Starting phenix.real_space_refine on Sat May 24 23:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwb_35052/05_2025/8hwb_35052.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwb_35052/05_2025/8hwb_35052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwb_35052/05_2025/8hwb_35052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwb_35052/05_2025/8hwb_35052.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwb_35052/05_2025/8hwb_35052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwb_35052/05_2025/8hwb_35052.cif" } resolution = 3.9 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= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 Mg 4 5.21 5 S 144 5.16 5 C 16283 2.51 5 N 4370 2.21 5 O 4916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "B" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "D" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "E" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "F" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "K" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1876 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.21, per 1000 atoms: 0.59 Number of scatterers: 25740 At special positions: 0 Unit cell: (130.305, 127.02, 175.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 23 15.00 Mg 4 11.99 O 4916 8.00 N 4370 7.00 C 16283 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: 5.83 Conformation dependent library (CDL) restraints added in 3.0 seconds 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 45 sheets defined 42.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 384 removed outlier: 4.405A pdb=" N SER A 381 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU A 382 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 528 through 532 removed outlier: 4.126A pdb=" N ILE A 531 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 578 removed outlier: 3.659A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.106A pdb=" N GLY A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.515A pdb=" N PHE A 668 " --> pdb=" O TYR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.825A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 398 Processing helix chain 'B' and resid 429 through 435 removed outlier: 4.082A pdb=" N LYS B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.715A pdb=" N LYS B 450 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.633A pdb=" N ILE B 531 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.727A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 660 removed outlier: 3.955A pdb=" N GLY B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.568A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 removed outlier: 3.592A pdb=" N TYR B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 4.048A pdb=" N ASN C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.703A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 398 Processing helix chain 'C' and resid 429 through 435 removed outlier: 4.377A pdb=" N LYS C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 528 through 532 removed outlier: 3.989A pdb=" N ILE C 531 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 removed outlier: 3.513A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.799A pdb=" N ARG C 619 " --> pdb=" O ASN C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 660 removed outlier: 4.403A pdb=" N GLY C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.538A pdb=" N PHE C 668 " --> pdb=" O TYR C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 692 removed outlier: 3.826A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 689 through 692' Processing helix chain 'C' and resid 693 through 699 removed outlier: 3.654A pdb=" N TYR C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.714A pdb=" N GLN D 25 " --> pdb=" O SER D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 removed outlier: 3.560A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 104 removed outlier: 3.504A pdb=" N GLN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 4.441A pdb=" N ASN D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 removed outlier: 4.450A pdb=" N ARG D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 203 through 208 removed outlier: 4.086A pdb=" N LEU D 208 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.763A pdb=" N CYS D 314 " --> pdb=" O PRO D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.578A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.636A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 398 removed outlier: 3.514A pdb=" N ASP D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 435 removed outlier: 4.159A pdb=" N LYS D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 528 through 532 removed outlier: 3.866A pdb=" N ILE D 531 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 576 Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.621A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 654 through 659 Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 689 through 692 removed outlier: 4.020A pdb=" N GLU D 692 " --> pdb=" O THR D 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 693 through 700 removed outlier: 3.816A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.732A pdb=" N ARG E 24 " --> pdb=" O PRO E 20 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 20 through 25' Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 78 through 105 Processing helix chain 'E' and resid 108 through 119 removed outlier: 4.279A pdb=" N ASN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 150 through 160 Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 203 through 208 removed outlier: 3.830A pdb=" N LEU E 208 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 