Starting phenix.real_space_refine on Sun Jul 5 08:40:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y07_72387/07_2026/9y07_72387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y07_72387/07_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_72387/07_2026/9y07_72387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y07_72387/07_2026/9y07_72387.map" model { file = "/net/cci-nas-00/data/ceres_data/9y07_72387/07_2026/9y07_72387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y07_72387/07_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-6108/lib/python3.11/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: 5.22, per 1000 atoms: 0.20 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: 1.87 Conformation dependent library (CDL) restraints added in 943.0 milliseconds 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: 0.70 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: 4.97 Time building geometry restraints manager: 2.44 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=" O3B AGS E 902 " pdb=" PB AGS E 902 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" O3B AGS B 902 " pdb=" PB AGS B 902 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" O3B AGS E 901 " pdb=" PB AGS E 901 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" O3B AGS D 901 " pdb=" PB AGS D 901 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" O3B AGS F 902 " pdb=" PB AGS F 902 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.12e+01 ... (remaining 26425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 34999 2.02 - 4.05: 558 4.05 - 6.07: 105 6.07 - 8.09: 48 8.09 - 10.11: 44 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 - 34.71: 16200 34.71 - 69.41: 262 69.41 - 104.11: 68 104.11 - 138.82: 18 138.82 - 173.52: 18 Dihedral angle restraints: 16566 sinusoidal: 7128 harmonic: 9438 Sorted by residual: dihedral pdb=" O2B AGS C 902 " pdb=" O3B AGS C 902 " pdb=" PB AGS C 902 " pdb=" PG AGS C 902 " ideal model delta sinusoidal sigma weight residual 7.37 -179.11 -173.52 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS F 902 " pdb=" O3B AGS F 902 " pdb=" PB AGS F 902 " pdb=" PG AGS F 902 " ideal model delta sinusoidal sigma weight residual 7.37 179.65 -172.28 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2B AGS A 902 " pdb=" O3B AGS A 902 " pdb=" PB AGS A 902 " pdb=" PG AGS A 902 " ideal model delta sinusoidal sigma weight residual 7.37 179.27 -171.90 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 16563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3187 0.054 - 0.107: 695 0.107 - 0.161: 102 0.161 - 0.215: 0 0.215 - 0.268: 12 Chirality restraints: 3996 Sorted by residual: chirality pdb=" C3' AGS E 901 " pdb=" C2' AGS E 901 " pdb=" C4' AGS E 901 " pdb=" O3' AGS E 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' AGS D 901 " pdb=" C2' AGS D 901 " pdb=" C4' AGS D 901 " pdb=" O3' AGS D 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' AGS B 901 " pdb=" C2' AGS B 901 " pdb=" C4' AGS B 901 " pdb=" O3' AGS B 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3993 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: 0.01 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: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.670 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.005 0.094 26430 Z= 0.220 Angle : 0.742 10.114 35754 Z= 0.349 Chirality : 0.046 0.268 3996 Planarity : 0.005 0.064 4668 Dihedral : 16.869 173.525 10446 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 0.00451 / 0.22 (26430) covalent geometry : angle 0.74197 / 0.35 (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 : 1.033 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: 0.7134 time to fit residues: 464.3532 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 : 0.686 ------------------------------------------------------------------------------- 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: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3670 r_free = 0.3670 target = 0.125791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.090339 restraints weight = 37143.883| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.80 r_work: 0.2943 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26430 Z= 0.171 Angle : 0.599 7.704 35754 Z= 0.301 Chirality : 0.044 0.158 3996 Planarity : 0.005 0.063 4668 Dihedral : 18.281 175.533 4005 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.64 % Favored : 96.15 % Rotamer: Outliers : 2.20 % Allowed : 10.15 % 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: 1.16 (0.16), residues: 3270 helix: 1.05 (0.13), residues: 1704 sheet: 0.38 (0.26), residues: 396 loop : 0.76 (0.21), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 359 TYR 0.019 0.002 TYR E 203 PHE 0.011 0.001 PHE A 563 TRP 0.025 0.003 TRP C 551 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (26430) covalent geometry : angle 0.59883 / 0.30 (35754) hydrogen bonds : bond 0.04272 / 2.86 ( 1246) hydrogen bonds : angle 4.29449 / 3.05 ( 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 368 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: A 305 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: A 397 GLU cc_start: 0.8605 (tt0) cc_final: 0.8177 (tp30) REVERT: A 454 TRP cc_start: 0.8994 (t-100) cc_final: 0.8715 (t-100) REVERT: A 560 ARG cc_start: 0.8415 (mtm110) cc_final: 0.7821 (mmt180) REVERT: A 611 MET cc_start: 0.7458 (mtm) cc_final: 0.7164 (mtt) REVERT: A 668 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8696 (mmpt) REVERT: B 288 LYS cc_start: 0.8712 (mptt) cc_final: 0.8289 (mmtt) REVERT: B 366 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: B 388 MET cc_start: 0.9011 (ptp) cc_final: 0.8712 (ptm) REVERT: C 288 LYS cc_start: 0.8606 (mptt) cc_final: 0.8248 (mmtt) REVERT: C 701 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: D 283 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7812 (mm-30) REVERT: D 292 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 305 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: D 397 GLU cc_start: 0.8617 (tt0) cc_final: 0.8110 (tp30) REVERT: D 402 GLU cc_start: 0.8747 (tt0) cc_final: 0.8331 (mt-10) REVERT: D 454 TRP cc_start: 0.9000 (t-100) cc_final: 0.8723 (t-100) REVERT: D 560 ARG cc_start: 0.8428 (mtm110) cc_final: 0.7828 (mmt180) REVERT: D 611 MET cc_start: 0.7468 (mtm) cc_final: 0.7174 (mtt) REVERT: E 288 LYS cc_start: 0.8652 (mptt) cc_final: 0.8241 (mmtt) REVERT: E 366 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: E 388 MET cc_start: 0.8960 (ptp) cc_final: 0.8734 (ptm) REVERT: F 288 LYS cc_start: 0.8563 (mptt) cc_final: 0.8216 (mmtt) REVERT: F 701 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8210 (tt0) outliers start: 60 outliers final: 20 residues processed: 341 average time/residue: 0.6621 time to fit residues: 258.0743 Evaluate side-chains 304 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 305 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 388 MET 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 305 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 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 388 MET Chi-restraints excluded: chain F residue 474 VAL 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: 0.1980 chunk 68 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 307 optimal weight: 0.0020 chunk 165 optimal weight: 0.2980 chunk 168 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 250 optimal weight: 0.6980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3681 r_free = 0.3681 target = 0.126438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.091574 restraints weight = 37156.071| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.78 r_work: 0.2967 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26430 Z= 0.123 Angle : 0.552 8.016 35754 Z= 0.272 Chirality : 0.043 0.171 3996 Planarity : 0.005 0.060 4668 Dihedral : 17.580 176.165 3996 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % Rotamer: Outliers : 2.01 % Allowed : 11.21 % Favored : 86.78 % 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: 1.33 (0.16), residues: 3270 helix: 1.22 (0.13), residues: 1704 sheet: 0.39 (0.27), residues: 378 loop : 0.81 (0.21), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 256 TYR 0.020 0.001 TYR E 203 PHE 0.009 0.001 PHE B 758 TRP 0.015 0.002 TRP B 551 HIS 0.010 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (26430) covalent geometry : angle 0.55161 / 0.27 (35754) hydrogen bonds : bond 0.03676 / 2.46 ( 1246) hydrogen bonds : angle 4.09604 / 2.91 ( 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 353 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 298 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: A 397 GLU cc_start: 0.8615 (tt0) cc_final: 0.8136 (tp30) REVERT: A 454 TRP cc_start: 0.8967 (t-100) cc_final: 0.8655 (t-100) REVERT: A 560 ARG cc_start: 0.8400 (mtm110) cc_final: 0.7781 (mmt180) REVERT: A 611 MET cc_start: 0.7388 (mtm) cc_final: 0.7162 (mtt) REVERT: B 288 LYS cc_start: 0.8740 (mptt) cc_final: 0.8329 (mmtt) REVERT: B 388 MET cc_start: 0.9107 (ptp) cc_final: 0.8813 (ptm) REVERT: C 288 LYS cc_start: 0.8637 (mptt) cc_final: 0.8257 (mmtt) REVERT: D 283 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: D 292 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8221 (mm-30) REVERT: D 397 GLU cc_start: 