Starting phenix.real_space_refine on Sat Jun 6 06:33:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y07_72387/06_2026/9y07_72387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y07_72387/06_2026/9y07_72387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y07_72387/06_2026/9y07_72387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y07_72387/06_2026/9y07_72387.map" model { file = "/net/cci-nas-00/data/ceres_data/9y07_72387/06_2026/9y07_72387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y07_72387/06_2026/9y07_72387.cif" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 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 36 5.49 5 Mg 12 5.21 5 S 144 5.16 5 C 16254 2.51 5 N 4566 2.21 5 O 4986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25998 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "B" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "C" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "D" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "E" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "F" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.02, per 1000 atoms: 0.23 Number of scatterers: 25998 At special positions: 0 Unit cell: (141, 145, 95, 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 36 15.00 Mg 12 11.99 O 4986 8.00 N 4566 7.00 C 16254 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6120 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 12 sheets defined 56.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 226 removed outlier: 4.333A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.315A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.736A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.558A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.064A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.876A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.527A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.113A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.834A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 557 through 569 Processing helix chain 'A' and resid 578 through 584 removed outlier: 4.112A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.086A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 683 through 706 removed outlier: 3.753A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.694A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.896A pdb=" N ARG A 766 " --> pdb=" O GLN A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.384A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.262A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.724A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.012A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.999A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.517A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.068A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.792A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 557 through 569 Processing helix chain 'B' and resid 578 through 584 removed outlier: 4.009A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 4.133A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.630A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.818A pdb=" N ARG B 766 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.358A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.225A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.808A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.025A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.792A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 removed outlier: 3.517A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.113A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.808A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 557 through 569 Processing helix chain 'C' and resid 578 through 584 removed outlier: 4.023A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 610 removed outlier: 4.114A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 683 through 706 removed outlier: 3.723A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.721A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 Processing helix chain 'C' and resid 762 through 766 removed outlier: 4.048A pdb=" N ARG C 766 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 210 through 226 removed outlier: 4.331A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.317A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.741A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.561A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.061A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.870A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.859A pdb=" N ARG D 358 " --> pdb=" O ASP D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.528A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.113A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.830A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 544 through 550 Processing helix chain 'D' and resid 557 through 569 Processing helix chain 'D' and resid 578 through 584 removed outlier: 4.109A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 610 removed outlier: 4.078A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 683 through 706 removed outlier: 3.751A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.698A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'D' and resid 762 through 766 removed outlier: 3.901A pdb=" N ARG D 766 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.389A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.267A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 271 through 277 removed outlier: 