removed outlier: 3.714A pdb=" N LEU E 230 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 254 removed outlier: 3.561A pdb=" N ILE E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE E 254 " --> pdb=" O VAL E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.725A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.942A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 398 removed outlier: 3.513A pdb=" N ARG E 389 " --> pdb=" O CYS E 385 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 435 removed outlier: 4.078A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.665A pdb=" N LYS E 450 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 475 through 488 removed outlier: 3.516A pdb=" N ARG E 479 " --> pdb=" O ASN E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 528 through 533 removed outlier: 4.323A pdb=" N ILE E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 546 removed outlier: 3.571A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 removed outlier: 3.503A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 642 Processing helix chain 'E' and resid 654 through 659 Processing helix chain 'E' and resid 664 through 680 removed outlier: 3.538A pdb=" N PHE E 668 " --> pdb=" O TYR E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 692 removed outlier: 4.008A pdb=" N GLU E 692 " --> pdb=" O THR E 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 689 through 692' Processing helix chain 'E' and resid 693 through 698 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.841A pdb=" N ASN F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.850A pdb=" N SER F 380 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 376 through 381' Processing helix chain 'F' and resid 385 through 398 removed outlier: 3.516A pdb=" N ASP F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.772A pdb=" N ASP F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 removed outlier: 3.953A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 474 No H-bonds generated for 'chain 'F' and resid 472 through 474' Processing helix chain 'F' and resid 475 through 488 removed outlier: 3.508A pdb=" N ARG F 479 " --> pdb=" O ASN F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 528 through 532 removed outlier: 3.917A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.731A pdb=" N ILE F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 641 Processing helix chain 'F' and resid 654 through 659 Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 689 through 692 Processing helix chain 'F' and resid 693 through 699 removed outlier: 3.514A pdb=" N ALA F 697 " --> pdb=" O ILE F 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 removed outlier: 3.505A pdb=" N GLY K 7 " --> pdb=" O ALA K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 26 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 78 through 104 removed outlier: 3.508A pdb=" N ASP K 88 " --> pdb=" O THR K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 119 removed outlier: 3.511A pdb=" N VAL K 112 " --> pdb=" O ILE K 108 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN K 119 " --> pdb=" O SER K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 150 Processing helix chain 'K' and resid 150 through 160 Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 203 through 208 removed outlier: 4.208A pdb=" N LEU K 208 " --> pdb=" O GLU K 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 415 removed outlier: 3.657A pdb=" N GLY A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.511A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 582 through 583 removed outlier: 3.778A pdb=" N ASN A 594 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA7, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.961A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.899A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N SER B 556 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'B' and resid 629 through 631 Processing sheet with id=AB2, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AB3, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.916A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 419 " --> pdb=" O TYR C 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 525 through 526 removed outlier: 6.685A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB6, first strand: chain 'C' and resid 629 through 631 removed outlier: 6.750A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 32 through 35 removed outlier: 4.744A pdb=" N PHE D 12 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 64 through 73 removed outlier: 11.026A pdb=" N VAL D 65 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP D 139 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE D 67 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER D 132 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N HIS D 134 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR D 123 " --> pdb=" O HIS D 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 64 through 73 removed outlier: 11.026A pdb=" N VAL D 65 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP D 139 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE D 67 " --> pdb=" O PHE D 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 294 through 299 removed outlier: 3.694A pdb=" N LYS D 317 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC3, first strand: chain 'D' and resid 412 through 415 removed outlier: 4.002A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 419 " --> pdb=" O TYR D 428 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 525 through 526 removed outlier: 6.856A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC6, first strand: chain 'D' and resid 629 through 