Starting phenix.real_space_refine on Tue Aug 26 12:29:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcq_28990/08_2025/8fcq_28990.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcq_28990/08_2025/8fcq_28990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fcq_28990/08_2025/8fcq_28990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcq_28990/08_2025/8fcq_28990.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcq_28990/08_2025/8fcq_28990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcq_28990/08_2025/8fcq_28990.cif" } resolution = 3.93 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 189 5.16 5 C 23162 2.51 5 N 6477 2.21 5 O 7052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36904 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "F" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "E" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "C" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "G" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2740 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.69, per 1000 atoms: 0.29 Number of scatterers: 36904 At special positions: 0 Unit cell: (182.646, 190.152, 117.594, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 189 16.00 P 24 15.00 O 7052 8.00 N 6477 7.00 C 23162 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: 3.31 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 40 sheets defined 52.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.587A 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 233 removed outlier: 4.026A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.830A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.861A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.156A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.642A pdb=" N ALA B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 612 through 615 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 748 through 762 Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 5.043A 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 233 removed outlier: 4.217A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 427 through 430 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.650A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.656A 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 543 through 553 Processing helix chain 'A' and resid 557 through 570 removed outlier: 4.168A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.530A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (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 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.509A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.027A 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 227 through 232 Processing helix chain 'F' and resid 250 through 263 removed outlier: 3.580A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.886A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 431 removed outlier: 4.476A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.694A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.512A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.114A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 609 Processing helix chain 'F' and resid 610 through 611 No H-bonds generated for 'chain 'F' and resid 610 through 611' Processing helix chain 'F' and resid 612 through 615 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.772A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (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 671 through 679 Processing helix chain 'F' and resid 683 through 707 Processing helix chain 'F' and resid 732 through 740 Processing helix chain 'F' and resid 748 through 763 Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.716A 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 233 removed outlier: 3.949A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 removed outlier: 3.535A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.533A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.835A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.769A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.931A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 384 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 431 removed outlier: 3.676A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP E 431 " --> pdb=" O MET E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.600A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.512A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.848A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 612 through 615 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 705 Processing helix chain 'E' and resid 732 through 740 Processing helix chain 'E' and resid 748 through 762 removed outlier: 4.200A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.698A 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 233 removed outlier: 4.107A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.616A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 318 through 334 Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 