Starting phenix.real_space_refine on Tue Oct 15 01:49:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvi_36675/10_2024/8jvi_36675.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvi_36675/10_2024/8jvi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvi_36675/10_2024/8jvi_36675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvi_36675/10_2024/8jvi_36675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvi_36675/10_2024/8jvi_36675.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jvi_36675/10_2024/8jvi_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-5477/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: 16.13, per 1000 atoms: 0.83 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: 5.18 Conformation dependent library (CDL) restraints added in 2.4 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: 2.18 Creating SS restraints... Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.141A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.571A pdb=" N ILE B 227 " --> pdb=" O MET B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.611A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 260 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.726A pdb=" N THR B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.403A pdb=" N MET B 449 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 removed outlier: 4.074A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 490 removed outlier: 3.679A pdb=" N TYR B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 534 removed outlier: 3.656A pdb=" N ASP B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 532 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 570 removed outlier: 3.862A pdb=" N TYR B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 586 removed outlier: 3.745A pdb=" N VAL B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 594 removed outlier: 4.119A pdb=" N ARG B 594 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 613 Processing helix chain 'B' and resid 613 through 634 Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.798A pdb=" N ILE B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 689 removed outlier: 3.617A pdb=" N SER B 687 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 725 removed outlier: 3.676A pdb=" N PHE B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 748 removed outlier: 3.712A pdb=" N LYS B 734 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 735 " --> pdb=" O HIS B 731 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'B' and resid 767 through 771 Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 168 through 176 removed outlier: 4.138A pdb=" N PHE C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.047A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 233 through 237 removed outlier: 4.100A pdb=" N ARG C 237 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.577A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.009A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.668A pdb=" N GLN C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.619A pdb=" N THR C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 335 through 356 removed outlier: 4.315A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 442 through 450 removed outlier: 3.640A pdb=" N ARG C 446 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU C 448 " --> pdb=" O ASN C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 removed outlier: 4.171A pdb=" N GLU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 490 Processing helix chain 'C' and resid 507 through 531 removed outlier: 3.633A pdb=" N ASP C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 534 No H-bonds generated for 'chain 'C' and resid 532 through 534' Processing helix chain 'C' and resid 546 through 570 removed outlier: 3.568A pdb=" N LEU C 551 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 590 removed outlier: 3.567A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.559A pdb=" N ARG C 594 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY C 595 " --> pdb=" O PHE C 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 591 through 595' Processing helix chain 'C' and resid 596 through 614 removed outlier: 3.981A pdb=" N TYR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 633 Processing helix chain 'C' and resid 665 through 679 Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.671A pdb=" N SER C 687 " --> pdb=" O GLU C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 748 removed outlier: 4.523A pdb=" N PHE C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 709 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C 710 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET C 718 " --> pdb=" O LEU C 714 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY C 723 " --> pdb=" O GLY C 719 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN C 724 " --> pdb=" O GLU C 720 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LYS C 727 " --> pdb=" O GLY C 723 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU C 728 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 747 " --> pdb=" O ASP C 743 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing helix chain 'C' and resid 767 through 771 Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 168 through 176 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.141A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.572A pdb=" N ILE D 227 " --> pdb=" O MET D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.611A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.726A pdb=" N THR D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 445 through 450 removed outlier: 4.403A pdb=" N MET D 449 " --> pdb=" O ASN D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 4.074A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 490 removed outlier: 3.679A pdb=" N TYR D 490 " --> pdb=" O THR D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 534 removed outlier: 3.656A pdb=" N ASP