631 Processing sheet with id=AC7, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AC8, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.557A pdb=" N GLU E 33 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE E 12 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 64 through 73 removed outlier: 10.981A pdb=" N VAL E 65 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ASP E 139 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE E 67 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 64 through 73 removed outlier: 10.981A pdb=" N VAL E 65 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ASP E 139 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE E 67 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 124 through 125 removed outlier: 3.572A pdb=" N LYS E 124 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 294 through 295 Processing sheet with id=AD4, first strand: chain 'E' and resid 294 through 295 Processing sheet with id=AD5, first strand: chain 'E' and resid 339 through 341 removed outlier: 3.520A pdb=" N LYS E 356 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 351 " --> pdb=" O SER E 354 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.644A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 419 " --> pdb=" O TYR E 428 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 525 through 527 removed outlier: 6.752A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 604 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AD9, first strand: chain 'E' and resid 629 through 631 removed outlier: 7.001A pdb=" N HIS E 629 " --> pdb=" O LYS E 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 340 through 341 removed outlier: 3.578A pdb=" N LEU F 340 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 412 through 415 Processing sheet with id=AE3, first strand: chain 'F' and resid 525 through 527 removed outlier: 3.596A pdb=" N PHE F 554 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 628 through 631 removed outlier: 6.437A pdb=" N HIS F 629 " --> pdb=" O LYS F 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'K' and resid 33 through 35 removed outlier: 3.587A pdb=" N GLU K 33 " --> pdb=" O VAL K 13 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL K 13 " --> pdb=" O GLU K 33 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE K 12 " --> pdb=" O SER K 55 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 64 through 68 removed outlier: 7.099A pdb=" N THR K 140 " --> pdb=" O ILE K 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 64 through 68 removed outlier: 7.099A pdb=" N THR K 140 " --> pdb=" O ILE K 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 71 through 73 removed outlier: 3.544A pdb=" N PHE K 133 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 124 through 125 removed outlier: 3.517A pdb=" N LYS K 124 " --> pdb=" O VAL K 196 " (cutoff:3.500A) 871 hydrogen bonds defined for protein. 2400 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: 9.87 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6639 1.33 - 1.45: 4767 1.45 - 1.58: 14628 1.58 - 1.70: 40 1.70 - 1.82: 207 Bond restraints: 26281 Sorted by residual: bond pdb=" C GLU D 237 " pdb=" N PRO D 238 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.26e-02 6.30e+03 6.07e+00 bond pdb=" N LEU A 577 " pdb=" CA LEU A 577 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.35e-02 5.49e+03 6.03e+00 bond pdb=" N LEU E 321 " pdb=" CA LEU E 321 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" N SER K 160 " pdb=" CA SER K 160 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.50e+00 bond pdb=" N LEU C 700 " pdb=" CA LEU C 700 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.45e+00 ... (remaining 26276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 35150 2.38 - 4.76: 394 4.76 - 7.14: 40 7.14 - 9.51: 6 9.51 - 11.89: 3 Bond angle restraints: 35593 Sorted by residual: angle pdb=" CA PRO E 29 " pdb=" N PRO E 29 " pdb=" CD PRO E 29 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" N LEU F 700 " pdb=" CA LEU F 700 " pdb=" C LEU F 700 " ideal model delta sigma weight residual 113.50 108.43 5.07 1.23e+00 6.61e-01 1.70e+01 angle pdb=" CA GLU D 382 " pdb=" CB GLU D 382 " pdb=" CG GLU D 382 " ideal model delta sigma weight residual 114.10 122.19 -8.09 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N PHE B 698 " pdb=" CA PHE B 698 " pdb=" C PHE B 698 " ideal model delta sigma weight residual 112.23 107.20 5.03 1.26e+00 6.30e-01 1.60e+01 angle pdb=" N MET F 458 " pdb=" CA MET F 458 " pdb=" CB MET F 458 " ideal model delta sigma weight residual 110.01 115.80 -5.79 1.45e+00 4.76e-01 1.59e+01 ... (remaining 35588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 15412 31.41 - 62.82: 670 62.82 - 94.23: 44 94.23 - 125.64: 1 125.64 - 157.05: 2 Dihedral angle restraints: 16129 sinusoidal: 6838 harmonic: 9291 Sorted by residual: dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 62.95 157.05 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DT S 2 " pdb=" C3' DT S 2 " pdb=" O3' DT S 2 " pdb=" P DT S 3 " ideal model delta sinusoidal sigma weight residual 220.00 67.88 152.12 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" CA ASP A 335 " pdb=" CB ASP A 335 " pdb=" CG ASP A 335 " pdb=" OD1 ASP A 335 " ideal model delta sinusoidal sigma weight residual -30.00 -90.06 60.06 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 16126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2683 0.038 - 0.076: 949 0.076 - 0.113: 313 0.113 - 0.151: 34 0.151 - 0.189: 5 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA LEU A 700 " pdb=" N LEU A 700 " pdb=" C LEU A 700 " pdb=" CB LEU A 700 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB ILE A 681 " pdb=" CA ILE A 