Starting phenix.real_space_refine on Tue Jun 17 02:31:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jvi_36675/06_2025/8jvi_36675.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jvi_36675/06_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_36675/06_2025/8jvi_36675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jvi_36675/06_2025/8jvi_36675.map" model { file = "/net/cci-nas-00/data/ceres_data/8jvi_36675/06_2025/8jvi_36675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jvi_36675/06_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-5710/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: 17.70, per 1000 atoms: 0.91 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: 5.10 Conformation dependent library (CDL) restraints added in 2.5 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: 1.94 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: 6.12 Time building geometry restraints manager: 5.96 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 50.060 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.090 ------------------------------------------------------------------------------- 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 : 1.925 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: 0.2899 time to fit residues: 144.0222 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 : 1.948 ------------------------------------------------------------------------------- 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 = 0.210205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151637 restraints weight = 24784.759| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.27 r_work: 0.3504 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20006 Z= 0.213 Angle : 0.669 8.527 27120 Z= 0.341 Chirality : 0.041 0.149 3090 Planarity : 0.005 0.081 3358 Dihedral : 7.192 57.262 2808 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.28 % Allowed : 7.99 % Favored : 90.73 % 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: 0.85 (0.13), residues: 1446 sheet: -3.61 (0.50), residues: 92 loop : -1.16 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 785 HIS 0.006 0.001 HIS B 326 PHE 0.022 0.002 PHE A 624 TYR 0.022 0.002 TYR B 628 ARG 0.004 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 1110) hydrogen bonds : angle 4.37750 ( 3168) covalent geometry : bond 0.00501 (20006) covalent geometry : angle 0.66889 (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 314 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 578 MET cc_start: 0.6556 (ttt) cc_final: 0.6342 (ttt) REVERT: C 225 GLU cc_start: 0.8271 (mt-10) cc_final: 0.6874 (pm20) REVERT: C 482 MET cc_start: 0.6879 (mmp) cc_final: 0.6678 (mmp) REVERT: C 685 MET cc_start: 0.7231 (tpp) cc_final: 0.7000 (tpp) REVERT: D 182 ASP cc_start: 0.7055 (m-30) cc_final: 0.6832 (m-30) REVERT: D 695 PHE cc_start: 0.7718 (t80) cc_final: 0.7314 (t80) REVERT: D 718 MET cc_start: 0.6645 (ppp) cc_final: 0.6008 (tpt) REVERT: A 225 GLU cc_start: 0.8271 (mt-10) cc_final: 0.6974 (pm20) REVERT: A 449 MET cc_start: 0.8264 (mtp) cc_final: 0.7814 (mtp) outliers start: 27 outliers final: 17 residues processed: 298 average time/residue: 0.5874 time to fit residues: 276.0721 Evaluate side-chains 283 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 266 time to evaluate : 2.507 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 222 optimal weight: 0.4980 chunk 236 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 8 optimal weight: 0.0060 chunk 80 optimal weight: 0.6980 overall best weight: 0.3374 ------------------------------------------------------------------------------- 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 ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.215492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153957 restraints weight = 24844.405| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.16 r_work: 0.3535 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20006 Z= 0.112 Angle : 0.564 10.053 27120 Z= 0.289 Chirality : 0.037 0.159 3090 Planarity : 0.004 0.054 3358 Dihedral : 5.997 39.475 2798 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.09 % Allowed : 10.45 % Favored : 88.46 % 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: 0.13 (0.18), residues: 2384 helix: 1.04 (0.14), residues: 1442 sheet: -2.49 (0.57), residues: 68 loop : -1.29 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 733 HIS 0.004 0.001 HIS C 252 PHE 0.023 0.001 PHE C 624 TYR 0.028 0.001 TYR D 628 ARG 0.013 0.000 ARG B 746 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 1110) hydrogen bonds : angle 4.08551 ( 3168) covalent geometry : bond 0.00237 (20006) covalent geometry : angle 0.56441 (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 305 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 587 MET cc_start: 0.7658 (mpp) cc_final: 0.7421 (mpp) REVERT: B 683 LEU cc_start: 0.6462 (pp) cc_final: 0.5774 (mt) REVERT: B 743 ASP cc_start: 0.8326 (m-30) cc_final: 0.8054 (m-30) REVERT: C 224 ARG cc_start: 0.7620 (ttt180) cc_final: 0.6726 (mmp80) REVERT: C 225 GLU cc_start: 0.8146 (mt-10) cc_final: 0.6701 (pm20) REVERT: C 685 MET cc_start: 0.7330 (tpp) cc_final: 