D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 532 " --> pdb=" O ASN D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 570 removed outlier: 3.863A pdb=" N TYR D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 586 removed outlier: 3.745A pdb=" N VAL D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 594 removed outlier: 4.120A pdb=" N ARG D 594 " --> pdb=" O TYR D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 613 Processing helix chain 'D' and resid 613 through 634 Processing helix chain 'D' and resid 665 through 679 removed outlier: 3.798A pdb=" N ILE D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 689 removed outlier: 3.617A pdb=" N SER D 687 " --> pdb=" O GLU D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 725 removed outlier: 3.675A pdb=" N PHE D 695 " --> pdb=" O TYR D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 748 removed outlier: 3.712A pdb=" N LYS D 734 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 735 " --> pdb=" O HIS D 731 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D 736 " --> pdb=" O ILE D 732 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 Processing helix chain 'D' and resid 767 through 771 Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 168 through 176 removed outlier: 4.138A pdb=" N PHE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.047A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.100A pdb=" N ARG A 237 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.577A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.009A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.668A pdb=" N GLN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 297 through 306 removed outlier: 3.619A pdb=" N THR A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 335 through 356 removed outlier: 4.316A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.639A pdb=" N ARG A 446 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 448 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 4.171A pdb=" N GLU A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 490 Processing helix chain 'A' and resid 507 through 531 removed outlier: 3.633A pdb=" N ASP A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.568A pdb=" N LEU A 551 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.567A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.559A pdb=" N ARG A 594 " --> pdb=" O TYR A 591 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY A 595 " --> pdb=" O PHE A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 595' Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.981A pdb=" N TYR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 633 Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 683 through 687 removed outlier: 3.672A pdb=" N SER A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 748 removed outlier: 4.546A pdb=" N PHE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 710 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A 724 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LYS A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'A' and resid 767 through 771 Processing sheet with id=AA1, first strand: chain 'B' and resid 405 through 410 removed outlier: 6.912A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.713A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 405 through 410 removed outlier: 6.912A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 410 removed outlier: 6.713A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 5.95 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 148 through 491 or resid 506 through 685 or (resid 686 thr \ ough 688 and (name N or name CA or name C or name O or name CB )) or resid 689 t \ hrough 788 or resid 1201)) selection = (chain 'B' and (resid 148 through 491 or resid 506 through 635 or resid 664 thro \ ugh 788 or resid 1201)) selection = (chain 'C' and (resid 148 through 491 or resid 506 through 685 or (resid 686 thr \ ough 688 and (name N or name CA or name C or name O or name CB )) or resid 689 t \ hrough 788 or resid 1201)) selection = (chain 'D' and (resid 148 through 491 or resid 506 through 635 or resid 664 thro \ ugh 788 or resid 1201)) } 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: 1.050 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: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.700 Find NCS groups from input model: 1.040 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.040 ------------------------------------------------------------------------------- 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= 0.701 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 *********************** 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 fitting. rotamer outliers: 19 poor density : 310 time to evaluate : 2.411 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: 0.3199 time to fit residues: 158.1653 Evaluate side-chains 272 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 2.163 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20006 Z= 0.323 Angle : 0.668 8.561 27120 Z= 0.341 Chirality : 0.041 0.145 3090 Planarity : 0.005 0.081 3358 Dihedral : 7.207 57.706 2808 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.28 % Allowed : 7.95 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2384 helix: 0.86 (0.13), residues: 1444 sheet: -3.61 (0.50), residues: 92 loop : -1.17 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 785 HIS 0.006 0.001 HIS B 326 PHE 0.022 0.002 PHE A 624 TYR 0.020 0.002 TYR B 628 ARG 0.004 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 288 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 225 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7139 (pm20) REVERT: C 482 MET cc_start: 0.6680 (mmp) cc_final: 0.6385 (mmp) REVERT: D 695 PHE cc_start: 0.7706 (t80) cc_final: 0.7384 (t80) REVERT: A 225 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7223 (pm20) REVERT: A 449 MET cc_start: 0.7934 (mtp) cc_final: 0.7603 (mtp) outliers start: 27 outliers