681 " pdb=" CG1 ILE A 681 " pdb=" CG2 ILE A 681 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CA LEU A 577 " pdb=" N LEU A 577 " pdb=" C LEU A 577 " pdb=" CB LEU A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.27e-01 ... (remaining 3981 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 28 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO E 29 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 455 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.49e+01 pdb=" N PRO F 456 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO F 456 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 456 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 300 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ASN E 300 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN E 300 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY E 301 " -0.012 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 191 2.50 - 3.10: 18496 3.10 - 3.70: 38565 3.70 - 4.30: 52984 4.30 - 4.90: 88127 Nonbonded interactions: 198363 Sorted by model distance: nonbonded pdb=" O3A ATP D1001 " pdb="MG MG D1002 " model vdw 1.900 2.170 nonbonded pdb=" O2B ATP C1001 " pdb="MG MG C1002 " model vdw 1.937 2.170 nonbonded pdb=" O3G ATP C1001 " pdb="MG MG C1002 " model vdw 1.971 2.170 nonbonded pdb=" O2B ATP B1001 " pdb="MG MG B1002 " model vdw 1.991 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.013 2.170 ... (remaining 198358 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 323 through 701) selection = (chain 'B' and resid 323 through 701) selection = (chain 'C' and resid 323 through 701) selection = chain 'F' } ncs_group { reference = (chain 'D' and resid 1 through 700) selection = (chain 'E' and resid 1 through 700) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 56.920 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.003 0.084 26281 Z= 0.154 Angle : 0.633 11.893 35593 Z= 0.358 Chirality : 0.042 0.189 3984 Planarity : 0.004 0.108 4537 Dihedral : 16.504 157.050 10087 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 0.59 % Allowed : 18.73 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.13 (0.15), residues: 3133 helix: 0.54 (0.17), residues: 1040 sheet: -1.30 (0.25), residues: 452 loop : -1.44 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 675 HIS 0.014 0.001 HIS F 629 PHE 0.015 0.001 PHE E 240 TYR 0.019 0.001 TYR F 645 ARG 0.004 0.000 ARG D 159 Details of bonding type rmsd hydrogen bonds : bond 0.22460 ( 852) hydrogen bonds : angle 7.10244 ( 2400) covalent geometry : bond 0.00305 (26281) covalent geometry : angle 0.63344 (35593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.7815 (mmm) cc_final: 0.7591 (tpp) REVERT: A 593 ASN cc_start: 0.8654 (m-40) cc_final: 0.8290 (t0) REVERT: A 618 MET cc_start: 0.7102 (ptp) cc_final: 0.6864 (pmm) REVERT: D 1 MET cc_start: 0.3721 (ttt) cc_final: 0.3517 (ttt) REVERT: E 116 MET cc_start: 0.7572 (ptp) cc_final: 0.7011 (ppp) REVERT: E 223 LEU cc_start: 0.8394 (mm) cc_final: 0.8129 (tp) REVERT: E 455 SER cc_start: 0.7647 (OUTLIER) cc_final: 0.7308 (t) outliers start: 17 outliers final: 5 residues processed: 240 average time/residue: 0.3501 time to fit residues: 136.4906 Evaluate side-chains 216 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 498 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.6980 chunk 235 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 125 optimal weight: 7.9990 chunk 243 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 0.0970 chunk 181 optimal weight: 0.0670 chunk 282 optimal weight: 9.9990 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 ASN E 573 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 629 HIS F 641 ASN ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.104496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075597 restraints weight = 71402.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077674 restraints weight = 41003.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079039 restraints weight = 28632.965| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26281 Z= 0.114 Angle : 0.547 9.717 35593 Z= 0.284 Chirality : 0.042 0.170 3984 Planarity : 0.004 0.075 4537 Dihedral : 10.096 156.864 3679 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 1.53 % Allowed : 17.13 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.00 (0.15), residues: 3133 helix: 0.65 (0.16), residues: 1061 sheet: -1.19 (0.24), residues: 457 loop : -1.40 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 350 HIS 0.009 0.001 HIS F 548 PHE 0.017 0.001 PHE K 100 TYR 0.020 0.001 TYR E 82 ARG 0.005 0.000 ARG F 389 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 852) hydrogen bonds : angle 5.00227 ( 2400) covalent geometry : bond 0.00252 (26281) covalent geometry : angle 0.54707 (35593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.6204 (t0) cc_final: 0.5978 (t0) REVERT: A 593 ASN cc_start: 0.8722 (m-40) cc_final: 0.8261 (t0) REVERT: A 618 MET cc_start: 0.7323 (ptp) cc_final: 0.6864 (pmm) REVERT: A 656 ASP cc_start: 0.8832 (p0) cc_final: 0.8457 (t0) REVERT: C 343 GLU cc_start: 0.7807 (mp0) cc_final: 0.7477 (mp0) REVERT: D 62 TYR cc_start: 0.6899 (m-80) cc_final: 0.6674 (m-80) REVERT: D 144 MET cc_start: 0.8683 (tpt) cc_final: 0.8480 (tpt) REVERT: D 150 MET cc_start: 0.7901 (mmm) cc_final: 0.7546 (mmm) REVERT: D 377 LYS cc_start: 0.8606 (tptt) cc_final: 0.8403 (tptt) REVERT: D 684 MET cc_start: 0.8591 (ttp) cc_final: 0.8294 (ttp) REVERT: E 223 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8179 (tp) REVERT: E 455 SER cc_start: 0.6587 (OUTLIER) cc_final: 0.5420 (t) REVERT: E 618 MET cc_start: 0.7793 (mtm) cc_final: 0.7366 (mtm) REVERT: K 1 MET cc_start: 0.2757 (tpp) cc_final: 0.1798 (tpp) outliers start: 44 outliers final: 24 residues processed: 266 average time/residue: 0.3266 time to fit residues: 144.8190 Evaluate side-chains 228 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 548 HIS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain K residue 135 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 308 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 303 optimal weight: 0.8980 chunk 169 optimal weight: 0.0770 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 ASN E 546 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.073358 restraints weight = 72264.