354 through 359 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 431 removed outlier: 3.672A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP D 431 " --> pdb=" O MET D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.203A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 612 through 615 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 705 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 762 removed outlier: 3.871A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.758A 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 233 removed outlier: 4.121A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.758A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 334 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 431 removed outlier: 4.283A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.915A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 706 removed outlier: 3.585A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'G' and resid 50 through 68 Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.721A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 165 removed outlier: 3.924A pdb=" N ASN G 165 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 188 Processing helix chain 'G' and resid 191 through 194 Processing helix chain 'G' and resid 201 through 208 removed outlier: 3.934A pdb=" N GLU G 206 " --> pdb=" O LYS G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 221 Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 250 through 262 Processing helix chain 'G' and resid 281 through 285 Processing helix chain 'G' and resid 289 through 294 Processing helix chain 'G' and resid 296 through 316 Processing helix chain 'G' and resid 319 through 328 removed outlier: 3.953A pdb=" N GLU G 326 " --> pdb=" O MET G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 358 through 370 removed outlier: 3.913A pdb=" N VAL G 362 " --> pdb=" O ARG G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 421 removed outlier: 4.230A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 435 Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.895A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 156 removed outlier: 5.545A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.186A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.405A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 25 through 29 removed outlier: 7.207A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.637A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.692A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.074A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 389 through 390 removed outlier: 7.277A pdb=" N LYS A 389 " --> pdb=" O VAL A 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.500A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 25 through 29 removed outlier: 7.394A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 109 through 110 removed outlier: 6.739A pdb=" N LYS F 109 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.594A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AB9, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.324A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.592A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 25 through 30 removed outlier: 7.802A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LYS E 81 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER E 42 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP E 74 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU E 41 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 151 through 156 removed outlier: 6.984A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AC5, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.753A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.196A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.475A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 25 through 30 removed outlier: 7.430A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 151 through 156 removed outlier: 5.393A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AD2, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AD3, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.211A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.469A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 25 through 29 removed outlier: 7.441A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.820A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AD8, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AD9, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.109A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.374A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AE3, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AE4, first strand: chain 'G' and resid 386 through 387 removed outlier: 4.407A pdb=" N LEU G 379 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ALA G 404 " --> pdb=" O TYR G 336 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU G 338 " --> pdb=" O ALA G 404 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU G 406 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG G 340 " --> pdb=" O LEU G 406 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N PHE G 408 " --> pdb=" O ARG G 340 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG G 342 " --> pdb=" O PHE G 408 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N TRP G 410 " --> pdb=" O ARG G 342 " (cutoff:3.500A) 1712 hydrogen bonds defined for protein. 