final: 18 residues processed: 299 average time/residue: 0.3276 time to fit residues: 148.7357 Evaluate side-chains 285 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 267 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 527 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 338 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1713 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= 0.226 Angle : 0.597 10.051 27120 Z= 0.305 Chirality : 0.039 0.156 3090 Planarity : 0.004 0.061 3358 Dihedral : 6.099 40.435 2800 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.37 % Allowed : 11.02 % Favored : 87.61 % 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: -0.02 (0.18), residues: 2384 helix: 0.94 (0.14), residues: 1438 sheet: -3.01 (0.53), residues: 78 loop : -1.29 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 733 HIS 0.005 0.001 HIS B 326 PHE 0.022 0.001 PHE C 624 TYR 0.031 0.002 TYR D 628 ARG 0.009 0.000 ARG B 746 *********************** 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 308 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 279 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 683 LEU cc_start: 0.6429 (pp) cc_final: 0.5718 (mt) REVERT: C 225 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7073 (pm20) REVERT: D 447 HIS cc_start: 0.7028 (OUTLIER) cc_final: 0.6713 (m90) REVERT: D 695 PHE cc_start: 0.7721 (t80) cc_final: 0.7400 (t80) REVERT: A 224 ARG cc_start: 0.7384 (ttt180) cc_final: 0.7174 (mmp80) REVERT: A 225 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7118 (pm20) REVERT: A 449 MET cc_start: 0.7826 (mtp) cc_final: 0.7583 (mtp) outliers start: 29 outliers final: 21 residues processed: 293 average time/residue: 0.3360 time to fit residues: 150.3671 Evaluate side-chains 285 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 263 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 476 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 628 TYR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 0.3980 chunk 104 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 447 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20006 Z= 0.332 Angle : 0.643 10.253 27120 Z= 0.326 Chirality : 0.041 0.167 3090 Planarity : 0.004 0.043 3358 Dihedral : 5.881 40.890 2796 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.80 % Allowed : 12.39 % 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: -0.13 (0.18), residues: 2384 helix: 0.87 (0.13), residues: 1428 sheet: -3.40 (0.51), residues: 88 loop : -1.27 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 733 HIS 0.006 0.001 HIS B 326 PHE 0.024 0.002 PHE C 751 TYR 0.031 0.002 TYR D 628 ARG 0.005 0.000 ARG B 746 *********************** 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 315 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 277 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 225 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7113 (pm20) REVERT: C 347 ASP cc_start: 0.7932 (m-30) cc_final: 0.7632 (m-30) REVERT: C 379 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8394 (ttpt) REVERT: D 447 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6826 (m90) REVERT: D 736 GLN cc_start: 0.7912 (pm20) cc_final: 0.7670 (pm20) REVERT: A 224 ARG cc_start: 0.7471 (ttt180) cc_final: 0.7189 (mmp80) REVERT: A 225 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7132 (pm20) outliers start: 38 outliers final: 24 residues processed: 296 average time/residue: 0.3191 time to fit residues: 146.1190 Evaluate side-chains 285 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 259 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain 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 379 LYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 527 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 160 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 302 ASN C 736 GLN D 387 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20006 Z= 0.204 Angle : 0.585 10.650 27120 Z= 0.297 Chirality : 0.039 0.217 3090 Planarity : 0.004 0.041 3358 Dihedral : 5.736 40.463 2796 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.80 % Allowed : 13.91 % Favored : 84.30 % 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: 0.03 (0.18), residues: 2384 helix: 0.97 (0.13), residues: 1432 sheet: -2.60 (0.58), residues: 78 loop : -1.27 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 733 HIS 0.004 0.001 HIS C 252 PHE 0.020 0.001 PHE C 624 TYR 0.020 0.001 TYR C 702 ARG 0.004 0.000 ARG B 746 *********************** 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 323 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 285 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 447 HIS cc_start: 0.7111 (OUTLIER) cc_final: 0.6901 (m90) REVERT: B 736 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: C 225 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7093 (pm20) REVERT: D 447 HIS cc_start: 0.7090 (OUTLIER) cc_final: 0.6811 (m90) REVERT: D 695 PHE cc_start: 0.7772 (t80) cc_final: 0.7543 (t80) REVERT: D 736 GLN cc_start: 0.7774 (pm20) cc_final: 0.7467 (mp10) REVERT: A 224 ARG cc_start: 0.7410 (ttt180) cc_final: 0.7144 (mmp80) REVERT: A 225 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7034 (pm20) outliers start: 38 outliers final: 24 residues processed: 302 average time/residue: 0.3261 time to fit residues: 152.0477 Evaluate side-chains 296 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 2.329 ------------------------------------------------------------------------------- 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 447 HIS Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 736 GLN 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 247 GLU Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 767 SER 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 357 PHE 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 78 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN D 387 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20006 