0.8611 (tt0) cc_final: 0.8146 (tp30) REVERT: D 402 GLU cc_start: 0.8798 (tt0) cc_final: 0.8487 (mt-10) REVERT: D 454 TRP cc_start: 0.8962 (t-100) cc_final: 0.8658 (t-100) REVERT: D 560 ARG cc_start: 0.8381 (mtm110) cc_final: 0.7795 (mmt180) REVERT: E 283 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: E 288 LYS cc_start: 0.8737 (mptt) cc_final: 0.8329 (mmtt) REVERT: E 366 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8650 (mt-10) REVERT: E 388 MET cc_start: 0.9040 (ptp) cc_final: 0.8763 (ptm) REVERT: E 508 MET cc_start: 0.8129 (tmt) cc_final: 0.7919 (ppp) REVERT: F 288 LYS cc_start: 0.8624 (mptt) cc_final: 0.8245 (mmtt) outliers start: 55 outliers final: 20 residues processed: 329 average time/residue: 0.6283 time to fit residues: 236.9859 Evaluate side-chains 298 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 474 VAL Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL 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 269 ILE Chi-restraints excluded: chain E residue 283 GLU 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 332 MET Chi-restraints excluded: chain F residue 358 ARG 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: 0.5980 chunk 93 optimal weight: 0.0020 chunk 121 optimal weight: 0.9980 chunk 297 optimal weight: 0.6980 chunk 244 optimal weight: 0.0270 chunk 266 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.3246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 285 ASN E 226 HIS E 285 ASN ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.091996 restraints weight = 37107.961| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.79 r_work: 0.2975 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26430 Z= 0.111 Angle : 0.521 6.795 35754 Z= 0.259 Chirality : 0.042 0.157 3996 Planarity : 0.005 0.056 4668 Dihedral : 17.282 176.431 3996 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.27 % Favored : 96.51 % Rotamer: Outliers : 1.90 % Allowed : 12.42 % Favored : 85.68 % 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: 1.37 (0.13), residues: 1710 sheet: 0.31 (0.27), residues: 378 loop : 0.86 (0.21), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.015 0.001 TYR B 203 PHE 0.008 0.001 PHE B 758 TRP 0.013 0.001 TRP B 551 HIS 0.014 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (26430) covalent geometry : angle 0.52108 / 0.26 (35754) hydrogen bonds : bond 0.03340 / 2.24 ( 1246) hydrogen bonds : angle 3.97162 / 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 364 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 312 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: A 397 GLU cc_start: 0.8602 (tt0) cc_final: 0.8165 (tp30) REVERT: A 454 TRP cc_start: 0.8949 (t-100) cc_final: 0.8631 (t-100) REVERT: A 560 ARG cc_start: 0.8393 (mtm110) cc_final: 0.7787 (mmt180) REVERT: A 765 SER cc_start: 0.9018 (m) cc_final: 0.8800 (p) REVERT: B 226 HIS cc_start: 0.7856 (m-70) cc_final: 0.7556 (m-70) REVERT: B 288 LYS cc_start: 0.8798 (mptt) cc_final: 0.8375 (mmtt) REVERT: B 366 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8657 (mt-10) REVERT: B 388 MET cc_start: 0.9127 (ptp) cc_final: 0.8912 (ptp) REVERT: C 225 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.8160 (ptp-170) REVERT: C 288 LYS cc_start: 0.8684 (mptt) cc_final: 0.8321 (mmtt) REVERT: C 534 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: D 283 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: D 292 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8254 (mm-30) REVERT: D 397 GLU cc_start: 0.8587 (tt0) cc_final: 0.8103 (tp30) REVERT: D 454 TRP cc_start: 0.8959 (t-100) cc_final: 0.8640 (t-100) REVERT: D 560 ARG cc_start: 0.8381 (mtm110) cc_final: 0.7789 (mmt180) REVERT: D 765 SER cc_start: 0.9003 (m) cc_final: 0.8762 (p) REVERT: E 288 LYS cc_start: 0.8788 (mptt) cc_final: 0.8367 (mmtt) REVERT: E 366 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8656 (mt-10) REVERT: E 388 MET cc_start: 0.9084 (ptp) cc_final: 0.8880 (ptp) REVERT: E 397 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8046 (tm-30) REVERT: E 508 MET cc_start: 0.8055 (tmt) cc_final: 0.7828 (ppp) REVERT: F 288 LYS cc_start: 0.8686 (mptt) cc_final: 0.8320 (mmtt) REVERT: F 534 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8356 (tt0) outliers start: 52 outliers final: 17 residues processed: 339 average time/residue: 0.6434 time to fit residues: 250.7332 Evaluate side-chains 301 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 603 GLN 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 268 LEU 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 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 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: 