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075410 restraints weight = 41649.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076735 restraints weight = 29193.229| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26281 Z= 0.152 Angle : 0.549 8.992 35593 Z= 0.284 Chirality : 0.042 0.162 3984 Planarity : 0.004 0.068 4537 Dihedral : 9.815 156.864 3674 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 2.71 % Allowed : 16.72 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.92 (0.15), residues: 3133 helix: 0.74 (0.16), residues: 1081 sheet: -1.23 (0.24), residues: 472 loop : -1.36 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 350 HIS 0.015 0.001 HIS F 548 PHE 0.013 0.001 PHE K 100 TYR 0.018 0.001 TYR A 482 ARG 0.004 0.000 ARG F 389 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 852) hydrogen bonds : angle 4.80723 ( 2400) covalent geometry : bond 0.00351 (26281) covalent geometry : angle 0.54947 (35593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 210 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8349 (mmm) cc_final: 0.8132 (mmm) REVERT: A 534 ASP cc_start: 0.6478 (t70) cc_final: 0.6187 (t0) REVERT: A 593 ASN cc_start: 0.8794 (m-40) cc_final: 0.8385 (t0) REVERT: A 656 ASP cc_start: 0.8882 (p0) cc_final: 0.8516 (t0) REVERT: A 684 MET cc_start: 0.5634 (tpt) cc_final: 0.5358 (tpt) REVERT: B 575 LYS cc_start: 0.8637 (mttm) cc_final: 0.8433 (mmtm) REVERT: C 340 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8667 (mt) REVERT: C 343 GLU cc_start: 0.7868 (mp0) cc_final: 0.7550 (mp0) REVERT: C 450 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8360 (mttt) REVERT: D 62 TYR cc_start: 0.6907 (m-80) cc_final: 0.6673 (m-80) REVERT: D 150 MET cc_start: 0.7952 (mmm) cc_final: 0.7623 (mmm) REVERT: D 322 ASP cc_start: 0.7993 (p0) cc_final: 0.7677 (p0) REVERT: D 377 LYS cc_start: 0.8696 (tptt) cc_final: 0.8377 (tptm) REVERT: E 223 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8286 (tp) REVERT: E 618 MET cc_start: 0.7912 (mtm) cc_final: 0.7549 (mtm) outliers start: 78 outliers final: 50 residues processed: 265 average time/residue: 0.3130 time to fit residues: 140.3528 Evaluate side-chains 242 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 72 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 310 optimal weight: 0.0270 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 296 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 270 optimal weight: 8.9990 chunk 274 optimal weight: 10.0000 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 597 HIS ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.102549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.073679 restraints weight = 72131.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.075755 restraints weight = 41589.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077113 restraints weight = 29128.162| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26281 Z= 0.124 Angle : 0.524 9.150 35593 Z= 0.270 Chirality : 0.042 0.163 3984 Planarity : 0.004 0.067 4537 Dihedral : 9.552 156.257 3673 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 2.64 % Allowed : 17.38 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.78 (0.15), residues: 3133 helix: 0.91 (0.16), residues: 1064 sheet: -1.18 (0.24), residues: 474 loop : -1.30 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 350 HIS 0.004 0.001 HIS F 548 PHE 0.011 0.001 PHE D 100 TYR 0.016 0.001 TYR A 482 ARG 0.005 0.000 ARG F 389 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 852) hydrogen bonds : angle 4.57784 ( 2400) covalent geometry : bond 0.00288 (26281) covalent geometry : angle 0.52380 (35593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 217 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8383 (mmm) cc_final: 0.8162 (mmm) REVERT: A 534 ASP cc_start: 0.6754 (t70) cc_final: 0.6425 (t0) REVERT: A 593 ASN cc_start: 0.8803 (m-40) cc_final: 0.8268 (t0) REVERT: A 618 MET cc_start: 0.7276 (ptp) cc_final: 0.7031 (pmm) REVERT: A 656 ASP cc_start: 0.8880 (p0) cc_final: 0.8548 (t0) REVERT: C 340 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8708 (mt) REVERT: D 62 TYR cc_start: 0.6908 (m-80) cc_final: 0.6693 (m-80) REVERT: D 110 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8224 (tp30) REVERT: D 150 MET cc_start: 0.8061 (mmm) cc_final: 0.7608 (mmm) REVERT: D 399 MET cc_start: 0.8431 (mtt) cc_final: 0.8216 (mtt) REVERT: E 116 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7435 (ppp) REVERT: E 223 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8287 (tp) REVERT: E 300 ASN cc_start: 0.8326 (t0) cc_final: 0.8039 (t0) REVERT: E 618 MET cc_start: 0.7926 (mtm) cc_final: 0.7496 (mtm) outliers start: 76 outliers final: 47 residues processed: 272 average time/residue: 0.3146 time to fit residues: 143.1649 Evaluate side-chains 244 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain K residue 135 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 157 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 281 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 292 optimal weight: 4.