3.723A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.018A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 4.004A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 425 removed outlier: 3.515A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.069A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.795A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 544 through 550 Processing helix chain 'E' and resid 557 through 569 Processing helix chain 'E' and resid 578 through 584 removed outlier: 4.049A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 4.088A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 683 through 705 Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.635A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 Processing helix chain 'E' and resid 762 through 766 removed outlier: 3.949A pdb=" N ARG E 766 " --> pdb=" O GLN E 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 210 through 226 removed outlier: 4.295A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.266A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.806A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.035A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.883A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 448 through 456 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.116A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.813A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 550 Processing helix chain 'F' and resid 557 through 569 Processing helix chain 'F' and resid 578 through 584 removed outlier: 4.017A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 4.118A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 683 through 706 removed outlier: 3.728A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.719A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.159A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.603A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.156A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 543 removed outlier: 6.584A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.133A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 541 removed outlier: 6.618A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.148A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 543 removed outlier: 6.607A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.163A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 543 removed outlier: 6.606A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.144A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 541 removed outlier: 6.624A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1246 hydrogen bonds defined for protein. 3531 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: 4.86 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 8997 1.37 - 1.51: 7239 1.51 - 1.66: 9960 1.66 - 1.80: 172 1.80 - 1.95: 62 Bond restraints: 26430 Sorted by residual: bond pdb=" CB TRP B 551 " pdb=" CG TRP B 551 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.68e+00 bond pdb=" CB TRP E 551 " pdb=" CG TRP E 551 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.40e+00 bond pdb=" CB TRP D 551 " pdb=" CG TRP D 551 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.35e+00 bond pdb=" CB TRP A 551 " pdb=" CG TRP A 551 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.35e+00 bond pdb=" CB TRP F 551 " pdb=" CG TRP F 551 " ideal model delta sigma weight residual 1.498 1.464 0.034 3.10e-02 1.04e+03 1.20e+00 ... (remaining 26425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 34822 1.46 - 2.93: 770 2.93 - 4.39: 107 4.39 - 5.86: 44 5.86 - 7.32: 11 Bond angle restraints: 35754 Sorted by residual: angle pdb=" C ARG C 599 " pdb=" CA ARG C 599 " pdb=" CB ARG C 599 " ideal model delta sigma weight residual 117.23 109.91 7.32 1.36e+00 5.41e-01 2.90e+01 angle pdb=" C ARG F 599 " pdb=" CA ARG F 599 " pdb=" CB ARG F 599 " ideal model delta sigma weight residual 117.23 109.91 7.32 1.36e+00 5.41e-01 2.90e+01 angle pdb=" C ARG E 599 " pdb=" CA ARG E 599 " pdb=" CB ARG E 599 " ideal model delta sigma weight residual 117.23 109.92 7.31 1.36e+00 5.41e-01 2.89e+01 angle pdb=" C ARG A 599 " pdb=" CA ARG A 599 " pdb=" CB ARG A 599 " ideal model delta sigma weight residual 117.23 109.95 7.28 1.36e+00 5.41e-01 2.87e+01 angle pdb=" C ARG D 599 " pdb=" CA ARG D 599 " pdb=" CB ARG D 599 " ideal model delta sigma weight residual 117.23 110.00 7.23 1.36e+00 5.41e-01 2.83e+01 ... (remaining 35749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 14847 17.06 - 34.11: 1200 34.11 - 51.17: 224 51.17 - 68.22: 43 68.22 - 85.28: 36 Dihedral angle restraints: 16350 sinusoidal: 6912 harmonic: 9438 Sorted by residual: dihedral pdb=" CA ALA F 297 " pdb=" C ALA F 297 " pdb=" N PRO F 298 " pdb=" CA PRO F 298 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ALA C 297 " pdb=" C ALA C 297 " pdb=" N PRO C 298 " pdb=" CA PRO C 298 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ALA D 297 " pdb=" C ALA D 297 " pdb=" N PRO D 298 " pdb=" CA PRO D 298 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 16347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2404 0.031 - 0.061: 972 0.061 - 0.092: 400 0.092 - 0.122: 217 0.122 - 0.153: 27 Chirality restraints: 4020 Sorted by residual: chirality pdb=" CA TRP F 551 " pdb=" N TRP F 551 " pdb=" C TRP F 551 " pdb=" CB TRP F 551 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA TRP A 551 " pdb=" N TRP A 551 " pdb=" C TRP A 551 " pdb=" CB TRP A 551 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA TRP C 551 " pdb=" N TRP C 551 " pdb=" C TRP C 551 " pdb=" CB TRP C 551 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 4017 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 