2.9990 chunk 226 optimal weight: 0.7980 chunk 134 optimal weight: 0.3980 chunk 231 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 227 optimal weight: 0.0270 chunk 99 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN D 568 GLN E 568 GLN F 226 HIS F 568 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.090717 restraints weight = 37187.332| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.80 r_work: 0.2953 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26430 Z= 0.122 Angle : 0.526 6.773 35754 Z= 0.260 Chirality : 0.042 0.167 3996 Planarity : 0.005 0.055 4668 Dihedral : 17.185 175.264 3996 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.51 % Rotamer: Outliers : 2.31 % Allowed : 13.15 % Favored : 84.54 % 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: 1.52 (0.16), residues: 3270 helix: 1.43 (0.13), residues: 1716 sheet: 0.30 (0.27), residues: 378 loop : 0.85 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 256 TYR 0.010 0.001 TYR D 244 PHE 0.009 0.001 PHE B 758 TRP 0.012 0.002 TRP E 551 HIS 0.010 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (26430) covalent geometry : angle 0.52564 / 0.26 (35754) hydrogen bonds : bond 0.03359 / 2.26 ( 1246) hydrogen bonds : angle 3.89895 / 2.77 ( 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 352 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: A 288 LYS cc_start: 0.8907 (mttp) cc_final: 0.8256 (mmtt) REVERT: A 397 GLU cc_start: 0.8610 (tt0) cc_final: 0.8127 (tp30) REVERT: A 454 TRP cc_start: 0.8978 (t-100) cc_final: 0.8662 (t-100) REVERT: A 560 ARG cc_start: 0.8380 (mtm110) cc_final: 0.7776 (mmt180) REVERT: A 765 SER cc_start: 0.8952 (m) cc_final: 0.8719 (p) REVERT: B 288 LYS cc_start: 0.8779 (mptt) cc_final: 0.8421 (mmtt) REVERT: B 366 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8773 (mt-10) REVERT: C 288 LYS cc_start: 0.8729 (mptt) cc_final: 0.8377 (mmtt) REVERT: D 283 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: D 288 LYS cc_start: 0.8920 (mttp) cc_final: 0.8148 (mmtt) REVERT: D 292 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8269 (mm-30) REVERT: D 397 GLU cc_start: 0.8613 (tt0) cc_final: 0.8171 (tp30) REVERT: D 454 TRP cc_start: 0.8980 (t-100) cc_final: 0.8667 (t-100) REVERT: D 560 ARG cc_start: 0.8379 (mtm110) cc_final: 0.7792 (mmt180) REVERT: D 765 SER cc_start: 0.8952 (m) cc_final: 0.8719 (p) REVERT: E 288 LYS cc_start: 0.8775 (mptt) cc_final: 0.8382 (mmtt) REVERT: E 366 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8703 (mt-10) REVERT: E 397 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8098 (tm-30) REVERT: E 508 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7820 (ppp) REVERT: F 288 LYS cc_start: 0.8726 (mptt) cc_final: 0.8373 (mmtt) REVERT: F 388 MET cc_start: 0.8830 (ptp) cc_final: 0.8613 (ptm) REVERT: F 534 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8347 (tt0) outliers start: 63 outliers final: 29 residues processed: 325 average time/residue: 0.6613 time to fit residues: 245.8784 Evaluate side-chains 306 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 633 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 366 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain C residue 268 LEU 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 757 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 633 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 366 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 MET 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 757 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 50 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 153 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 GLN ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN D 603 GLN ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.089052 restraints weight = 37094.516| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.80 r_work: 0.2927 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26430 Z= 0.141 Angle : 0.538 10.581 35754 Z= 0.266 Chirality : 0.043 0.143 3996 Planarity : 0.005 0.055 4668 Dihedral : 17.129 174.001 3996 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.46 % Favored : 96.36 % Rotamer: Outliers : 2.71 % Allowed : 13.44 % Favored : 83.85 % 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: 1.52 (0.16), residues: 3270 helix: 1.44 (0.13), residues: 1716 sheet: 0.31 (0.27), residues: 378 loop : 0.83 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 256 TYR 0.011 0.001 TYR D 244 PHE 0.010 0.001 PHE B 758 TRP 0.013 0.002 TRP B 551 HIS 0.008 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (26430) covalent geometry : angle 0.53760 / 0.27 (35754) hydrogen bonds : bond 0.03435 / 2.31 ( 1246) hydrogen bonds : angle 3.86924 / 2.75 ( 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 357 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 283 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: A 288 LYS cc_start: 0.8919 (mttp) cc_final: 0.8276 (mmtt) REVERT: A 397 GLU cc_start: 0.8651 (tt0) cc_final: 0.8092 (tp30) REVERT: A 454 TRP cc_start: 0.9008 (t-100) cc_final: 0.8655 (t-100) REVERT: A 560 ARG cc_start: 0.8370 (mtm110) cc_final: 0.7750 (mmt180) REVERT: A 765 SER cc_start: 0.8988 (m) cc_final: 0.8744 (p) REVERT: B 288 LYS cc_start: 0.8853 (mptt) cc_final: 0.8443 (mmtt) REVERT: C 292 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8214 (mm-30) REVERT: C 295 LYS cc_start: 0.9274 (ttmm) cc_final: 0.9038 (ttpt) REVERT: C 509 THR cc_start: 0.9081 (t) cc_final: 0.8818 (t) REVERT: C 534 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: C 611 MET cc_start: 0.7464 (mtp) cc_final: 0.7173 (mmt) REVERT: D 283 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: D 288 LYS cc_start: 0.8956 (mttp) cc_final: 0.8187 (mmtt) REVERT: D 292 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8260 (mm-30) REVERT: D 397 GLU cc_start: 0.8623 (tt0) cc_final: 0.8104 (tp30) REVERT: D 454 TRP cc_start: 0.9011 (t-100) cc_final: 0.8657 (t-100) REVERT: D 560 ARG cc_start: 0.8383 (mtm110) cc_final: 0.7783 (mmt180) REVERT: D 765 SER cc_start: 0.8964 (m) cc_final: 0.8718 (p) REVERT: E 288 LYS cc_start: 0.8806 (mptt) cc_final: 0.8395 (mmtt) REVERT: E 366 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8744 (mt-10) REVERT: E 397 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8124 (tm-30) REVERT: E 508 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7778 (ppp) REVERT: F 509 THR cc_start: 0.9093 (t) cc_final: 0.8824 (t) REVERT: F 534 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: F 611 MET cc_start: 0.7484 (mtp) cc_final: 0.7177 (mmt) outliers start: 74 outliers final: 32 residues processed: 330 average time/residue: 0.6557 time to fit residues: 248.8004 Evaluate side-chains 308 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE 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 268 LEU 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 757 MET Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 611 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 E residue 508 MET 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 534 GLU Chi-restraints excluded: chain F residue 672 LEU 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: 0.6980 chunk 243 optimal weight: 0.0020 chunk 275 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3654 r_free = 0.3654 target = 0.124203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.089627 restraints weight = 37180.016| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.79 r_work: 0.2934 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2880 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= 0.124 Angle : 0.537 8.343 35754 Z= 0.265 Chirality : 0.042 0.185 3996 Planarity : 0.005 0.056 4668 Dihedral : 17.126 174.857 3996 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.51 % Rotamer: Outliers : 2.20 % Allowed : 14.65 % Favored : 83.15 % 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: 1.52 (0.16), residues: 3270 helix: 1.48 (0.13), residues: 1716 sheet: 0.26 (0.27), residues: 378 loop : 0.77 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.010 0.001 TYR D 244 PHE 0.010 0.001 PHE F 674 TRP 0.012 0.002 TRP E 551 HIS 0.007 0.001 HIS D 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (26430) covalent geometry : angle 0.53681 / 0.26 (35754) hydrogen bonds : bond 0.03294 / 2.22 ( 1246) hydrogen bonds : angle 3.85521 / 2.73 ( 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 335 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: A 288 LYS cc_start: 0.8915 (mttp) cc_final: 0.8260 (mmtt) REVERT: A 397 GLU cc_start: 0.8635 (tt0) cc_final: 0.8132 (tp30) REVERT: A 454 TRP cc_start: 0.8998 (t-100) cc_final: 0.8651 (t-100) REVERT: A 560 ARG cc_start: 0.8353 (mtm110) cc_final: 0.7776 (mmt180) REVERT: A 765 SER cc_start: 0.8962 (m) cc_final: 0.8753 (p) REVERT: B 288 LYS cc_start: 0.8852 (mptt) cc_final: 0.8440 (mmtt) REVERT: C 292 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8209 (mm-30) REVERT: C 295 LYS cc_start: 0.9269 (ttmm) cc_final: 0.9043 (ttpt) REVERT: C 509 THR cc_start: 0.9063 (t) cc_final: 0.8861 (t) REVERT: C 603 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: C 611 MET cc_start: 0.7484 (mtp) cc_final: 0.7248 (mmt) REVERT: C 668 LYS cc_start: 0.9107 (mmtm) cc_final: 0.8904 (mmtm) REVERT: C 678 