0.7073 (tpp) REVERT: D 182 ASP cc_start: 0.6952 (m-30) cc_final: 0.6700 (m-30) REVERT: D 718 MET cc_start: 0.6721 (ppp) cc_final: 0.6178 (tpt) REVERT: A 224 ARG cc_start: 0.7562 (ttt180) cc_final: 0.6733 (mmp80) REVERT: A 225 GLU cc_start: 0.8152 (mt-10) cc_final: 0.6720 (pm20) outliers start: 23 outliers final: 16 residues processed: 291 average time/residue: 0.4180 time to fit residues: 189.6281 Evaluate side-chains 283 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 267 time to evaluate : 2.358 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 20.0000 chunk 4 optimal weight: 0.0980 chunk 109 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 137 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 447 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.214889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156328 restraints weight = 24949.032| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.51 r_work: 0.3570 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20006 Z= 0.110 Angle : 0.558 10.694 27120 Z= 0.283 Chirality : 0.038 0.166 3090 Planarity : 0.004 0.042 3358 Dihedral : 5.645 37.977 2796 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.42 % Allowed : 11.16 % Favored : 87.42 % 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: 0.21 (0.18), residues: 2384 helix: 1.14 (0.13), residues: 1438 sheet: -2.24 (0.59), residues: 68 loop : -1.34 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 785 HIS 0.005 0.001 HIS A 252 PHE 0.024 0.001 PHE A 751 TYR 0.029 0.001 TYR D 628 ARG 0.005 0.000 ARG B 746 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 1110) hydrogen bonds : angle 3.99462 ( 3168) covalent geometry : bond 0.00244 (20006) covalent geometry : angle 0.55807 (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 312 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 224 ARG cc_start: 0.7576 (ttt180) cc_final: 0.6759 (mmp80) REVERT: C 225 GLU cc_start: 0.8100 (mt-10) cc_final: 0.6665 (pm20) REVERT: C 685 MET cc_start: 0.7123 (tpp) cc_final: 0.6906 (tpp) REVERT: D 182 ASP cc_start: 0.6831 (m-30) cc_final: 0.6572 (m-30) REVERT: D 447 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7629 (m90) REVERT: D 736 GLN cc_start: 0.8179 (pm20) cc_final: 0.7771 (mp10) REVERT: A 224 ARG cc_start: 0.7615 (ttt180) cc_final: 0.6818 (mmp80) REVERT: A 225 GLU cc_start: 0.8094 (mt-10) cc_final: 0.6752 (pm20) outliers start: 30 outliers final: 22 residues processed: 294 average time/residue: 0.3382 time to fit residues: 151.7863 Evaluate side-chains 284 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 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 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 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 449 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 130 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 219 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 302 ASN C 447 HIS C 736 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 447 HIS A 736 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.214009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157516 restraints weight = 24834.664| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.14 r_work: 0.3549 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20006 Z= 0.121 Angle : 0.568 11.008 27120 Z= 0.287 Chirality : 0.038 0.208 3090 Planarity : 0.004 0.038 3358 Dihedral : 5.510 37.838 2796 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.37 % Allowed : 12.82 % Favored : 85.81 % 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: 0.26 (0.18), residues: 2384 helix: 1.18 (0.13), residues: 1438 sheet: -2.09 (0.60), residues: 68 loop : -1.31 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 785 HIS 0.005 0.001 HIS C 252 PHE 0.020 0.001 PHE A 624 TYR 0.034 0.001 TYR D 628 ARG 0.004 0.000 ARG B 746 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 1110) hydrogen bonds : angle 3.92974 ( 3168) covalent geometry : bond 0.00276 (20006) covalent geometry : angle 0.56815 (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 303 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 ARG cc_start: 0.7654 (ttm170) cc_final: 0.7271 (ttm-80) REVERT: B 736 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: C 224 ARG cc_start: 0.7595 (ttt180) cc_final: 0.6786 (mmp80) REVERT: C 225 GLU cc_start: 0.8082 (mt-10) cc_final: 0.6735 (pm20) REVERT: D 182 ASP cc_start: 0.6906 (m-30) cc_final: 0.6629 (m-30) REVERT: D 447 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7532 (m90) REVERT: D 736 GLN cc_start: 0.8191 (pm20) cc_final: 0.7769 (mp10) REVERT: A 224 ARG cc_start: 0.7599 (ttt180) cc_final: 0.6834 (mmp80) REVERT: A 225 GLU cc_start: 0.8082 (mt-10) cc_final: 0.6794 (pm20) REVERT: A 732 ILE cc_start: 0.8067 (mp) cc_final: 0.7859 (tp) outliers start: 29 outliers final: 24 residues processed: 288 average time/residue: 0.3333 time to fit residues: 146.9228 Evaluate side-chains 294 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 2.138 ------------------------------------------------------------------------------- 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 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 