4803 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: 10.37 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7661 1.33 - 1.45: 7790 1.45 - 1.57: 21739 1.57 - 1.69: 36 1.69 - 1.81: 301 Bond restraints: 37527 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 37522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 49745 2.49 - 4.97: 873 4.97 - 7.46: 89 7.46 - 9.94: 30 9.94 - 12.43: 9 Bond angle restraints: 50746 Sorted by residual: angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 113.28 123.95 -10.67 1.22e+00 6.72e-01 7.64e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 111.87 122.42 -10.55 1.41e+00 5.03e-01 5.60e+01 angle pdb=" CA GLY D 591 " pdb=" C GLY D 591 " pdb=" O GLY D 591 " ideal model delta sigma weight residual 122.23 118.56 3.67 6.90e-01 2.10e+00 2.83e+01 angle pdb=" N LYS G 333 " pdb=" CA LYS G 333 " pdb=" C LYS G 333 " ideal model delta sigma weight residual 112.23 118.42 -6.19 1.26e+00 6.30e-01 2.41e+01 angle pdb=" C LEU A 429 " pdb=" N ILE A 430 " pdb=" CA ILE A 430 " ideal model delta sigma weight residual 122.66 127.29 -4.63 9.70e-01 1.06e+00 2.28e+01 ... (remaining 50741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 22929 35.37 - 70.75: 242 70.75 - 106.12: 45 106.12 - 141.49: 9 141.49 - 176.87: 8 Dihedral angle restraints: 23233 sinusoidal: 9775 harmonic: 13458 Sorted by residual: dihedral pdb=" O1B ADP D 901 " pdb=" O3A ADP D 901 " pdb=" PB ADP D 901 " pdb=" PA ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 116.87 -176.87 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual 300.00 123.88 176.11 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 115.25 -175.25 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 23230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4074 0.047 - 0.094: 990 0.094 - 0.142: 463 0.142 - 0.189: 184 0.189 - 0.236: 12 Chirality restraints: 5723 Sorted by residual: chirality pdb=" CA ILE A 590 " pdb=" N ILE A 590 " pdb=" C ILE A 590 " pdb=" CB ILE A 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE E 590 " pdb=" N ILE E 590 " pdb=" C ILE E 590 " pdb=" CB ILE E 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE F 590 " pdb=" N ILE F 590 " pdb=" C ILE F 590 " pdb=" CB ILE F 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 5720 not shown) Planarity restraints: 6650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C GLU G 254 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU G 254 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG G 255 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 534 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C GLU F 534 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU F 534 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS F 535 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 360 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C PHE C 360 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE C 360 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY C 361 " 0.013 2.00e-02 2.50e+03 ... (remaining 6647 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 13625 2.89 - 3.39: 35881 3.39 - 3.89: 63456 3.89 - 4.40: 72768 4.40 - 4.90: 118287 Nonbonded interactions: 304017 Sorted by model distance: nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.387 3.120 nonbonded pdb=" OD2 ASP C 368 " pdb=" NZ LYS C 565 " model vdw 2.401 3.120 nonbonded pdb=" OD2 ASP D 368 " pdb=" NZ LYS D 565 " model vdw 2.408 3.120 nonbonded pdb=" NZ LYS C 62 " pdb=" OD2 ASP C 98 " model vdw 2.413 3.120 nonbonded pdb=" OE2 GLU E 30 " pdb=" NZ LYS E 217 " model vdw 2.424 3.120 ... (remaining 304012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 39.890 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.111 37527 Z= 0.609 Angle : 0.848 12.426 50746 Z= 0.520 Chirality : 0.058 0.236 5723 Planarity : 0.004 0.033 6650 Dihedral : 12.291 176.869 14503 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.70 % Favored : 98.23 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 0.31 (0.11), residues: 4639 helix: -0.25 (0.10), residues: 2069 sheet: 0.68 (0.17), residues: 778 loop : 0.89 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 424 TYR 0.001 0.000 TYR D 173 PHE 0.001 0.000 PHE C 52 TRP 0.001 0.000 TRP F 476 HIS 0.001 0.000 HIS D 406 Details of bonding type rmsd covalent geometry : bond 0.01076 (37527) covalent geometry : angle 0.84774 (50746) hydrogen bonds : bond 0.20841 ( 1712) hydrogen bonds : angle 6.59389 ( 4803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1442 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1441 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 VAL cc_start: 0.7923 (t) cc_final: 0.7379 (t) REVERT: B 244 TYR cc_start: 0.6516 (p90) cc_final: 0.6227 (p90) REVERT: B 332 MET cc_start: 0.7472 (mmm) cc_final: 0.6880 (mmm) REVERT: B 654 VAL cc_start: 0.6785 (t) cc_final: 0.6577 (t) REVERT: A 252 THR cc_start: 0.7013 (p) cc_final: 0.6533 (t) REVERT: A 302 PHE cc_start: 0.5466 (t80) cc_final: 0.4905 (t80) REVERT: F 133 VAL cc_start: 0.7334 (t) cc_final: 0.7121 (t) REVERT: F 188 PRO cc_start: 0.7304 (Cg_exo) cc_final: 0.7039 (Cg_endo) REVERT: F 198 LEU cc_start: 0.7056 (mt) cc_final: 0.6801 (mt) REVERT: F 371 ILE cc_start: 0.8324 (mt) cc_final: 0.7848 (mp) REVERT: F 430 ILE cc_start: 0.7756 (mt) cc_final: 0.7358 (mm) REVERT: E 153 LEU cc_start: 0.5934 (tp) cc_final: 0.5427 (tp) REVERT: E 244 TYR cc_start: 0.7631 (p90) cc_final: 0.7269 (p90) REVERT: E 332 MET cc_start: 0.7866 (mmm) cc_final: 0.7579 (mmm) REVERT: D 201 VAL cc_start: 0.7321 (t) cc_final: 0.7009 (t) REVERT: D 399 VAL cc_start: 0.8141 (t) cc_final: 0.7869 (t) REVERT: D 644 TYR cc_start: 0.6779 (t80) cc_final: 0.6435 (t80) REVERT: C 51 LEU cc_start: 0.5447 (pp) cc_final: 0.5224 (pp) REVERT: C 275 MET cc_start: 0.6891 (mmm) cc_final: 0.6489 (mmm) REVERT: C 363 PHE cc_start: 0.6807 (m-80) cc_final: 0.6552 (m-10) outliers start: 1 outliers final: 0 residues processed: 1442 average time/residue: 0.2739 time to fit residues: 609.3578 Evaluate side-chains 732 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 732 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS F 660 ASN E 285 ASN E 296 ASN D 226 HIS ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS C 443 ASN G 67 GLN G 148 HIS G 328 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.102781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.082403 restraints weight = 146851.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.084693 restraints weight = 85007.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.086189 restraints weight = 57888.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.087177 restraints weight = 44195.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.087751 restraints weight = 36796.406| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 37527 Z= 0.185 Angle : 0.760 11.391 50746 Z= 0.376 Chirality : 0.047 0.239 5723 Planarity : 0.005 0.056 6650 Dihedral : 9.935 173.752 5191 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.29 % Favored : 98.69 % Rotamer: Outliers : 2.44 % Allowed : 12.11 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 1.18 (0.12), residues: 4639 helix: 0.85 (0.11), residues: 2087 sheet: 0.80 (0.17), residues: 770 loop : 0.98 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 635 TYR 0.028 0.002 TYR C 495 PHE 0.030 0.002 PHE E 139 TRP 0.028 0.002 TRP A 454 HIS 0.010 0.001 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00408 (37527) covalent geometry : angle 0.76009 (50746) hydrogen bonds : bond 0.05627 ( 1712) hydrogen bonds : angle 4.87191 ( 4803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 779 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.4564 (m-40) cc_final: 0.4216 (t0) REVERT: B 268 LEU cc_start: 0.9153 (tt) cc_final: 0.8943 (tt) REVERT: B 454 TRP cc_start: 0.8443 (t60) cc_final: 0.7539 (t-100) REVERT: B 495 TYR cc_start: 0.8192 (m-10) cc_final: 0.7752 (m-80) REVERT: B 527 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9122 (mm) REVERT: B 546 GLU cc_start: 0.8712 (tp30) cc_final: 0.8300 (tp30) REVERT: B 567 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8328 (ttp80) REVERT: B 611 MET cc_start: 0.7512 (mmm) cc_final: 0.7307 (mmm) REVERT: A 143 TYR cc_start: 0.7286 (m-80) cc_final: 0.6817 (m-80) REVERT: A 244 TYR cc_start: 0.6342 (p90) cc_final: 0.4884 (p90) REVERT: A 438 ASP cc_start: 0.8557 (t0) cc_final: 0.8143 (t70) REVERT: A 449 MET cc_start: 0.6996 (tpp) cc_final: 0.6448 (tpp) REVERT: A 736 PHE cc_start: 0.8074 (m-80) cc_final: 0.7834 (m-10) REVERT: F 162 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6820 (mt-10) REVERT: F 198 LEU cc_start: 0.8368 (mt) cc_final: 0.6870 (mt) REVERT: F 291 GLU cc_start: 0.8420 (tp30) cc_final: 0.7973 (tm-30) REVERT: F 388 MET cc_start: 0.7928 (mtp) cc_final: 0.7640 (mmm) REVERT: F 426 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8365 (mtmt) REVERT: F 449 MET cc_start: 0.8210 (tpp) cc_final: 0.7878 (tpp) REVERT: F 466 GLU cc_start: 0.6563 (pp20) cc_final: 0.6140 (tm-30) REVERT: F 491 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8867 (mp0) REVERT: F 508 MET cc_start: 0.6071 (mmp) cc_final: 0.5638 (mmt) REVERT: F 561 GLU cc_start: 0.9450 (mp0) cc_final: 0.9246 (mp0) REVERT: F 650 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7639 (tm-30) REVERT: E 323 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7832 (ttm110) REVERT: E 332 MET cc_start: 0.8941 (mmm) cc_final: 0.8501 (mmm) REVERT: E 366 GLU cc_start: 0.7873 (pt0) cc_final: 0.7577 (pt0) REVERT: E 424 ARG cc_start: 0.8438 (mtm-85) cc_final: 0.8012 (ttp-110) REVERT: E 550 MET cc_start: 0.8969 (mtt) cc_final: 0.8662 (mtm) REVERT: D 109 LYS cc_start: 0.8106 (tppt) cc_final: 0.7377 (ptpt) REVERT: D 366 GLU cc_start: 0.8216 (pp20) cc_final: 0.7344 (pp20) REVERT: D 476 TRP cc_start: 0.7950 (m100) cc_final: 0.7507 (m100) REVERT: D 484 