MET cc_start: 0.8599 (mmp) cc_final: 0.8293 (mmm) REVERT: D 283 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: D 288 LYS cc_start: 0.8947 (mttp) cc_final: 0.8184 (mmtt) REVERT: D 292 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8198 (mm-30) REVERT: D 397 GLU cc_start: 0.8604 (tt0) cc_final: 0.8084 (tp30) REVERT: D 454 TRP cc_start: 0.8998 (t-100) cc_final: 0.8656 (t-100) REVERT: D 560 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7785 (mmt180) REVERT: D 765 SER cc_start: 0.8976 (m) cc_final: 0.8756 (p) REVERT: E 288 LYS cc_start: 0.8819 (mptt) cc_final: 0.8407 (mmtt) REVERT: E 366 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8735 (mt-10) REVERT: E 397 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8102 (tm-30) REVERT: E 508 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7780 (ppp) REVERT: F 611 MET cc_start: 0.7482 (mtp) cc_final: 0.7173 (mmt) REVERT: F 678 MET cc_start: 0.8584 (mmm) cc_final: 0.8297 (mmm) REVERT: F 737 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7709 (mt-10) outliers start: 60 outliers final: 38 residues processed: 315 average time/residue: 0.6196 time to fit residues: 224.9291 Evaluate side-chains 310 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 266 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 601 ILE Chi-restraints excluded: chain A residue 603 GLN 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 474 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 301 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 603 GLN 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 320 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 611 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 E residue 508 MET Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 332 MET 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 672 LEU Chi-restraints excluded: chain F residue 737 GLU 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: 0.7980 chunk 80 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 152 optimal weight: 0.0980 chunk 105 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3648 r_free = 0.3648 target = 0.123620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.088890 restraints weight = 37196.325| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.81 r_work: 0.2924 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26430 Z= 0.128 Angle : 0.537 8.216 35754 Z= 0.265 Chirality : 0.042 0.144 3996 Planarity : 0.005 0.055 4668 Dihedral : 17.058 175.879 3996 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.45 % Rotamer: Outliers : 2.09 % Allowed : 14.65 % Favored : 83.26 % 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: 1.52 (0.16), residues: 3270 helix: 1.48 (0.13), residues: 1716 sheet: 0.28 (0.27), residues: 378 loop : 0.78 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 256 TYR 0.012 0.001 TYR B 203 PHE 0.010 0.001 PHE B 758 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 0.00303 / 0.13 (26430) covalent geometry : angle 0.53726 / 0.26 (35754) hydrogen bonds : bond 0.03298 / 2.22 ( 1246) hydrogen bonds : angle 3.83412 / 2.72 ( 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 336 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: A 288 LYS cc_start: 0.8923 (mttp) cc_final: 0.8264 (mmtt) REVERT: A 397 GLU cc_start: 0.8650 (tt0) cc_final: 0.8084 (tp30) REVERT: A 454 TRP cc_start: 0.9009 (t-100) cc_final: 0.8657 (t-100) REVERT: A 560 ARG cc_start: 0.8366 (mtm110) cc_final: 0.7771 (mmt180) REVERT: A 765 SER cc_start: 0.8952 (m) cc_final: 0.8748 (p) REVERT: B 288 LYS cc_start: 0.8872 (mptt) cc_final: 0.8439 (mmtt) REVERT: C 241 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8412 (mm) REVERT: C 292 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8228 (mm-30) REVERT: C 295 LYS cc_start: 0.9275 (ttmm) cc_final: 0.9057 (ttpt) REVERT: C 388 MET cc_start: 0.8931 (ptp) cc_final: 0.8504 (ptm) REVERT: C 534 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: C 603 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: C 668 LYS cc_start: 0.9092 (mmtm) cc_final: 0.8876 (mmtm) REVERT: C 678 MET cc_start: 0.8618 (mmp) cc_final: 0.8313 (mmm) REVERT: D 283 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: D 288 LYS cc_start: 0.8952 (mttp) cc_final: 0.8188 (mmtt) REVERT: D 292 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8208 (mm-30) REVERT: D 397 GLU cc_start: 0.8614 (tt0) cc_final: 0.8046 (tp30) REVERT: D 454 TRP cc_start: 0.9008 (t-100) cc_final: 0.8658 (t-100) REVERT: D 560 ARG cc_start: 0.8377 (mtm110) cc_final: 0.7760 (mmt180) REVERT: E 397 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8078 (tm-30) REVERT: E 508 