710 LEU 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 527 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 209 THR 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 449 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 184 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 226 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 447 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.213281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159270 restraints weight = 24641.436| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.96 r_work: 0.3556 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20006 Z= 0.122 Angle : 0.564 11.222 27120 Z= 0.284 Chirality : 0.038 0.182 3090 Planarity : 0.003 0.038 3358 Dihedral : 5.436 38.061 2796 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.89 % Allowed : 13.77 % Favored : 84.34 % 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: 1.19 (0.13), residues: 1440 sheet: -1.98 (0.60), residues: 68 loop : -1.24 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 785 HIS 0.004 0.001 HIS A 252 PHE 0.028 0.001 PHE C 751 TYR 0.025 0.001 TYR D 628 ARG 0.003 0.000 ARG D 779 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 1110) hydrogen bonds : angle 3.89063 ( 3168) covalent geometry : bond 0.00281 (20006) covalent geometry : angle 0.56438 (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 322 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 699 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8125 (mp) REVERT: C 224 ARG cc_start: 0.7615 (ttt180) cc_final: 0.6817 (mmp80) REVERT: C 225 GLU cc_start: 0.8045 (mt-10) cc_final: 0.6734 (pm20) REVERT: C 449 MET cc_start: 0.8204 (mtp) cc_final: 0.7956 (mtp) REVERT: D 182 ASP cc_start: 0.6892 (m-30) cc_final: 0.6599 (m-30) REVERT: D 447 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7595 (m90) REVERT: D 730 LYS cc_start: 0.8608 (tppt) cc_final: 0.7943 (ptpt) REVERT: D 736 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: A 224 ARG cc_start: 0.7638 (ttt180) cc_final: 0.6868 (mmp80) REVERT: A 225 GLU cc_start: 0.8064 (mt-10) cc_final: 0.6809 (pm20) REVERT: A 437 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8661 (tt) REVERT: A 628 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6915 (t80) outliers start: 40 outliers final: 26 residues processed: 301 average time/residue: 0.3124 time to fit residues: 144.0463 Evaluate side-chains 300 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 269 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 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 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 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 209 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 39 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.211435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151999 restraints weight = 24539.447| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.35 r_work: 0.3519 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20006 Z= 0.151 Angle : 0.598 11.494 27120 Z= 0.300 Chirality : 0.039 0.222 3090 Planarity : 0.004 0.038 3358 Dihedral : 5.464 38.566 2796 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.84 % Allowed : 14.90 % Favored : 83.25 % 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: 0.28 (0.18), residues: 2384 helix: 1.14 (0.13), residues: 1438 sheet: -2.37 (0.57), residues: 78 loop : -1.14 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 785 HIS 0.004 0.001 HIS B 252 PHE 0.024 0.001 PHE D 172 TYR 0.031 0.002 TYR A 439 ARG 0.003 0.000 ARG C 271 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 1110) hydrogen bonds : angle 3.96064 ( 3168) covalent geometry : bond 0.00357 (20006) covalent geometry : angle 0.59783 (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 314 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8673 (mt) REVERT: B 699 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8163 (mp) REVERT: C 224 ARG cc_start: 0.7641 (ttt180) cc_final: 0.6812 (mmp80) REVERT: C 225 GLU cc_start: 0.8093 (mt-10) cc_final: 0.6783 (pm20) REVERT: C 271 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7906 (ttp80) REVERT: C 449 MET cc_start: 0.8307 (mtp) cc_final: 0.7906 (mtp) REVERT: D 182 ASP cc_start: 0.6937 (m-30) cc_final: 0.6621 (m-30) REVERT: D 213 LEU cc_start: 0.8470 (mp) cc_final: 0.8066 (mp) REVERT: D 447 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7651 (m90) REVERT: D 736 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: A 224 ARG cc_start: 0.7627 (ttt180) cc_final: 0.6845 (mmp80) REVERT: A 225 GLU cc_start: 0.8155 (mt-10) cc_final: 0.6855 (pm20) REVERT: A 437 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8656 (tt) REVERT: A 628 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6887 (t80) REVERT: A 732 ILE cc_start: 0.8138 (mp) cc_final: 0.7828 (tp) outliers start: 39 outliers final: 27 residues processed: 294 average time/residue: 0.3159 time to fit residues: 141.9093 Evaluate side-chains 299 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 437 LEU Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 