460 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO D 461 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 461 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 461 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 460 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 461 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 460 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO C 461 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 461 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 461 " 0.034 5.00e-02 4.00e+02 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 276 2.57 - 3.16: 21436 3.16 - 3.74: 43618 3.74 - 4.32: 59922 4.32 - 4.90: 94660 Nonbonded interactions: 219912 Sorted by model distance: nonbonded pdb=" O2G AGS C 902 " pdb="MG MG C 904 " model vdw 1.993 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 903 " model vdw 1.997 2.170 nonbonded pdb=" OG1 THR B 252 " pdb="MG MG B 903 " model vdw 1.998 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 903 " model vdw 2.017 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 903 " model vdw 2.019 2.170 ... (remaining 219907 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 24.210 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 0.040 26430 Z= 0.124 Angle : 0.565 7.325 35754 Z= 0.311 Chirality : 0.043 0.153 4020 Planarity : 0.005 0.064 4668 Dihedral : 13.367 85.276 10230 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.03 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 3270 helix: 0.91 (0.13), residues: 1734 sheet: 0.46 (0.27), residues: 396 loop : 0.71 (0.21), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 256 TYR 0.010 0.002 TYR B 244 PHE 0.010 0.001 PHE E 758 TRP 0.038 0.003 TRP C 551 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (26430) covalent geometry : angle 0.56526 / 0.31 (35754) hydrogen bonds : bond 0.14065 / 9.52 ( 1246) hydrogen bonds : angle 5.12871 / 3.69 ( 3531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8528 (tt0) cc_final: 0.8122 (tp30) REVERT: A 398 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 454 TRP cc_start: 0.8973 (t-100) cc_final: 0.8714 (t-100) REVERT: A 509 THR cc_start: 0.8981 (m) cc_final: 0.8739 (t) REVERT: A 560 ARG cc_start: 0.8479 (mtm110) cc_final: 0.7946 (mmt180) REVERT: B 288 LYS cc_start: 0.8641 (mptt) cc_final: 0.8367 (mmtt) REVERT: B 388 MET cc_start: 0.8977 (ptp) cc_final: 0.8754 (ptm) REVERT: B 398 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7448 (tm-30) REVERT: B 454 TRP cc_start: 0.9050 (t-100) cc_final: 0.8748 (t-100) REVERT: C 288 LYS cc_start: 0.8527 (mptt) cc_final: 0.8287 (mmtt) REVERT: C 398 GLN cc_start: 0.8618 (tm-30) cc_final: 0.7987 (tp-100) REVERT: D 292 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8277 (mm-30) REVERT: D 397 GLU cc_start: 0.8544 (tt0) cc_final: 0.8076 (tp30) REVERT: D 454 TRP cc_start: 0.8971 (t-100) cc_final: 0.8705 (t-100) REVERT: D 509 THR cc_start: 0.8973 (m) cc_final: 0.8721 (t) REVERT: D 560 ARG cc_start: 0.8429 (mtm110) cc_final: 0.7904 (mmt180) REVERT: E 288 LYS cc_start: 0.8630 (mptt) cc_final: 0.8356 (mmtt) REVERT: E 388 MET cc_start: 0.8935 (ptp) cc_final: 0.8726 (ptm) REVERT: E 398 GLN cc_start: 0.8634 (tm-30) cc_final: 0.7363 (tm-30) REVERT: E 454 TRP cc_start: 0.9046 (t-100) cc_final: 0.8746 (t-100) REVERT: F 288 LYS cc_start: 0.8428 (mptt) cc_final: 0.8164 (mmtt) REVERT: F 398 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8010 (tp-100) REVERT: F 663 LYS cc_start: 0.9203 (mptt) cc_final: 0.8990 (mmtm) outliers start: 0 outliers final: 4 residues processed: 578 average time/residue: 0.8578 time to fit residues: 554.2788 Evaluate side-chains 315 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 311 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 624 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.0050 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 337 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 260 ASN B 337 GLN C 215 GLN C 337 GLN D 226 HIS D 337 GLN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN E 337 GLN F 215 GLN F 337 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092506 restraints weight = 37200.219| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.80 r_work: 0.2980 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26430 Z= 0.139 Angle : 0.564 7.104 35754 Z= 0.288 Chirality : 0.043 0.159 4020 Planarity : 0.005 0.061 4668 Dihedral : 8.632 59.898 3789 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.55 % Favored : 96.24 % Rotamer: Outliers : 1.87 % Allowed : 10.48 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.16), residues: 3270 helix: 1.06 (0.13), residues: 1740 sheet: 0.36 (0.26), residues: 396 loop : 0.82 (0.21), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 359 TYR 0.016 0.002 TYR E 203 PHE 0.009 0.001 PHE A 563 TRP 0.021 0.002 TRP C 551 HIS 0.006 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (26430) covalent geometry : angle 0.56376 / 0.29 (35754) hydrogen bonds : bond 0.04341 / 2.91 ( 1246) hydrogen bonds : angle 4.34669 / 3.09 ( 3531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 316 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7795 (mm-30) REVERT: A 305 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: A 397 GLU cc_start: 0.8578 (tt0) cc_final: 0.8163 (tp30) REVERT: A 454 TRP cc_start: 0.8936 (t-100) cc_final: 0.8673 (t-100) REVERT: A 560 ARG cc_start: 0.8379 (mtm110) cc_final: 0.7808 (mmt180) REVERT: A 668 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8668 (mmpt) REVERT: B 288 LYS cc_start: 0.8583 (mptt) cc_final: 0.8204 (mmtt) REVERT: B 366 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: B 388 MET cc_start: 0.8990 (ptp) cc_final: 0.8779 (ptm) REVERT: C 288 LYS cc_start: 0.8548 (mptt) cc_final: 0.8217 (mmtt) REVERT: C 358 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8219 (mtm180) REVERT: D 283 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: D 292 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8230 (mm-30) REVERT: D 305 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: D 397 GLU cc_start: 0.8606 (tt0) cc_final: 0.8144 (tp30) REVERT: D 402 GLU cc_start: 0.8764 (tt0) cc_final: 0.8340 (mt-10) REVERT: D 454 TRP cc_start: 0.8942 (t-100) cc_final: 0.8680 (t-100) REVERT: D 560 ARG cc_start: 0.8394 (mtm110) cc_final: 0.7799 (mmt180) REVERT: D 668 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8656 (mmpt) REVERT: E 288 LYS cc_start: 0.8588 (mptt) cc_final: 0.8208 (mmtt) REVERT: E 366 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: E 388 MET cc_start: 0.8931 (ptp) cc_final: 0.8699 (ptm) REVERT: F 288 LYS cc_start: 0.8533 (mptt) cc_final: 0.8206 (mmtt) REVERT: F 358 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8226 (mtm180) REVERT: F 701 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8152 (tt0) outliers start: 51 outliers final: 9 residues processed: 342 average time/residue: 0.7610 time to fit residues: 295.5021 Evaluate side-chains 297 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 279 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 701 GLU Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 292 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 307 optimal weight: 0.2980 chunk 165 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 250 optimal weight: 0.0270 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS C 226 HIS C 285 ASN C 568 GLN D 285 ASN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 226 HIS F 285 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091327 restraints weight = 37362.274| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.79 r_work: 0.2961 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26430 Z= 0.134 Angle : 0.543 7.411 35754 Z= 0.273 Chirality : 0.043 0.181 4020 Planarity : 0.005 0.060 4668 Dihedral : 8.282 56.008 3780 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.30 % Favored : 96.48 % Rotamer: Outliers : 1.79 % Allowed : 11.28 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.16), residues: 3270 helix: 1.22 (0.13), residues: 1704 sheet: 0.45 (0.27), residues: 378 loop : 0.82 (0.21), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 744 TYR 0.021 0.001 TYR E 203 PHE 0.009 0.001 PHE B 758 TRP 0.016 0.002 TRP B 551 HIS 0.007 0.001 HIS E 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (26430) covalent geometry : angle 0.54285 / 0.27 (35754) hydrogen bonds : bond 0.03807 / 2.55 ( 1246) hydrogen bonds : angle 4.08169 / 2.90 ( 3531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 298 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: A 397 GLU cc_start: 0.8615 (tt0) cc_final: 0.8136 (tp30) REVERT: A 454 TRP cc_start: 0.8963 (t-100) cc_final: 0.8663 (t-100) REVERT: A 560 ARG cc_start: 0.8399 (mtm110) cc_final: 0.7813 (mmt180) REVERT: B 288 LYS cc_start: 0.8748 (mptt) cc_final: 0.8325 (mmtt) REVERT: B 366 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8681 (mt-10) REVERT: B 388 MET cc_start: 0.9060 (ptp) cc_final: 0.8692 (ptm) REVERT: B 508 MET cc_start: 0.8151 (tmt) cc_final: 0.7947 (ppp) REVERT: C 288 LYS cc_start: 0.8635 (mptt) cc_final: 0.8257 (mmtt) REVERT: C 701 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: D 283 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: D 292 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8223 (mm-30) REVERT: D 397 GLU cc_start: 0.8599 (tt0) cc_final: 0.8115 (tp30) REVERT: D 402 GLU cc_start: 0.8811 (tt0) cc_final: 0.8498 (mt-10) REVERT: D 454 TRP cc_start: 0.8970 (t-100) cc_final: 0.8674 (t-100) REVERT: D 560 ARG cc_start: 0.8387 (mtm110) cc_final: 0.7795 (mmt180) REVERT: E 288 LYS cc_start: 0.8747 (mptt) cc_final: 0.8324 (mmtt) REVERT: E 366 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8637 (mt-10) REVERT: E 388 MET cc_start: 0.9034 (ptp) cc_final: 0.8756 (ptm) REVERT: E 757 MET cc_start: 0.8779 (tmm) cc_final: 0.8558 (tmm) REVERT: F 288 LYS cc_start: 0.8624 (mptt) cc_final: 0.8248 (mmtt) outliers start: 49 outliers final: 15 residues processed: 329 average time/residue: 0.7161 time to fit residues: 268.2964 Evaluate side-chains 292 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 103 optimal weight: 4.9990 chunk 323 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 297 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 266 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS B 285 ASN C 226 HIS E 226 HIS E 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089326 restraints weight = 37122.683| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.79 r_work: 0.2930 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26430 Z= 0.148 Angle : 0.542 7.887 35754 Z= 0.272 Chirality : 0.043 0.149 4020 Planarity : 0.005 0.060 4668 Dihedral : 8.228 55.198 3780 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.46 % Favored : 96.33 % Rotamer: Outliers : 1.83 % Allowed : 12.53 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.16), residues: 3270 helix: 1.32 (0.13), residues: 1704 sheet: 0.40 (0.27), residues: 378 loop : 0.87 (0.21), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.010 0.001 TYR E 203 PHE 0.010 0.001 PHE B 758 TRP 0.017 0.002 TRP E 551 HIS 0.010 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (26430) covalent geometry : angle 0.54171 / 0.27 (35754) hydrogen bonds : bond 0.03658 / 2.45 ( 1246) hydrogen bonds : angle 3.97553 / 2.82 ( 3531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 