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN F 548 HIS ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.072031 restraints weight = 72154.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.074050 restraints weight = 42054.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075366 restraints weight = 29671.217| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26281 Z= 0.162 Angle : 0.557 9.998 35593 Z= 0.286 Chirality : 0.042 0.177 3984 Planarity : 0.004 0.064 4537 Dihedral : 9.525 156.551 3673 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 2.98 % Allowed : 17.76 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.77 (0.15), residues: 3133 helix: 0.94 (0.16), residues: 1075 sheet: -1.18 (0.24), residues: 478 loop : -1.33 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 350 HIS 0.012 0.001 HIS F 548 PHE 0.015 0.001 PHE F 543 TYR 0.019 0.001 TYR A 482 ARG 0.006 0.000 ARG K 24 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 852) hydrogen bonds : angle 4.60833 ( 2400) covalent geometry : bond 0.00376 (26281) covalent geometry : angle 0.55670 (35593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 199 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8507 (mmm) cc_final: 0.8273 (mmm) REVERT: A 583 ILE cc_start: 0.6339 (OUTLIER) cc_final: 0.6035 (tp) REVERT: A 593 ASN cc_start: 0.8846 (m-40) cc_final: 0.8313 (t0) REVERT: A 656 ASP cc_start: 0.8887 (p0) cc_final: 0.8586 (t0) REVERT: C 340 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8837 (mt) REVERT: D 62 TYR cc_start: 0.6938 (m-80) cc_final: 0.6718 (m-80) REVERT: D 110 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8242 (tp30) REVERT: D 150 MET cc_start: 0.7942 (mmm) cc_final: 0.7510 (mmm) REVERT: E 116 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7366 (ppp) REVERT: E 223 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8312 (tp) REVERT: E 618 MET cc_start: 0.8023 (mtm) cc_final: 0.7584 (mtm) outliers start: 86 outliers final: 60 residues processed: 263 average time/residue: 0.3193 time to fit residues: 141.7640 Evaluate side-chains 250 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 548 HIS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 131 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN F 347 HIS ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 573 ASN K 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073307 restraints weight = 71816.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075364 restraints weight = 41504.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076679 restraints weight = 29172.989| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26281 Z= 0.107 Angle : 0.530 9.868 35593 Z= 0.270 Chirality : 0.042 0.179 3984 Planarity : 0.004 0.063 4537 Dihedral : 9.319 156.275 3673 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 2.60 % Allowed : 18.94 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.67 (0.15), residues: 3133 helix: 0.99 (0.16), residues: 1083 sheet: -1.08 (0.24), residues: 479 loop : -1.26 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 350 HIS 0.011 0.001 HIS F 548 PHE 0.020 0.001 PHE F 543 TYR 0.014 0.001 TYR A 482 ARG 0.003 0.000 ARG C 595 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 852) hydrogen bonds : angle 4.38357 ( 2400) covalent geometry : bond 0.00246 (26281) covalent geometry : angle 0.52954 (35593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 207 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8506 (mmm) cc_final: 0.8284 (mmm) REVERT: A 593 ASN cc_start: 0.8852 (m-40) cc_final: 0.8328 (t0) REVERT: A 618 MET cc_start: 0.7288 (ptp) cc_final: 0.7040 (pmm) REVERT: A 656 ASP cc_start: 0.8837 (p0) cc_final: 0.8591 (t0) REVERT: C 340 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8806 (mt) REVERT: C 450 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8270 (mttp) REVERT: C 557 GLU cc_start: 0.6553 (pm20) cc_final: 0.6333 (pm20) REVERT: D 62 TYR cc_start: 0.6927 (m-80) cc_final: 0.6684 (m-80) REVERT: D 110 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8239 (tp30) REVERT: D 150 MET cc_start: 0.7794 (mmm) cc_final: 0.7417 (mmm) REVERT: E 116 MET cc_start: 0.8018 (ptp) cc_final: 0.7652 (ppp) REVERT: E 170 ASP cc_start: 0.7907 (t0) cc_final: 0.6794 (p0) REVERT: E 223 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8300 (tp) REVERT: E 618 MET cc_start: 0.7995 (mtm) cc_final: 0.7467 (mtm) REVERT: F 632 GLN cc_start: 0.1775 (OUTLIER) cc_final: 0.1212 (mp-120) REVERT: F 682 PRO cc_start: 0.7970 (Cg_endo) cc_final: 0.7719 (Cg_exo) outliers start: 75 outliers final: 55 residues processed: 264 average time/residue: 0.3066 time to fit residues: 137.3425 Evaluate side-chains 246 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain F residue 645 TYR Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 261 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 215 optimal weight: 0.0770 chunk 268 optimal weight: 10.0000 chunk 21 optimal weight: 0.0770 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 ASN E 201 HIS ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.075032 restraints weight = 71668.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.077114 restraints weight = 40823.