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 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 209 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 695 PHE Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 66 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 211 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 528 ASN D 550 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.212463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.156747 restraints weight = 24673.826| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.01 r_work: 0.3541 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20006 Z= 0.128 Angle : 0.594 11.774 27120 Z= 0.296 Chirality : 0.039 0.288 3090 Planarity : 0.003 0.038 3358 Dihedral : 5.443 38.284 2796 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.89 % Allowed : 15.52 % Favored : 82.59 % 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: 1.16 (0.13), residues: 1438 sheet: -1.79 (0.63), residues: 68 loop : -1.19 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 785 HIS 0.003 0.001 HIS C 326 PHE 0.028 0.001 PHE C 751 TYR 0.033 0.001 TYR C 628 ARG 0.004 0.000 ARG A 746 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 1110) hydrogen bonds : angle 3.96996 ( 3168) covalent geometry : bond 0.00298 (20006) covalent geometry : angle 0.59395 (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 317 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 699 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8165 (mp) REVERT: B 761 MET cc_start: 0.8198 (mmm) cc_final: 0.7780 (mmm) REVERT: C 224 ARG cc_start: 0.7626 (ttt180) cc_final: 0.6823 (mmp80) REVERT: C 225 GLU cc_start: 0.8061 (mt-10) cc_final: 0.6772 (pm20) REVERT: C 271 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7864 (ttp80) REVERT: C 449 MET cc_start: 0.8251 (mtp) cc_final: 0.7856 (mtp) REVERT: C 669 PHE cc_start: 0.8768 (t80) cc_final: 0.8548 (t80) REVERT: D 182 ASP cc_start: 0.6872 (m-30) cc_final: 0.6572 (m-30) REVERT: D 447 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7629 (m90) REVERT: D 683 LEU cc_start: 0.6327 (pp) cc_final: 0.5661 (mt) REVERT: D 730 LYS cc_start: 0.8573 (tppt) cc_final: 0.7928 (ptpt) REVERT: D 736 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: A 224 ARG cc_start: 0.7673 (ttt180) cc_final: 0.6879 (mmp80) REVERT: A 225 GLU cc_start: 0.8114 (mt-10) cc_final: 0.6852 (pm20) REVERT: A 437 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 628 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7097 (t80) REVERT: A 732 ILE cc_start: 0.8113 (mp) cc_final: 0.7847 (tp) outliers start: 40 outliers final: 28 residues processed: 294 average time/residue: 0.3140 time to fit residues: 141.9284 Evaluate side-chains 302 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 699 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 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 C residue 746 ARG 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 527 THR Chi-restraints excluded: chain D residue 551 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 264 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 6.9990 chunk 132 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.213767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160857 restraints weight = 24475.092| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.86 r_work: 0.3575 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20006 Z= 0.116 Angle : 0.589 11.817 27120 Z= 0.293 Chirality : 0.038 0.187 3090 Planarity : 0.003 0.038 3358 Dihedral : 5.380 37.809 2796 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.56 % Allowed : 16.23 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.18), residues: 2384 helix: 1.15 (0.13), residues: 1440 sheet: -1.57 (0.66), residues: 68 loop : -1.14 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 785 HIS 0.004 0.001 HIS D 252 PHE 0.029 0.001 PHE D 172 TYR 0.021 0.001 TYR B 628 ARG 0.004 0.000 ARG A 746 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 1110) hydrogen bonds : angle 3.95607 ( 3168) covalent geometry : bond 0.00264 (20006) covalent geometry : angle 0.58913 (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 308 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 699 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 761 MET cc_start: 0.8111 (mmm) cc_final: 0.7695 (mmm) REVERT: C 224 ARG cc_start: 0.7618 (ttt180) cc_final: 0.6812 (mmp80) REVERT: C 225 GLU cc_start: 0.7996 (mt-10) cc_final: 0.6619 (pm20) REVERT: C 271 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7826 (ttp80) REVERT: C 375 MET cc_start: 0.8463 (mtm) cc_final: 0.8239 (mtp) REVERT: C 449 MET cc_start: 0.8135 (mtp) cc_final: 0.7827 (mtp) REVERT: C 669 PHE cc_start: 0.8724 (t80) cc_final: 0.8511 (t80) REVERT: D 182 ASP cc_start: 0.6779 (m-30) cc_final: 0.6495 (m-30) REVERT: D 447 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7641 (m90) REVERT: D 683 LEU cc_start: 0.6458 (pp) cc_final: 0.5816 (mt) REVERT: D 730 LYS cc_start: 0.8542 (tppt) cc_final: 0.7916 (ptpt) REVERT: D 736 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: A 224 ARG cc_start: 0.7657 (ttt180) cc_final: 0.6885 (mmp80) REVERT: A 225 GLU cc_start: 