307 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7728 (mm-30) REVERT: A 397 GLU cc_start: 0.8615 (tt0) cc_final: 0.8062 (tp30) REVERT: A 454 TRP cc_start: 0.9004 (t-100) cc_final: 0.8699 (t-100) REVERT: A 560 ARG cc_start: 0.8401 (mtm110) cc_final: 0.7827 (mmt180) REVERT: A 765 SER cc_start: 0.8986 (m) cc_final: 0.8725 (p) REVERT: B 288 LYS cc_start: 0.8783 (mptt) cc_final: 0.8325 (mmtt) REVERT: B 366 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8720 (mt-10) REVERT: B 388 MET cc_start: 0.9146 (ptp) cc_final: 0.8749 (ptm) REVERT: C 225 ARG cc_start: 0.8463 (mtm-85) cc_final: 0.8220 (ptp-170) REVERT: C 288 LYS cc_start: 0.8733 (mptt) cc_final: 0.8273 (mmtt) REVERT: C 388 MET cc_start: 0.8931 (ptp) cc_final: 0.8625 (ptm) REVERT: C 534 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: D 283 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: D 292 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8280 (mm-30) REVERT: D 397 GLU cc_start: 0.8603 (tt0) cc_final: 0.8097 (tp30) REVERT: D 454 TRP cc_start: 0.9005 (t-100) cc_final: 0.8704 (t-100) REVERT: D 560 ARG cc_start: 0.8383 (mtm110) cc_final: 0.7793 (mmt180) REVERT: D 765 SER cc_start: 0.8976 (m) cc_final: 0.8713 (p) REVERT: E 288 LYS cc_start: 0.8757 (mptt) cc_final: 0.8307 (mmtt) REVERT: E 366 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8701 (mt-10) REVERT: E 388 MET cc_start: 0.9140 (ptp) cc_final: 0.8909 (ptp) REVERT: E 397 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8124 (tm-30) REVERT: F 288 LYS cc_start: 0.8736 (mptt) cc_final: 0.8309 (mmtt) REVERT: F 534 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8322 (tt0) outliers start: 50 outliers final: 21 residues processed: 337 average time/residue: 0.7439 time to fit residues: 285.4791 Evaluate side-chains 307 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 268 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 227 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN D 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.088379 restraints weight = 37198.838| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.79 r_work: 0.2911 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26430 Z= 0.156 Angle : 0.548 6.827 35754 Z= 0.273 Chirality : 0.043 0.147 4020 Planarity : 0.005 0.058 4668 Dihedral : 8.240 55.548 3780 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.45 % Rotamer: Outliers : 2.23 % Allowed : 13.04 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.16), residues: 3270 helix: 1.36 (0.13), residues: 1716 sheet: 0.18 (0.26), residues: 396 loop : 0.82 (0.21), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 766 TYR 0.011 0.001 TYR C 203 PHE 0.011 0.001 PHE B 758 TRP 0.014 0.002 TRP E 551 HIS 0.008 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (26430) covalent geometry : angle 0.54778 / 0.27 (35754) hydrogen bonds : bond 0.03639 / 2.44 ( 1246) hydrogen bonds : angle 3.92652 / 2.78 ( 3531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 277 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: A 288 LYS cc_start: 0.8932 (mttp) cc_final: 0.8286 (mmtt) REVERT: A 397 GLU cc_start: 0.8628 (tt0) cc_final: 0.8059 (tp30) REVERT: A 454 TRP cc_start: 0.9025 (t-100) cc_final: 0.8710 (t-100) REVERT: A 560 ARG cc_start: 0.8413 (mtm110) cc_final: 0.7816 (mmt180) REVERT: A 765 SER cc_start: 0.8988 (m) cc_final: 0.8734 (p) REVERT: B 288 LYS cc_start: 0.8830 (mptt) cc_final: 0.8400 (mmtt) REVERT: B 366 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8753 (mt-10) REVERT: B 388 MET cc_start: 0.9163 (ptp) cc_final: 0.8780 (ptm) REVERT: B 397 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 225 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8231 (ptp-170) REVERT: C 358 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8262 (mtm180) REVERT: C 388 MET cc_start: 0.8942 (ptp) cc_final: 0.8632 (ptm) REVERT: C 534 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: C 611 MET cc_start: 0.7478 (mtp) cc_final: 0.7010 (mmt) REVERT: D 283 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: D 288 LYS cc_start: 0.8967 (mttp) cc_final: 0.8220 (mmtt) REVERT: D 292 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8285 (mm-30) REVERT: D 397 GLU cc_start: 0.8634 (tt0) cc_final: 0.8103 (tp30) REVERT: D 454 TRP cc_start: 0.9029 (t-100) cc_final: 0.8718 (t-100) REVERT: D 560 ARG cc_start: 0.8397 (mtm110) cc_final: 0.7821 (mmt180) REVERT: D 765 SER cc_start: 0.9008 (m) cc_final: 0.8761 (p) REVERT: E 288 LYS cc_start: 0.8810 (mptt) cc_final: 0.8352 (mmtt) REVERT: E 366 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8708 (mt-10) REVERT: E 388 MET cc_start: 0.9157 (ptp) cc_final: 0.8948 (ptp) REVERT: E 397 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8130 (tm-30) REVERT: F 358 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8191 (mtm180) REVERT: F 534 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: F 611 MET cc_start: 0.7536 (mtp) cc_final: 0.7272 (mmt) outliers start: 61 outliers final: 26 residues processed: 315 average time/residue: 0.7703 time to fit residues: 275.2353 Evaluate side-chains 293 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 50 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 GLN ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.086662 restraints weight = 37255.415| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.80 r_work: 0.2879 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26430 Z= 0.179 Angle : 0.562 7.299 35754 Z= 0.281 Chirality : 0.044 0.175 4020 Planarity : 0.005 0.063 4668 Dihedral : 8.361 56.726 3780 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.45 % Rotamer: Outliers : 2.34 % Allowed : 13.44 