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078494 restraints weight = 28455.992| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 26281 Z= 0.094 Angle : 0.516 9.715 35593 Z= 0.263 Chirality : 0.041 0.181 3984 Planarity : 0.003 0.061 4537 Dihedral : 9.056 156.252 3671 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 2.08 % Allowed : 19.56 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.54 (0.15), residues: 3133 helix: 1.05 (0.16), residues: 1085 sheet: -0.97 (0.24), residues: 485 loop : -1.16 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.003 0.000 HIS D 290 PHE 0.020 0.001 PHE E 120 TYR 0.016 0.001 TYR K 82 ARG 0.003 0.000 ARG K 167 Details of bonding type rmsd hydrogen bonds : bond 0.02746 ( 852) hydrogen bonds : angle 4.17511 ( 2400) covalent geometry : bond 0.00210 (26281) covalent geometry : angle 0.51564 (35593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9538 (tp) cc_final: 0.9314 (tp) REVERT: A 534 ASP cc_start: 0.6895 (t70) cc_final: 0.6463 (t0) REVERT: A 593 ASN cc_start: 0.8833 (m-40) cc_final: 0.8329 (t0) REVERT: A 618 MET cc_start: 0.7321 (ptp) cc_final: 0.7056 (pmm) REVERT: A 656 ASP cc_start: 0.8796 (p0) cc_final: 0.8588 (t0) REVERT: B 615 ASN cc_start: 0.8600 (t0) cc_final: 0.8372 (p0) REVERT: B 618 MET cc_start: 0.7583 (mtm) cc_final: 0.7284 (mtm) REVERT: C 340 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8688 (mt) REVERT: D 62 TYR cc_start: 0.6911 (m-80) cc_final: 0.6709 (m-80) REVERT: D 110 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8244 (tp30) REVERT: D 150 MET cc_start: 0.7939 (mmm) cc_final: 0.7680 (mmm) REVERT: E 116 MET cc_start: 0.7902 (ptp) cc_final: 0.7566 (ppp) REVERT: E 170 ASP cc_start: 0.7927 (t0) cc_final: 0.6854 (p0) REVERT: E 223 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8293 (tp) REVERT: E 618 MET cc_start: 0.7929 (mtm) cc_final: 0.7439 (mtm) REVERT: F 632 GLN cc_start: 0.2014 (OUTLIER) cc_final: 0.1376 (mp-120) REVERT: F 682 PRO cc_start: 0.7951 (Cg_endo) cc_final: 0.7722 (Cg_exo) REVERT: K 1 MET cc_start: 0.2916 (tpp) cc_final: 0.2533 (tpp) outliers start: 60 outliers final: 45 residues processed: 268 average time/residue: 0.3184 time to fit residues: 142.3665 Evaluate side-chains 242 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain F residue 645 TYR Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 298 optimal weight: 0.4980 chunk 171 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 264 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 118 optimal weight: 20.0000 chunk 246 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 328 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.102269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074186 restraints weight = 72392.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076165 restraints weight = 42976.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077478 restraints weight = 30612.494| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26281 Z= 0.123 Angle : 0.545 10.564 35593 Z= 0.275 Chirality : 0.042 0.212 3984 Planarity : 0.003 0.058 4537 Dihedral : 9.026 156.618 3671 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.91 % Rotamer: Outliers : 2.19 % Allowed : 20.08 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.51 (0.15), residues: 3133 helix: 1.08 (0.16), residues: 1093 sheet: -1.01 (0.24), residues: 500 loop : -1.14 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 350 HIS 0.008 0.001 HIS F 548 PHE 0.018 0.001 PHE E 120 TYR 0.015 0.001 TYR A 482 ARG 0.005 0.000 ARG K 152 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 852) hydrogen bonds : angle 4.25401 ( 2400) covalent geometry : bond 0.00289 (26281) covalent geometry : angle 0.54453 (35593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.7008 (t70) cc_final: 0.6592 (t0) REVERT: A 593 ASN cc_start: 0.8829 (m-40) cc_final: 0.8300 (t0) REVERT: A 618 MET cc_start: 0.7300 (ptp) cc_final: 0.7037 (pmm) REVERT: B 615 ASN cc_start: 0.8582 (t0) cc_final: 0.8365 (p0) REVERT: B 618 MET cc_start: 0.7573 (mtm) cc_final: 0.7254 (mtm) REVERT: C 340 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8850 (mt) REVERT: D 62 TYR cc_start: 0.6861 (m-80) cc_final: 0.6632 (m-80) REVERT: D 110 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8250 (tp30) REVERT: D 116 MET cc_start: 0.7757 (ttp) cc_final: 0.7313 (ppp) REVERT: D 462 MET cc_start: 0.8784 (mmm) cc_final: 0.8382 (tpt) REVERT: E 116 MET cc_start: 0.7893 (ptp) cc_final: 0.7576 (ppp) REVERT: E 170 ASP cc_start: 0.7887 (t0) cc_final: 0.6965 (p0) REVERT: E 223 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8236 (tp) REVERT: E 618 MET cc_start: 0.7933 (mtm) cc_final: 0.7512 (mtm) REVERT: F 444 PHE cc_start: 0.6896 (p90) cc_final: 0.6235 (p90) REVERT: F 632 GLN cc_start: 0.2065 (OUTLIER) cc_final: 0.1434 (mp-120) REVERT: F 682 PRO cc_start: 0.7977 (Cg_endo) cc_final: 0.7755 (Cg_exo) REVERT: K 1 MET cc_start: 0.2916 (tpp) cc_final: 0.2504 (tpp) outliers start: 63 outliers final: 51 residues processed: 255 average time/residue: 0.3156 time to fit residues: 135.3275 Evaluate side-chains 256 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 548 HIS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 266 optimal weight: 0.1980 chunk 308 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.102720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074722 restraints weight = 72720.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076711 restraints weight = 42704.