Z= 0.225 Angle : 0.603 11.303 27120 Z= 0.304 Chirality : 0.039 0.195 3090 Planarity : 0.004 0.040 3358 Dihedral : 5.656 39.683 2796 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.08 % Allowed : 14.76 % Favored : 83.16 % 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: 0.01 (0.18), residues: 2384 helix: 0.95 (0.13), residues: 1434 sheet: -3.16 (0.53), residues: 88 loop : -1.19 (0.23), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 733 HIS 0.005 0.001 HIS C 252 PHE 0.019 0.001 PHE A 624 TYR 0.023 0.001 TYR D 628 ARG 0.007 0.000 ARG B 206 *********************** 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 319 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 275 time to evaluate : 2.181 Fit side-chains revert: symmetry clash REVERT: B 447 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6861 (m90) REVERT: B 730 LYS cc_start: 0.8345 (tppt) cc_final: 0.7971 (ptpt) REVERT: B 736 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: C 225 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7132 (pm20) REVERT: D 447 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6887 (m90) REVERT: D 730 LYS cc_start: 0.8370 (tppt) cc_final: 0.8016 (ptpt) REVERT: D 736 GLN cc_start: 0.7766 (pm20) cc_final: 0.7464 (mp10) REVERT: A 224 ARG cc_start: 0.7426 (ttt180) cc_final: 0.7147 (mmp80) REVERT: A 225 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7058 (pm20) REVERT: A 437 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8521 (tt) outliers start: 44 outliers final: 35 residues processed: 297 average time/residue: 0.3238 time to fit residues: 148.1388 Evaluate side-chains 304 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 265 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 HIS Chi-restraints excluded: chain B residue 470 SER 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 257 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 357 PHE 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 D residue 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 767 SER 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 357 PHE 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 710 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 0.3980 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 528 ASN D 550 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2459 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= 0.161 Angle : 0.578 11.424 27120 Z= 0.290 Chirality : 0.038 0.251 3090 Planarity : 0.003 0.040 3358 Dihedral : 5.549 38.529 2796 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 1.94 % Allowed : 16.13 % Favored : 81.93 % 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: 0.18 (0.18), residues: 2384 helix: 1.06 (0.13), residues: 1438 sheet: -2.06 (0.61), residues: 68 loop : -1.24 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 733 HIS 0.008 0.001 HIS B 252 PHE 0.029 0.001 PHE A 751 TYR 0.024 0.001 TYR B 628 ARG 0.003 0.000 ARG D 206 *********************** 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 319 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 278 time to evaluate : 2.422 Fit side-chains REVERT: B 447 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6759 (m90) REVERT: B 730 LYS cc_start: 0.8371 (tppt) cc_final: 0.8013 (ptpt) REVERT: B 736 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: C 224 ARG cc_start: 0.7389 (ttt180) cc_final: 0.7127 (mmp80) REVERT: C 225 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7126 (pm20) REVERT: D 213 LEU cc_start: 0.7832 (mp) cc_final: 0.6936 (mp) REVERT: D 447 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6928 (m90) REVERT: D 695 PHE cc_start: 0.7787 (t80) cc_final: 0.7574 (t80) REVERT: D 730 LYS cc_start: 0.8343 (tppt) cc_final: 0.8037 (ptpt) REVERT: D 736 GLN cc_start: 0.7760 (pm20) cc_final: 0.7468 (mp10) REVERT: A 225 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7081 (pm20) REVERT: A 437 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8451 (tt) outliers start: 41 outliers final: 26 residues processed: 301 average time/residue: 0.3317 time to fit residues: 153.1371 Evaluate side-chains 300 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 270 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 HIS Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 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 551 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 0.0020 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- 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 252 HIS ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20006 Z= 0.200 Angle : 0.591 11.735 27120 Z= 0.297 Chirality : 0.040 0.368 3090 Planarity : 0.004 0.039 3358 Dihedral : 5.496 38.004 2796 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.99 % Allowed : 16.60 % Favored : 81.41 % 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: 0.19 (0.18), residues: 2384 helix: 1.05 (0.13), residues: 1440 sheet: -2.81 (0.57), residues: 88 loop : -1.07 (0.24), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 785 HIS 0.004 0.001 HIS D 252 PHE 0.027 0.001 PHE D 172 TYR 0.023 0.001 TYR B 628 ARG 0.005 0.000 ARG C 779 *********************** 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 fitting. rotamer outliers: 42 poor density : 275 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: B 447 HIS cc_start: 0.7074 (OUTLIER) cc_final: 0.6805 (m90) REVERT: B 694 VAL cc_start: 0.7390 (m) cc_final: 0.7172 (m) REVERT: B 730 LYS cc_start: 0.8374 (tppt) cc_final: 0.8021 (ptpt) REVERT: B 736 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: C 224 ARG cc_start: 0.7391 (ttt180) cc_final: 0.7111 (mmp80) REVERT: C 225 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7131 (pm20) REVERT: D 447 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6915 (m90) REVERT: D 683 LEU cc_start: 0.6376 (pp) cc_final: 0.5713 (mt) REVERT: D 736 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: A 437 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8455 (tt) outliers start: 42 outliers final: 32 residues processed: 296 average time/residue: 0.2347 time to fit residues: 107.8373 Evaluate side-chains 299 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 262 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 HIS Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 578 MET 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 257 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 129 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 214 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 550 GLN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20006 Z= 0.177 Angle : 0.595 11.950 27120 Z= 0.296 Chirality : 0.039 0.189 3090 Planarity : 0.003 0.039 3358 Dihedral : 5.463 37.455 2796 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.75 % Allowed : 17.08 % Favored : 81.17 % 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: 1.09 (0.13), residues: 1440 sheet: -1.73 (0.65), residues: 68 loop : -1.19 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 733 HIS 0.004 0.001 HIS A 252 PHE 0.030 0.001 PHE C 751 TYR 0.031 0.001 TYR B 628 ARG 0.003 0.000 ARG C 271 *********************** 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 310 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 273 time to evaluate : 2.297 Fit side-chains revert: symmetry clash REVERT: B 447 HIS cc_start: 0.7131 (OUTLIER) cc_final: 0.6856 (m90) REVERT: B 694 VAL cc_start: 0.7445 (m) cc_final: 0.7223 (m) REVERT: B 730 LYS cc_start: 0.8373 (tppt) cc_final: 0.8025 (ptpt) REVERT: B 736 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7409 (mp10) REVERT: C 224 ARG cc_start: 0.7383 (ttt180) cc_final: 0.7110 (mmp80) REVERT: C 225 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7140 (pm20) REVERT: C 375 MET cc_start: 0.7741 (mtm) cc_final: 0.7534 (mtp) REVERT: D 447 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6882 (m90) REVERT: D 683 LEU cc_start: 0.6449 (pp) cc_final: 0.5779 (mt) REVERT: D 736 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: A 225 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6740 (pm20) REVERT: A 437 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8454 (tt) outliers start: 37 outliers final: 30 residues processed: 292 average time/residue: 0.2809 time to fit residues: 127.9917 Evaluate side-chains 298 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 263 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 HIS Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 470 SER 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 D residue 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 767 SER 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 437 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 239 optimal weight: 0.7980 chunk 220 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20006 Z= 0.185 Angle : 0.614 19.825 27120 Z= 0.303 Chirality : 0.039 0.201 3090 Planarity : 0.003 0.038 3358 Dihedral : 5.433 37.190 2796 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.75 % Allowed : 17.60 % Favored : 80.65 % 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: 1.11 (0.13), residues: 1438 sheet: -2.06 (0.62), residues: 78 loop : -1.13 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 785 HIS 0.003 0.001 HIS C 252 PHE 0.030 0.001 PHE D 172 TYR 0.036 0.001 TYR C 628 ARG 0.003 0.000 ARG C 779 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 267 time to evaluate : 2.282 Fit side-chains revert: symmetry clash REVERT: B 447 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6794 (m90) REVERT: B 567 TYR cc_start: 0.6189 (t80) cc_final: 0.5668 (t80) REVERT: B 694 VAL cc_start: 0.7451 (m) cc_final: 0.7221 (m) REVERT: B 730 LYS cc_start: 0.8359 (tppt) cc_final: 0.8017 (ptpt) REVERT: B 736 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: C 224 ARG cc_start: 0.7313 (ttt180) cc_final: 0.7090 (mmp80) REVERT: C 225 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7165 (pm20) REVERT: D 447 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6881 (m90) REVERT: D 683 LEU cc_start: 0.6475 (pp) cc_final: 0.5787 (mt) REVERT: D 736 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: A 225 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6787 (pm20) REVERT: A 375 MET cc_start: 0.7714 (mtm) cc_final: 0.7513 (mtp) REVERT: A 437 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8461 (tt) outliers start: 37 outliers final: 31 residues processed: 287 average time/residue: 0.3260 time to fit residues: 143.5857 Evaluate side-chains 293 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 257 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 447 HIS Chi-restraints excluded: chain B residue 578 MET 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 257 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 470 SER 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 D residue 247 GLU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9990 chunk 202 optimal weight: 0.0070 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.214004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158671 restraints weight = 24436.487| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.96 r_work: 0.3575 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2879 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= 0.162 Angle : 0.599 17.398 27120 Z= 0.297 Chirality : 0.038 0.188 3090 Planarity : 0.003 0.038 3358 Dihedral : 5.377 36.342 2796 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.70 % Allowed : 17.64 % Favored : 80.65 % 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: 0.36 (0.18), residues: 2384 helix: 1.20 (0.13), residues: 1438 sheet: -1.70 (0.66), residues: 68 loop : -1.19 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 733 HIS 0.002 0.000 HIS C 326 PHE 0.039 0.001 PHE D 172 TYR 0.033 0.001 TYR C 628 ARG 0.003 0.000 ARG C 779 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4370.68 seconds wall clock time: 161 minutes 56.02 seconds (9716.02 seconds total)