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.16), residues: 3270 helix: 1.36 (0.13), residues: 1716 sheet: 0.16 (0.26), residues: 396 loop : 0.76 (0.21), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 766 TYR 0.010 0.002 TYR D 244 PHE 0.011 0.002 PHE B 758 TRP 0.017 0.002 TRP E 551 HIS 0.007 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (26430) covalent geometry : angle 0.56172 / 0.28 (35754) hydrogen bonds : bond 0.03758 / 2.53 ( 1246) hydrogen bonds : angle 3.91216 / 2.77 ( 3531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 272 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 288 LYS cc_start: 0.8889 (mttp) cc_final: 0.8298 (mmtt) REVERT: A 397 GLU cc_start: 0.8643 (tt0) cc_final: 0.8043 (tp30) REVERT: A 560 ARG cc_start: 0.8424 (mtm110) cc_final: 0.7822 (mmt180) REVERT: A 765 SER cc_start: 0.9004 (m) cc_final: 0.8726 (p) REVERT: B 366 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8739 (mt-10) REVERT: B 388 MET cc_start: 0.9256 (ptp) cc_final: 0.9050 (ptp) REVERT: B 397 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8133 (tm-30) REVERT: C 225 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8174 (ptp-170) REVERT: C 241 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8495 (mm) REVERT: C 358 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8267 (mtm180) REVERT: C 388 MET cc_start: 0.8972 (ptp) cc_final: 0.8606 (ptm) REVERT: C 534 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: D 283 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: D 288 LYS cc_start: 0.8934 (mttp) cc_final: 0.8242 (mmtt) REVERT: D 292 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8287 (mm-30) REVERT: D 397 GLU cc_start: 0.8622 (tt0) cc_final: 0.8076 (tp30) REVERT: D 560 ARG cc_start: 0.8407 (mtm110) cc_final: 0.7795 (mmt180) REVERT: D 765 SER cc_start: 0.8984 (m) cc_final: 0.8748 (p) REVERT: E 366 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8764 (mt-10) REVERT: E 397 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8145 (tm-30) REVERT: F 241 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8486 (mm) REVERT: F 358 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8258 (mtm180) REVERT: F 534 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: F 737 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7725 (mt-10) outliers start: 64 outliers final: 32 residues processed: 315 average time/residue: 0.7253 time to fit residues: 260.2028 Evaluate side-chains 295 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 737 GLU Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 169 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 275 optimal weight: 0.9980 chunk 248 optimal weight: 0.0050 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 32 optimal weight: 0.0170 chunk 44 optimal weight: 0.8980 overall best weight: 0.5032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN B 660 ASN ** E 226 HIS ** 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 = 0.3634 r_free = 0.3634 target = 0.122715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088032 restraints weight = 37244.988| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.80 r_work: 0.2906 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 26430 Z= 0.125 Angle : 0.544 10.436 35754 Z= 0.270 Chirality : 0.042 0.189 4020 Planarity : 0.005 0.059 4668 Dihedral : 8.169 55.433 3780 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.45 % Rotamer: Outliers : 2.16 % Allowed : 14.10 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.16), residues: 3270 helix: 1.42 (0.13), residues: 1716 sheet: 0.24 (0.26), residues: 378 loop : 0.79 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.011 0.001 TYR E 203 PHE 0.010 0.001 PHE B 758 TRP 0.013 0.002 TRP E 551 HIS 0.007 0.001 HIS E 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (26430) covalent geometry : angle 0.54432 / 0.27 (35754) hydrogen bonds : bond 0.03398 / 2.29 ( 1246) hydrogen bonds : angle 3.89110 / 2.76 ( 3531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 265 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: A 288 LYS cc_start: 0.8944 (mttp) cc_final: 0.8282 (mmtt) REVERT: A 397 GLU cc_start: 0.8638 (tt0) cc_final: 0.8049 (tp30) REVERT: A 560 ARG cc_start: 0.8405 (mtm110) cc_final: 0.7796 (mmt180) REVERT: A 765 SER cc_start: 0.8972 (m) cc_final: 0.8765 (p) REVERT: B 366 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8754 (mt-10) REVERT: B 388 MET cc_start: 0.9269 (ptp) cc_final: 0.9068 (ptp) REVERT: B 397 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 225 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8197 (ptp-170) REVERT: C 241 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8403 (mm) REVERT: C 295 LYS cc_start: 0.9281 (ttmm) cc_final: 0.9064 (ttpt) REVERT: C 358 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8290 (mtm180) REVERT: C 388 MET cc_start: 0.9039 (ptp) cc_final: 0.8491 (ptm) REVERT: C 603 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: D 283 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: D 288 LYS cc_start: 0.8980 (mttp) cc_final: 0.8222 (mmtt) REVERT: D 292 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8192 (mm-30) REVERT: D 397 GLU cc_start: 0.8602 (tt0) cc_final: 0.8067 (tp30) REVERT: D 560 ARG cc_start: 0.8384 (mtm110) cc_final: 0.7773 (mmt180) REVERT: D 765 SER cc_start: 0.8970 (m) cc_final: 0.8767 (p) REVERT: E 366 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8723 (mt-10) REVERT: E 397 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8119 (tm-30) REVERT: F 358 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8204 (mtm180) REVERT: F 534 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: F 678 MET cc_start: 0.8584 (mmm) cc_final: 