmm) REVERT: C 224 ARG cc_start: 0.7646 (ttt180) cc_final: 0.6838 (mmp80) REVERT: C 225 GLU cc_start: 0.8064 (mt-10) cc_final: 0.6733 (pm20) REVERT: C 669 PHE cc_start: 0.8726 (t80) cc_final: 0.8525 (t80) REVERT: D 182 ASP cc_start: 0.6854 (m-30) cc_final: 0.6543 (m-30) REVERT: D 213 LEU cc_start: 0.8423 (mp) cc_final: 0.7810 (mp) REVERT: D 447 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7551 (m90) REVERT: D 578 MET cc_start: 0.6568 (ttp) cc_final: 0.6350 (ttt) REVERT: D 730 LYS cc_start: 0.8574 (tppt) cc_final: 0.7924 (ptpt) REVERT: D 736 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: A 224 ARG cc_start: 0.7673 (ttt180) cc_final: 0.6863 (mmp80) REVERT: A 225 GLU cc_start: 0.8102 (mt-10) cc_final: 0.6930 (pm20) REVERT: A 449 MET cc_start: 0.8150 (mtp) cc_final: 0.7938 (mtp) outliers start: 41 outliers final: 30 residues processed: 303 average time/residue: 0.3231 time to fit residues: 149.3186 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 : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 736 GLN 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 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 487 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 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 705 LEU 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 710 LEU Chi-restraints excluded: chain A residue 746 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 66 optimal weight: 0.9990 chunk 134 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 150 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 387 GLN D 550 GLN D 607 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.213244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 143)---------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151810 restraints weight = 24678.039| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.88 r_work: 0.3522 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2475 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= 0.112 Angle : 0.577 11.828 27120 Z= 0.291 Chirality : 0.039 0.356 3090 Planarity : 0.003 0.039 3358 Dihedral : 5.430 37.918 2796 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.66 % Allowed : 16.27 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.18), residues: 2384 helix: 1.13 (0.13), residues: 1442 sheet: -1.82 (0.64), residues: 68 loop : -1.15 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 785 HIS 0.003 0.001 HIS A 252 PHE 0.024 0.001 PHE D 172 TYR 0.028 0.001 TYR B 628 ARG 0.003 0.000 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 1110) hydrogen bonds : angle 3.97981 ( 3168) covalent geometry : bond 0.00251 (20006) covalent geometry : angle 0.57706 (27120) *********************** 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 310 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 ARG cc_start: 0.7339 (tpp80) cc_final: 0.6849 (tpp80) REVERT: B 213 LEU cc_start: 0.7975 (mp) cc_final: 0.7702 (tp) REVERT: B 699 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 730 LYS cc_start: 0.8568 (tppt) cc_final: 0.7859 (ptpt) REVERT: B 736 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: B 739 THR cc_start: 0.8847 (m) cc_final: 0.8610 (m) REVERT: B 761 MET cc_start: 0.8309 (mmm) cc_final: 0.7943 (mmm) REVERT: C 224 ARG cc_start: 0.7602 (ttt180) cc_final: 0.6769 (mmp80) REVERT: C 225 GLU cc_start: 0.8053 (mt-10) cc_final: 0.6647 (pm20) REVERT: C 669 PHE cc_start: 0.8799 (t80) cc_final: 0.8582 (t80) REVERT: D 182 ASP cc_start: 0.6957 (m-30) cc_final: 0.6639 (m-30) REVERT: D 447 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7729 (m90) REVERT: D 578 MET cc_start: 0.6477 (ttp) cc_final: 0.6264 (ttt) REVERT: D 730 LYS cc_start: 0.8533 (tppt) cc_final: 0.7869 (ptpt) REVERT: D 736 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: A 224 ARG cc_start: 0.7624 (ttt180) cc_final: 0.6797 (mmp80) REVERT: A 225 GLU cc_start: 0.8105 (mt-10) cc_final: 0.6782 (pm20) REVERT: A 449 MET cc_start: 0.8143 (mtp) cc_final: 0.7910 (mtp) outliers start: 35 outliers final: 28 residues processed: 293 average time/residue: 0.3126 time to fit residues: 139.1193 Evaluate side-chains 300 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 736 GLN 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 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 487 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 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 258 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 258 VAL 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 Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 746 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 11 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 163 optimal weight: 0.2980 overall best weight: 1.4602 ------------------------------------------------------------------------------- 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** D 387 GLN D 550 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.211009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150694 restraints weight = 24390.739| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.46 r_work: 0.3506 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20006 Z= 0.154 Angle : 0.607 11.695 27120 Z= 0.305 Chirality : 0.040 0.179 3090 Planarity : 0.003 0.038 3358 Dihedral : 5.465 38.355 2796 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.70 % Allowed : 16.27 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2384 helix: 1.08 (0.13), residues: 1438 sheet: -2.84 (0.57), residues: 88 loop : -1.05 (0.24), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 785 HIS 0.005 0.001 HIS B 326 PHE 0.030 0.001 PHE C 751 TYR 0.023 0.001 TYR D 628 ARG 0.006 0.000 ARG C 779 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 1110) hydrogen bonds : angle 4.00537 ( 3168) covalent geometry : bond 0.00365 (20006) covalent geometry : angle 0.60691 (27120) *********************** 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 