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8344 (t0) REVERT: D 508 MET cc_start: 0.7555 (tpt) cc_final: 0.7107 (tpt) REVERT: D 602 ASN cc_start: 0.8549 (m-40) cc_final: 0.8325 (m110) REVERT: D 740 MET cc_start: 0.8243 (tmm) cc_final: 0.8008 (tmm) REVERT: C 46 MET cc_start: 0.7006 (mtt) cc_final: 0.6704 (mtt) REVERT: C 200 GLU cc_start: 0.8177 (tp30) cc_final: 0.7879 (tp30) REVERT: C 275 MET cc_start: 0.8541 (mmm) cc_final: 0.8234 (mmm) REVERT: C 327 GLN cc_start: 0.9259 (tp40) cc_final: 0.8714 (tp40) REVERT: C 336 LYS cc_start: 0.8961 (pttt) cc_final: 0.8621 (mmtt) REVERT: C 482 LEU cc_start: 0.8660 (mt) cc_final: 0.8352 (mp) REVERT: C 522 CYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7963 (t) REVERT: C 564 ASP cc_start: 0.8512 (m-30) cc_final: 0.8259 (m-30) REVERT: C 579 LEU cc_start: 0.8478 (mt) cc_final: 0.8262 (mt) REVERT: G 134 LYS cc_start: 0.6691 (tptt) cc_final: 0.6272 (tptt) REVERT: G 159 MET cc_start: 0.7623 (mtt) cc_final: 0.7293 (ptp) outliers start: 97 outliers final: 53 residues processed: 838 average time/residue: 0.2499 time to fit residues: 335.0672 Evaluate side-chains 655 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 598 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 308 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 180 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 chunk 315 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 115 optimal weight: 0.0020 chunk 16 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 255 optimal weight: 5.9990 chunk 340 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 296 ASN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS F 443 ASN E 602 ASN E 750 ASN D 398 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 602 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.102535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.082367 restraints weight = 147390.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.084634 restraints weight = 85150.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.086126 restraints weight = 57993.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.087119 restraints weight = 44293.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.087747 restraints weight = 36756.124| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37527 Z= 0.143 Angle : 0.714 12.071 50746 Z= 0.345 Chirality : 0.047 0.251 5723 Planarity : 0.005 0.063 6650 Dihedral : 9.665 178.438 5191 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.52 % Allowed : 13.57 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 1.19 (0.12), residues: 4639 helix: 0.94 (0.11), residues: 2104 sheet: 0.88 (0.18), residues: 768 loop : 0.81 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 567 TYR 0.034 0.002 TYR D 244 PHE 0.032 0.002 PHE E 139 TRP 0.023 0.002 TRP F 454 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00312 (37527) covalent geometry : angle 0.71444 (50746) hydrogen bonds : bond 0.04544 ( 1712) hydrogen bonds : angle 4.67388 ( 4803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 691 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASN cc_start: 0.4763 (m-40) cc_final: 0.4444 (m-40) REVERT: B 212 GLN cc_start: 0.8471 (mp10) cc_final: 0.8256 (mp10) REVERT: B 268 LEU cc_start: 0.9131 (tt) cc_final: 0.8880 (tt) REVERT: B 379 GLU cc_start: 0.8262 (tt0) cc_final: 0.8012 (pt0) REVERT: B 491 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: B 495 TYR cc_start: 0.8339 (m-10) cc_final: 0.8118 (m-80) REVERT: B 546 GLU cc_start: 0.8679 (tp30) cc_final: 0.8251 (tp30) REVERT: B 567 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8189 (ttp80) REVERT: B 644 TYR cc_start: 0.8274 (t80) cc_final: 0.8058 (t80) REVERT: A 46 MET cc_start: 0.8828 (ttt) cc_final: 0.8594 (mmm) REVERT: A 63 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7815 (pttp) REVERT: A 143 TYR cc_start: 0.7291 (m-80) cc_final: 0.6816 (m-80) REVERT: A 388 MET cc_start: 0.5165 (mtt) cc_final: 0.4807 (mtt) REVERT: A 438 ASP cc_start: 0.8524 (t0) cc_final: 0.8138 (t70) REVERT: A 449 MET cc_start: 0.6372 (tpp) cc_final: 0.6155 (tmm) REVERT: A 598 ASP cc_start: 0.7115 (t0) cc_final: 0.6820 (p0) REVERT: A 608 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8404 (ppp) REVERT: F 136 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8919 (tptt) REVERT: F 162 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: F 198 LEU cc_start: 0.8400 (mt) cc_final: 0.6939 (mt) REVERT: F 267 PHE cc_start: 0.5840 (m-80) cc_final: 0.5632 (m-80) REVERT: F 275 MET cc_start: 0.9173 (mpp) cc_final: 0.8837 (mmp) REVERT: F 426 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8499 (mtmt) REVERT: F 487 ARG cc_start: 0.8804 (mmt-90) cc_final: 0.8314 (mmt-90) REVERT: F 508 MET cc_start: 0.6070 (mmp) cc_final: 0.5570 (mmt) REVERT: F 575 PHE cc_start: 0.9057 (t80) cc_final: 0.8621 (t80) REVERT: E 162 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7586 (mm-30) REVERT: E 244 TYR cc_start: 0.7843 (p90) cc_final: 0.7196 (p90) REVERT: E 332 MET cc_start: 0.9058 (mmm) cc_final: 0.8643 (mmm) REVERT: E 366 GLU cc_start: 0.7850 (pt0) cc_final: 0.7630 (pt0) REVERT: E 424 