0.8305 (mmm) outliers start: 59 outliers final: 28 residues processed: 305 average time/residue: 0.7477 time to fit residues: 258.9654 Evaluate side-chains 289 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 603 GLN Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 269 optimal weight: 0.6980 chunk 80 optimal weight: 0.0050 chunk 139 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.087819 restraints weight = 37294.483| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.79 r_work: 0.2908 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26430 Z= 0.132 Angle : 0.549 9.562 35754 Z= 0.272 Chirality : 0.043 0.171 4020 Planarity : 0.005 0.059 4668 Dihedral : 8.055 54.290 3780 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.55 % Favored : 96.27 % Rotamer: Outliers : 2.12 % Allowed : 14.36 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.16), residues: 3270 helix: 1.42 (0.13), residues: 1716 sheet: 0.24 (0.27), residues: 378 loop : 0.77 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 256 TYR 0.010 0.001 TYR C 203 PHE 0.021 0.001 PHE F 363 TRP 0.013 0.002 TRP B 551 HIS 0.006 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (26430) covalent geometry : angle 0.54927 / 0.27 (35754) hydrogen bonds : bond 0.03387 / 2.28 ( 1246) hydrogen bonds : angle 3.87994 / 2.75 ( 3531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: A 288 LYS cc_start: 0.8947 (mttp) cc_final: 0.8290 (mmtt) REVERT: A 397 GLU cc_start: 0.8641 (tt0) cc_final: 0.8050 (tp30) REVERT: A 560 ARG cc_start: 0.8394 (mtm110) cc_final: 0.7799 (mmt180) REVERT: A 765 SER cc_start: 0.8968 (m) cc_final: 0.8763 (p) REVERT: B 366 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8705 (mt-10) REVERT: B 388 MET cc_start: 0.9266 (ptp) cc_final: 0.9065 (ptp) REVERT: B 397 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8080 (tm-30) REVERT: B 744 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7686 (ptp-170) REVERT: C 225 ARG cc_start: 0.8514 (mtm-85) cc_final: 0.8178 (ptp-170) REVERT: C 241 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8426 (mm) REVERT: C 295 LYS cc_start: 0.9280 (ttmm) cc_final: 0.9068 (ttpt) REVERT: C 358 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8218 (mtm180) REVERT: C 388 MET cc_start: 0.9063 (ptp) cc_final: 0.8543 (ptm) REVERT: C 603 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: D 283 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: D 288 LYS cc_start: 0.8968 (mttp) cc_final: 0.8211 (mmtt) REVERT: D 292 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8191 (mm-30) REVERT: D 397 GLU cc_start: 0.8601 (tt0) cc_final: 0.8097 (tp30) REVERT: D 560 ARG cc_start: 0.8385 (mtm110) cc_final: 0.7789 (mmt180) REVERT: D 765 SER cc_start: 0.8978 (m) cc_final: 0.8771 (p) REVERT: E 217 LYS cc_start: 0.8343 (mttt) cc_final: 0.8110 (tppp) REVERT: E 397 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8104 (tm-30) REVERT: E 744 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7745 (ptp-170) REVERT: F 358 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8199 (mtm180) REVERT: F 534 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: F 678 MET cc_start: 0.8594 (mmm) cc_final: 0.8324 (mmm) outliers start: 58 outliers final: 31 residues processed: 310 average time/residue: 0.7399 time to fit residues: 260.6889 Evaluate side-chains 301 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 603 GLN Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 744 ARG Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 144 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 192 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 GLN ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN F 568 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.088447 restraints weight = 37260.032| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.80 r_work: 0.2917 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 26430 Z= 0.128 Angle : 0.558 9.051 35754 Z= 0.275 Chirality : 0.042 0.178 4020 Planarity : 0.005 0.059 4668 Dihedral : 7.974 53.617 3780 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.43 % Favored : 96.39 % Rotamer: Outliers : 1.72 % Allowed : 14.84 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 3270 helix: 1.44 (0.13), residues: 1716 sheet: 0.22 (0.26), residues: 378 loop : 0.75 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 256 TYR 0.010 0.001 TYR D 244 PHE 0.017 0.001 PHE F 363 TRP 0.015 0.002 TRP A 454 HIS 0.006 0.001 HIS D 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (26430) covalent geometry : angle 0.55821 / 0.28 (35754) hydrogen bonds : bond 0.03289 / 2.21 ( 1246) hydrogen bonds : angle 3.86057 / 2.74 ( 3531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: A 288 LYS cc_start: 0.8949 (mttp) cc_final: 0.8290 (mmtt) REVERT: A 397 GLU cc_start: 0.8638 (tt0) cc_final: 0.8054 (tp30) REVERT: A 402 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8508 (mt-10) REVERT: A 560 ARG cc_start: 0.8397 (mtm110) cc_final: 0.7796 (mmt180) REVERT: B 366 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8695 (mt-10) REVERT: B 397 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 225 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8176 (ptp-170) REVERT: C 241 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8397 (mm) REVERT: C 295 LYS cc_start: 0.9273 (ttmm) cc_final: 0.8903 (ttpt) REVERT: C 358 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8246 (mtm180) REVERT: C 388 MET cc_start: 0.9151 (ptp) cc_final: 0.8658 (ptm) REVERT: C 603 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: C 668 LYS cc_start: 0.9013 (mmtm) cc_final: 0.8799 (mmtm) REVERT: C 678 MET cc_start: 0.8590 (mmm) cc_final: 0.8356 (mmm) REVERT: D 283 