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7789 (ppp) REVERT: F 241 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8399 (mm) REVERT: F 388 MET cc_start: 0.8920 (ptp) cc_final: 0.8500 (ptp) REVERT: F 678 MET cc_start: 0.8555 (mmm) cc_final: 0.8288 (mmm) outliers start: 57 outliers final: 36 residues processed: 316 average time/residue: 0.6280 time to fit residues: 228.5499 Evaluate side-chains 307 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 264 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 603 GLN Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 332 MET 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 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 534 GLU 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 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 611 MET 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 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 241 ILE 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 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: 0.8980 chunk 11 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 196 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3638 r_free = 0.3638 target = 0.122935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.088171 restraints weight = 37103.772| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.80 r_work: 0.2911 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26430 Z= 0.143 Angle : 0.566 8.951 35754 Z= 0.278 Chirality : 0.043 0.164 3996 Planarity : 0.005 0.061 4668 Dihedral : 17.057 175.460 3996 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.48 % Rotamer: Outliers : 1.90 % Allowed : 15.31 % Favored : 82.78 % 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: 1.49 (0.16), residues: 3270 helix: 1.45 (0.13), residues: 1716 sheet: 0.30 (0.27), residues: 378 loop : 0.74 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 256 TYR 0.014 0.001 TYR B 203 PHE 0.011 0.001 PHE B 758 TRP 0.017 0.002 TRP E 551 HIS 0.006 0.001 HIS D 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (26430) covalent geometry : angle 0.56640 / 0.28 (35754) hydrogen bonds : bond 0.03400 / 2.29 ( 1246) hydrogen bonds : angle 3.85000 / 2.73 ( 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 327 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 275 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: A 288 LYS cc_start: 0.8938 (mttp) cc_final: 0.8280 (mmtt) REVERT: A 397 GLU cc_start: 0.8660 (tt0) cc_final: 0.8084 (tp30) REVERT: A 454 TRP cc_start: 0.9026 (t-100) cc_final: 0.8697 (t-100) REVERT: A 560 ARG cc_start: 0.8368 (mtm110) cc_final: 0.7766 (mmt180) REVERT: A 765 SER cc_start: 0.8970 (m) cc_final: 0.8757 (p) REVERT: B 288 LYS cc_start: 0.8895 (mptt) cc_final: 0.8460 (mmtt) REVERT: C 241 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8419 (mm) REVERT: C 534 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: C 603 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: C 668 LYS cc_start: 0.9058 (mmtm) cc_final: 0.8834 (mmtm) REVERT: C 678 MET cc_start: 0.8610 (mmp) cc_final: 0.8292 (mmm) REVERT: D 283 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: D 288 LYS cc_start: 0.8960 (mttp) cc_final: 0.8203 (mmtt) REVERT: D 292 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8202 (mm-30) REVERT: D 397 GLU cc_start: 0.8638 (tt0) cc_final: 0.8027 (tp30) REVERT: D 454 TRP cc_start: 0.9024 (t-100) cc_final: 0.8693 (t-100) REVERT: D 560 ARG cc_start: 0.8381 (mtm110) cc_final: 0.7795 (mmt180) REVERT: E 397 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8077 (tm-30) REVERT: E 508 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7786 (ppp) REVERT: F 241 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8422 (mm) REVERT: F 678 MET cc_start: 0.8562 (mmm) cc_final: 0.8310 (mmm) outliers start: 52 outliers final: 33 residues processed: 308 average time/residue: 0.6440 time to fit residues: 228.4054 Evaluate side-chains 306 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 611 MET Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 332 MET 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 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 534 GLU 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 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 611 MET 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 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 241 ILE 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 509 THR Chi-restraints excluded: chain F residue 672 LEU 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: 0.7980 chunk 244 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 