305 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 699 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 730 LYS cc_start: 0.8582 (tppt) cc_final: 0.7892 (ptpt) REVERT: C 215 ASP cc_start: 0.8903 (m-30) cc_final: 0.8703 (m-30) REVERT: C 224 ARG cc_start: 0.7646 (ttt180) cc_final: 0.6854 (mmp80) REVERT: C 225 GLU cc_start: 0.8093 (mt-10) cc_final: 0.6722 (pm20) REVERT: C 669 PHE cc_start: 0.8781 (t80) cc_final: 0.8564 (t80) REVERT: D 182 ASP cc_start: 0.6905 (m-30) cc_final: 0.6584 (m-30) REVERT: D 447 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7709 (m90) REVERT: D 578 MET cc_start: 0.6538 (ttp) cc_final: 0.6334 (ttt) REVERT: D 683 LEU cc_start: 0.6459 (pp) cc_final: 0.5752 (mt) REVERT: D 736 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 224 ARG cc_start: 0.7655 (ttt180) cc_final: 0.6857 (mmp80) REVERT: A 225 GLU cc_start: 0.8138 (mt-10) cc_final: 0.6824 (pm20) REVERT: A 732 ILE cc_start: 0.8198 (mp) cc_final: 0.7958 (tp) outliers start: 36 outliers final: 30 residues processed: 287 average time/residue: 0.3094 time to fit residues: 135.7339 Evaluate side-chains 297 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 470 SER 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 209 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 487 LEU 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 250 CYS Chi-restraints excluded: chain D residue 258 VAL 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 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE 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 Chi-restraints excluded: chain A residue 746 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 43 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 211 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 387 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.213901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157895 restraints weight = 24512.155| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.04 r_work: 0.3564 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20006 Z= 0.111 Angle : 0.602 20.207 27120 Z= 0.297 Chirality : 0.039 0.195 3090 Planarity : 0.003 0.038 3358 Dihedral : 5.404 37.271 2796 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.32 % Allowed : 17.12 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2384 helix: 1.18 (0.13), residues: 1442 sheet: -1.69 (0.66), residues: 68 loop : -1.13 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 733 HIS 0.004 0.001 HIS B 252 PHE 0.028 0.001 PHE D 172 TYR 0.021 0.001 TYR D 628 ARG 0.004 0.000 ARG C 779 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 1110) hydrogen bonds : angle 3.96768 ( 3168) covalent geometry : bond 0.00246 (20006) covalent geometry : angle 0.60233 (27120) ********************** 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 304 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 567 TYR cc_start: 0.6092 (t80) cc_final: 0.5536 (t80) REVERT: B 699 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8188 (mp) REVERT: B 730 LYS cc_start: 0.8565 (tppt) cc_final: 0.7888 (ptpt) REVERT: C 215 ASP cc_start: 0.8919 (m-30) cc_final: 0.8717 (m-30) REVERT: C 224 ARG cc_start: 0.7536 (ttt180) cc_final: 0.6764 (mmp80) REVERT: C 225 GLU cc_start: 0.8006 (mt-10) cc_final: 0.6632 (pm20) REVERT: C 669 PHE cc_start: 0.8733 (t80) cc_final: 0.8532 (t80) REVERT: D 182 ASP cc_start: 0.6787 (m-30) cc_final: 0.6496 (m-30) REVERT: D 447 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7607 (m90) REVERT: D 578 MET cc_start: 0.6464 (ttp) cc_final: 0.6040 (ttt) REVERT: D 683 LEU cc_start: 0.6606 (pp) cc_final: 0.5940 (mt) REVERT: D 730 LYS cc_start: 0.8551 (tppt) cc_final: 0.7899 (ptpt) REVERT: D 736 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: A 224 ARG cc_start: 0.7611 (ttt180) cc_final: 0.6822 (mmp80) REVERT: A 225 GLU cc_start: 0.8010 (mt-10) cc_final: 0.6779 (pm20) REVERT: A 449 MET cc_start: 0.8109 (mtp) cc_final: 0.7877 (mtp) outliers start: 28 outliers final: 24 residues processed: 290 average time/residue: 0.3258 time to fit residues: 143.8970 Evaluate side-chains 295 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 442 LYS Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 487 LEU 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 258 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 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 710 LEU Chi-restraints excluded: chain A residue 746 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 69 optimal weight: 0.6980 chunk 185 optimal weight: 0.0040 chunk 165 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 189 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 163 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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** D 528 ASN 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 = 0.4354 r_free = 0.4354 target = 0.214712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3835 r_free = 0.3835 target = 0.159109 restraints weight = 24678.896| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.09 r_work: 0.3560 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20006 Z= 0.107 Angle : 0.591 17.619 27120 Z= 0.294 Chirality : 0.039 0.363 3090 Planarity : 0.003 0.038 3358 Dihedral : 5.317 35.981 2796 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.23 % Allowed : 17.50 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2384 helix: 1.22 (0.13), residues: 1440 sheet: -1.41 (0.69), residues: 68 loop : -1.13 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 785 HIS 0.002 0.000 HIS B 326 PHE 0.030 0.001 PHE C 751 TYR 0.025 0.001 TYR C 628 ARG 0.003 0.000 ARG C 779 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 1110) hydrogen bonds : angle 3.93380 ( 3168) covalent geometry : bond 0.00235 (20006) covalent geometry : angle 0.59146 (27120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13133.30 seconds wall clock time: 226 minutes 37.45 seconds (13597.45 seconds total)