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: D 288 LYS cc_start: 0.8965 (mttp) cc_final: 0.8209 (mmtt) REVERT: D 292 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8212 (mm-30) REVERT: D 397 GLU cc_start: 0.8595 (tt0) cc_final: 0.8097 (tp30) REVERT: D 560 ARG cc_start: 0.8383 (mtm110) cc_final: 0.7787 (mmt180) REVERT: E 397 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8059 (tm-30) REVERT: E 744 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7699 (ptp-170) REVERT: F 358 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8190 (mtm180) REVERT: F 668 LYS cc_start: 0.9014 (mmtm) cc_final: 0.8802 (mmtm) REVERT: F 678 MET cc_start: 0.8576 (mmm) cc_final: 0.8310 (mmm) outliers start: 47 outliers final: 30 residues processed: 297 average time/residue: 0.7611 time to fit residues: 256.7051 Evaluate side-chains 292 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 603 GLN Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 744 ARG Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 194 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 67 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 303 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 77 optimal weight: 0.3980 chunk 238 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 226 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 = 0.3636 r_free = 0.3636 target = 0.122576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.088096 restraints weight = 37301.907| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.79 r_work: 0.2914 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 26430 Z= 0.133 Angle : 0.569 10.449 35754 Z= 0.279 Chirality : 0.042 0.186 4020 Planarity : 0.005 0.059 4668 Dihedral : 7.963 53.357 3780 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.46 % Favored : 96.36 % Rotamer: Outliers : 1.72 % Allowed : 15.05 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.16), residues: 3270 helix: 1.43 (0.13), residues: 1716 sheet: 0.23 (0.26), residues: 378 loop : 0.73 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 256 TYR 0.013 0.001 TYR F 244 PHE 0.015 0.001 PHE F 363 TRP 0.013 0.002 TRP B 551 HIS 0.006 0.001 HIS D 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (26430) covalent geometry : angle 0.56873 / 0.28 (35754) hydrogen bonds : bond 0.03306 / 2.23 ( 1246) hydrogen bonds : angle 3.86535 / 2.74 ( 3531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: A 288 LYS cc_start: 0.8942 (mttp) cc_final: 0.8283 (mmtt) REVERT: A 397 GLU cc_start: 0.8649 (tt0) cc_final: 0.8057 (tp30) REVERT: A 560 ARG cc_start: 0.8381 (mtm110) cc_final: 0.7779 (mmt180) REVERT: B 366 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8735 (mt-10) REVERT: B 397 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 744 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7665 (ptp-170) REVERT: C 225 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8151 (ptp-170) REVERT: C 241 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8415 (mm) REVERT: C 295 LYS cc_start: 0.9270 (ttmm) cc_final: 0.8899 (ttpt) REVERT: C 358 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8202 (mtm180) REVERT: C 388 MET cc_start: 0.9149 (ptp) cc_final: 0.8667 (ptm) REVERT: C 603 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8214 (mt0) REVERT: C 668 LYS cc_start: 0.9014 (mmtm) cc_final: 0.8799 (mmtm) REVERT: C 678 MET cc_start: 0.8594 (mmm) cc_final: 0.8355 (mmm) REVERT: D 283 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: D 288 LYS cc_start: 0.8954 (mttp) cc_final: 0.8194 (mmtt) REVERT: D 292 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8207 (mm-30) REVERT: D 397 GLU cc_start: 0.8591 (tt0) cc_final: 0.8092 (tp30) REVERT: D 560 ARG cc_start: 0.8385 (mtm110) cc_final: 0.7783 (mmt180) REVERT: E 397 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8056 (tm-30) REVERT: F 358 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8183 (mtm180) REVERT: F 668 LYS cc_start: 0.9017 (mmtm) cc_final: 0.8813 (mmtm) REVERT: F 678 MET cc_start: 0.8570 (mmm) cc_final: 0.8310 (mmm) outliers start: 47 outliers final: 33 residues processed: 289 average time/residue: 0.7592 time to fit residues: 250.0005 Evaluate side-chains 295 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 744 ARG Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 603 GLN Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 218 optimal weight: 7.9990 chunk 307 optimal weight: 0.0980 chunk 241 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 240 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 319 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 568 GLN ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.082827 restraints weight = 37316.282| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.79 r_work: 0.2815 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 26430 Z= 0.291 Angle : 0.692 11.013 35754 Z= 0.343 Chirality : 0.048 0.164 4020 Planarity : 0.006 0.093 4668 Dihedral : 9.073 59.975 3780 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.02 % Rotamer: Outliers : 1.79 % Allowed : 14.98 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3270 helix: 1.01 (0.13), residues: 1752 sheet: 0.20 (0.26), residues: 396 loop : 0.63 (0.21), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 766 TYR 0.014 0.002 TYR F 244 PHE 0.018 0.002 PHE F 758 TRP 0.022 0.003 TRP E 551 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.29 (26430) covalent geometry : angle 0.69198 / 0.34 (35754) hydrogen bonds : bond 0.04344 / 2.92 ( 1246) hydrogen bonds : angle 4.05297 / 2.87 ( 3531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8587.19 seconds wall clock time: 146 minutes 51.05 seconds (8811.05 seconds total)