0.0770 chunk 67 optimal weight: 2.9990 chunk 302 optimal weight: 0.4980 chunk 303 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3612 r_free = 0.3612 target = 0.120999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.085982 restraints weight = 37100.211| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.81 r_work: 0.2874 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26430 Z= 0.185 Angle : 0.605 10.878 35754 Z= 0.296 Chirality : 0.044 0.147 3996 Planarity : 0.005 0.078 4668 Dihedral : 17.015 172.067 3996 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.55 % Favored : 96.27 % Rotamer: Outliers : 1.83 % Allowed : 15.64 % Favored : 82.53 % 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: 1.37 (0.13), residues: 1716 sheet: 0.35 (0.27), residues: 378 loop : 0.68 (0.21), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 256 TYR 0.015 0.002 TYR C 203 PHE 0.013 0.002 PHE B 758 TRP 0.017 0.002 TRP B 551 HIS 0.005 0.001 HIS D 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (26430) covalent geometry : angle 0.60513 / 0.30 (35754) hydrogen bonds : bond 0.03649 / 2.46 ( 1246) hydrogen bonds : angle 3.89882 / 2.76 ( 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 319 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 288 LYS cc_start: 0.8891 (mttp) cc_final: 0.8314 (mmtt) REVERT: A 397 GLU cc_start: 0.8660 (tt0) cc_final: 0.8048 (tp30) REVERT: A 560 ARG cc_start: 0.8383 (mtm110) cc_final: 0.7798 (mmt180) REVERT: A 765 SER cc_start: 0.8967 (m) cc_final: 0.8671 (p) REVERT: C 241 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8494 (mm) REVERT: C 358 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8263 (mtm180) REVERT: C 534 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: C 603 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: C 668 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8858 (mmtm) REVERT: C 678 MET cc_start: 0.8630 (mmp) cc_final: 0.8288 (mmm) REVERT: D 288 LYS cc_start: 0.8921 (mttp) cc_final: 0.8237 (mmtt) REVERT: D 292 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8206 (mm-30) REVERT: D 397 GLU cc_start: 0.8677 (tt0) cc_final: 0.8055 (tp30) REVERT: D 560 ARG cc_start: 0.8406 (mtm110) cc_final: 0.7816 (mmt180) REVERT: E 397 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8078 (tm-30) REVERT: E 508 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7792 (ppp) REVERT: F 241 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8484 (mm) REVERT: F 358 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8195 (mtm180) REVERT: F 678 MET cc_start: 0.8611 (mmm) cc_final: 0.8357 (mmm) outliers start: 50 outliers final: 28 residues processed: 300 average time/residue: 0.6114 time to fit residues: 211.2041 Evaluate side-chains 291 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 611 MET 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 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 468 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 534 GLU 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 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 611 MET 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 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain F residue 241 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 509 THR 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: 0.6980 chunk 307 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 240 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3627 r_free = 0.3627 target = 0.122121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.087408 restraints weight = 36896.081| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.78 r_work: 0.2898 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 26430 Z= 0.141 Angle : 0.576 11.353 35754 Z= 0.281 Chirality : 0.043 0.169 3996 Planarity : 0.005 0.072 4668 Dihedral : 17.070 171.921 3996 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.48 % Rotamer: Outliers : 1.58 % Allowed : 16.37 % Favored : 82.05 % 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: 1.41 (0.16), residues: 3270 helix: 1.40 (0.13), residues: 1710 sheet: 0.27 (0.27), residues: 378 loop : 0.68 (0.21), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 256 TYR 0.012 0.001 TYR C 203 PHE 0.011 0.001 PHE B 758 TRP 0.015 0.002 TRP E 551 HIS 0.006 0.001 HIS A 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (26430) covalent geometry : angle 0.57550 / 0.28 (35754) hydrogen bonds : bond 0.03395 / 2.29 ( 1246) hydrogen bonds : angle 3.90382 / 2.77 ( 3531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7767.57 seconds wall clock time: 145 minutes 14.20 seconds (8714.20 seconds total)