0.8026 (mt-10) cc_final: 0.6811 (pm20) REVERT: A 375 MET cc_start: 0.8449 (mtm) cc_final: 0.8231 (mtp) REVERT: A 437 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8636 (tt) REVERT: A 628 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7624 (t80) REVERT: A 732 ILE cc_start: 0.8115 (mp) cc_final: 0.7879 (tp) outliers start: 33 outliers final: 26 residues processed: 291 average time/residue: 0.3174 time to fit residues: 141.9297 Evaluate side-chains 294 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 2.244 ------------------------------------------------------------------------------- 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 699 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 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 736 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 209 THR 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 437 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 43 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 211 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.213717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160636 restraints weight = 24526.576| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.08 r_work: 0.3551 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20006 Z= 0.119 Angle : 0.603 20.372 27120 Z= 0.298 Chirality : 0.039 0.388 3090 Planarity : 0.003 0.037 3358 Dihedral : 5.351 37.518 2796 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.51 % Allowed : 16.60 % Favored : 81.88 % 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: 0.34 (0.18), residues: 2384 helix: 1.14 (0.13), residues: 1440 sheet: -1.51 (0.67), residues: 68 loop : -1.13 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 785 HIS 0.003 0.001 HIS D 252 PHE 0.029 0.001 PHE C 751 TYR 0.022 0.001 TYR C 628 ARG 0.004 0.000 ARG A 746 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 1110) hydrogen bonds : angle 3.98282 ( 3168) covalent geometry : bond 0.00273 (20006) covalent geometry : angle 0.60348 (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 299 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 567 TYR cc_start: 0.6110 (t80) cc_final: 0.5498 (t80) REVERT: B 699 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8215 (mp) REVERT: B 761 MET cc_start: 0.8171 (mmm) cc_final: 0.7752 (mmm) REVERT: C 224 ARG cc_start: 0.7615 (ttt180) cc_final: 0.6809 (mmp80) REVERT: C 225 GLU cc_start: 0.8004 (mt-10) cc_final: 0.6632 (pm20) REVERT: C 271 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7869 (ttp80) REVERT: C 449 MET cc_start: 0.8169 (mtp) cc_final: 0.7857 (mtp) REVERT: C 669 PHE cc_start: 0.8744 (t80) cc_final: 0.8533 (t80) REVERT: D 182 ASP cc_start: 0.6812 (m-30) cc_final: 0.6510 (m-30) REVERT: D 447 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7645 (m90) REVERT: D 683 LEU cc_start: 0.6541 (pp) cc_final: 0.5915 (mt) REVERT: D 730 LYS cc_start: 0.8557 (tppt) cc_final: 0.7925 (ptpt) REVERT: D 736 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: A 224 ARG cc_start: 0.7617 (ttt180) cc_final: 0.6881 (mmp-170) REVERT: A 437 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8652 (tt) REVERT: A 628 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7541 (t80) REVERT: A 732 ILE cc_start: 0.8155 (mp) cc_final: 0.7908 (tp) outliers start: 32 outliers final: 23 residues processed: 282 average time/residue: 0.3241 time to fit residues: 141.3979 Evaluate side-chains 288 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 2.194 ------------------------------------------------------------------------------- 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 699 LEU Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 523 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 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 437 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 69 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 49 optimal weight: 0.0040 chunk 189 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 A 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.213594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.158037 restraints weight = 24590.385| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.98 r_work: 0.3566 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20006 Z= 0.123 Angle : 0.617 19.757 27120 Z= 0.302 Chirality : 0.039 0.189 3090 Planarity : 0.003 0.037 3358 Dihedral : 5.343 37.367 2796 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.42 % Allowed : 16.75 % Favored : 81.84 % 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: 0.29 (0.18), residues: 2384 helix: 1.12 (0.13), residues: 1438 sheet: -2.28 (0.62), residues: 78 loop : -1.09 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 785 HIS 0.003 0.001 HIS D 252 PHE 0.033 0.001 PHE D 172 TYR 0.021 0.001 TYR C 628 ARG 0.009 0.000 ARG C 779 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 1110) hydrogen bonds : angle 3.97299 ( 3168) covalent geometry : bond 0.00283 (20006) covalent geometry : angle 0.61730 (27120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13551.34 seconds wall clock time: 237 minutes 25.59 seconds (14245.59 seconds total)