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078025 restraints weight = 30305.175| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26281 Z= 0.104 Angle : 0.543 11.639 35593 Z= 0.274 Chirality : 0.041 0.193 3984 Planarity : 0.003 0.058 4537 Dihedral : 8.982 156.297 3671 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 2.08 % Allowed : 20.15 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.49 (0.15), residues: 3133 helix: 1.08 (0.16), residues: 1094 sheet: -0.97 (0.24), residues: 496 loop : -1.12 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.016 0.001 HIS F 548 PHE 0.019 0.001 PHE F 543 TYR 0.013 0.001 TYR A 482 ARG 0.006 0.000 ARG F 387 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 852) hydrogen bonds : angle 4.17584 ( 2400) covalent geometry : bond 0.00241 (26281) covalent geometry : angle 0.54342 (35593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.6957 (t70) cc_final: 0.6540 (t0) REVERT: A 593 ASN cc_start: 0.8810 (m-40) cc_final: 0.8259 (t0) REVERT: A 618 MET cc_start: 0.7331 (ptp) cc_final: 0.7074 (pmm) REVERT: B 615 ASN cc_start: 0.8575 (t0) cc_final: 0.8367 (p0) REVERT: B 618 MET cc_start: 0.7577 (mtm) cc_final: 0.7264 (mtm) REVERT: C 340 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8828 (mt) REVERT: D 62 TYR cc_start: 0.6841 (m-80) cc_final: 0.6615 (m-80) REVERT: D 110 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8239 (tp30) REVERT: D 116 MET cc_start: 0.7773 (ttp) cc_final: 0.7343 (ppp) REVERT: D 462 MET cc_start: 0.8767 (mmm) cc_final: 0.8391 (tpt) REVERT: E 116 MET cc_start: 0.7873 (ptp) cc_final: 0.7583 (ppp) REVERT: E 170 ASP cc_start: 0.7872 (t0) cc_final: 0.7048 (p0) REVERT: E 223 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8231 (tp) REVERT: E 618 MET cc_start: 0.7908 (mtm) cc_final: 0.7480 (mtm) REVERT: F 444 PHE cc_start: 0.6905 (p90) cc_final: 0.6328 (p90) REVERT: F 632 GLN cc_start: 0.2046 (OUTLIER) cc_final: 0.1432 (mp-120) REVERT: F 682 PRO cc_start: 0.7904 (Cg_endo) cc_final: 0.7684 (Cg_exo) REVERT: K 1 MET cc_start: 0.2907 (tpp) cc_final: 0.2525 (tpp) outliers start: 60 outliers final: 50 residues processed: 256 average time/residue: 0.3164 time to fit residues: 136.6726 Evaluate side-chains 252 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain F residue 645 TYR Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 69 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075411 restraints weight = 72516.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077654 restraints weight = 42907.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.078055 restraints weight = 28272.600| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 26281 Z= 0.103 Angle : 0.543 12.867 35593 Z= 0.272 Chirality : 0.041 0.180 3984 Planarity : 0.003 0.060 4537 Dihedral : 8.934 156.258 3671 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 2.05 % Allowed : 20.57 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.47 (0.15), residues: 3133 helix: 1.07 (0.16), residues: 1096 sheet: -0.96 (0.24), residues: 502 loop : -1.08 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.013 0.001 HIS F 548 PHE 0.017 0.001 PHE E 120 TYR 0.020 0.001 TYR E 82 ARG 0.005 0.000 ARG F 387 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 852) hydrogen bonds : angle 4.15990 ( 2400) covalent geometry : bond 0.00238 (26281) covalent geometry : angle 0.54262 (35593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 214 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 ASN cc_start: 0.8872 (m-40) cc_final: 0.8380 (t0) REVERT: A 618 MET cc_start: 0.7344 (ptp) cc_final: 0.6979 (pmm) REVERT: B 615 ASN cc_start: 0.8632 (t0) cc_final: 0.8403 (p0) REVERT: B 618 MET cc_start: 0.7646 (mtm) cc_final: 0.7319 (mtm) REVERT: C 340 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8829 (mt) REVERT: C 557 GLU cc_start: 0.6371 (pm20) cc_final: 0.6144 (pm20) REVERT: D 62 TYR cc_start: 0.6872 (m-80) cc_final: 0.6616 (m-80) REVERT: D 116 MET cc_start: 0.7853 (ttp) cc_final: 0.7382 (ppp) REVERT: D 462 MET cc_start: 0.8782 (mmm) cc_final: 0.8378 (tpt) REVERT: D 522 ASP cc_start: 0.8162 (t70) cc_final: 0.7922 (t0) REVERT: E 116 MET cc_start: 0.8001 (ptp) cc_final: 0.7699 (ppp) REVERT: E 170 ASP cc_start: 0.7846 (t0) cc_final: 0.7168 (p0) REVERT: E 223 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8286 (tp) REVERT: E 618 MET cc_start: 0.7978 (mtm) cc_final: 0.7505 (mtm) REVERT: F 444 PHE cc_start: 0.6935 (p90) cc_final: 0.6415 (p90) REVERT: F 631 SER cc_start: 0.6953 (t) cc_final: 0.6742 (m) REVERT: F 632 GLN cc_start: 0.1844 (OUTLIER) cc_final: 0.1252 (mp-120) REVERT: F 682 PRO cc_start: 0.7892 (Cg_endo) cc_final: 0.7683 (Cg_exo) REVERT: K 1 MET cc_start: 0.2940 (tpp) cc_final: 0.2564 (tpp) outliers start: 59 outliers final: 51 residues processed: 256 average time/residue: 0.3214 time to fit residues: 138.5786 Evaluate side-chains 256 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 548 HIS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain F residue 645 TYR Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 55 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 166 optimal weight: 0.0470 chunk 221 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 282 optimal weight: 0.0070 chunk 168 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 17 optimal weight: 0.4980 overall best weight: 0.7296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.103229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.075851 restraints weight = 72139.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077910 restraints weight = 42801.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078697 restraints weight = 27867.568| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26281 Z= 0.100 Angle : 0.543 12.318 35593 Z= 0.273 Chirality : 0.041 0.179 3984 Planarity : 0.003 0.062 4537 Dihedral : 8.886 156.193 3671 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 2.01 % Allowed : 20.74 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.45 (0.15), residues: 3133 helix: 1.04 (0.16), residues: 1102 sheet: -0.93 (0.24), residues: 502 loop : -1.05 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 350 HIS 0.015 0.001 HIS F 548 PHE 0.019 0.001 PHE K 100 TYR 0.020 0.001 TYR K 82 ARG 0.005 0.000 ARG F 387 Details of bonding type rmsd hydrogen bonds : bond 0.02796 ( 852) hydrogen bonds : angle 4.13474 ( 2400) covalent geometry : bond 0.00230 (26281) covalent geometry : angle 0.54273 (35593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7067.71 seconds wall clock time: 125 minutes 37.53 seconds (7537.53 seconds total)