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.8190 (ttm110) REVERT: E 550 MET cc_start: 0.9083 (mtt) cc_final: 0.8594 (mtm) REVERT: E 671 ASP cc_start: 0.8209 (t0) cc_final: 0.7832 (m-30) REVERT: D 109 LYS cc_start: 0.8153 (tppt) cc_final: 0.7839 (mmmt) REVERT: D 117 LEU cc_start: 0.7432 (mp) cc_final: 0.7067 (mt) REVERT: D 244 TYR cc_start: 0.7383 (p90) cc_final: 0.6269 (p90) REVERT: D 283 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: D 366 GLU cc_start: 0.8042 (pp20) cc_final: 0.7656 (pp20) REVERT: D 484 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8184 (t0) REVERT: D 602 ASN cc_start: 0.8507 (m-40) cc_final: 0.8292 (m110) REVERT: D 740 MET cc_start: 0.8193 (tmm) cc_final: 0.7923 (tmm) REVERT: C 46 MET cc_start: 0.7084 (mtt) cc_final: 0.6656 (mtt) REVERT: C 158 MET cc_start: 0.7781 (mmp) cc_final: 0.6050 (mmp) REVERT: C 200 GLU cc_start: 0.8090 (tp30) cc_final: 0.7792 (tp30) REVERT: C 275 MET cc_start: 0.8533 (mmm) cc_final: 0.8226 (mmm) REVERT: C 336 LYS cc_start: 0.8936 (pttt) cc_final: 0.8572 (mmpt) REVERT: C 466 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6512 (tm-30) REVERT: C 522 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7983 (t) REVERT: C 564 ASP cc_start: 0.8464 (m-30) cc_final: 0.8227 (m-30) outliers start: 100 outliers final: 59 residues processed: 757 average time/residue: 0.2120 time to fit residues: 262.0388 Evaluate side-chains 640 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 574 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain F residue 691 CYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 691 CYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 80 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 382 optimal weight: 4.9990 chunk 420 optimal weight: 4.9990 chunk 461 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 431 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 371 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 624 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN F 183 HIS F 398 GLN F 735 HIS E 384 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 183 HIS D 327 GLN D 404 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 337 GLN G 278 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.094229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.074063 restraints weight = 154862.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.076027 restraints weight = 92838.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.077317 restraints weight = 65171.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.078164 restraints weight = 50980.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.078704 restraints weight = 43318.536| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 37527 Z= 0.309 Angle : 0.864 12.474 50746 Z= 0.426 Chirality : 0.051 0.276 5723 Planarity : 0.006 0.071 6650 Dihedral : 9.814 177.622 5191 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.36 % Allowed : 13.30 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 0.52 (0.12), residues: 4639 helix: 0.43 (0.11), residues: 2119 sheet: 0.43 (0.18), residues: 757 loop : 0.46 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 89 TYR 0.027 0.003 TYR F 143 PHE 0.038 0.003 PHE B 563 TRP 0.020 0.002 TRP C 476 HIS 0.011 0.002 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00664 (37527) covalent geometry : angle 0.86358 (50746) hydrogen bonds : bond 0.04832 ( 1712) hydrogen bonds : angle 5.21016 ( 4803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 562 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 ASP cc_start: 0.6950 (t0) cc_final: 0.6725 (t0) REVERT: B 491 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: B 495 TYR cc_start: 0.8537 (m-10) cc_final: 0.7806 (m-80) REVERT: B 567 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8473 (ttp80) REVERT: B 577 ASP cc_start: 0.6812 (p0) cc_final: 0.6560 (p0) REVERT: B 644 TYR cc_start: 0.8340 (t80) cc_final: 0.8113 (t80) REVERT: A 46 MET cc_start: 0.9033 (ttt) cc_final: 0.8650 (mmm) REVERT: A 143 TYR cc_start: 0.7180 (m-80) cc_final: 0.6896 (m-80) REVERT: A 388 MET cc_start: 0.5055 (mtt) cc_final: 0.4585 (mtt) REVERT: A 438 ASP cc_start: 0.8698 (t0) cc_final: 0.8214 (t70) REVERT: A 576 PHE cc_start: 0.8524 (m-80) cc_final: 0.8168 (m-80) REVERT: A 598 ASP cc_start: 0.7442 (t0) cc_final: 0.6872 (p0) REVERT: A 602 ASN cc_start: 0.8275 (t0) cc_final: 0.8070 (t0) REVERT: F 158 MET cc_start: 0.7798 (mmp) cc_final: 0.6359 (mmp) REVERT: F 162 GLU cc_start: 0.7137 (pt0) cc_final: 0.6757 (mt-10) REVERT: F 198 LEU cc_start: 0.8652 (mt) cc_final: 0.7412 (mt) REVERT: F 442 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7966 (mtm) REVERT: F 487 ARG cc_start: 0.8783 (mmt-90) cc_final: 0.8389 (mmt-90) REVERT: F 599 ARG cc_start: 0.7612 (mpt180) cc_final: 0.7269 (mtt90) REVERT: F 618 PHE cc_start: 0.7933 (t80) cc_final: 0.7641 (t80) REVERT: E 244 TYR cc_start: 0.8223 (p90) cc_final: 0.7649 (p90) REVERT: E 305 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8039 (mt-10) REVERT: E 337 GLN cc_start: 0.8541 (mp10) cc_final: 0.8295 (tm-30) REVERT: E 366 GLU cc_start: 0.7983 (pt0) cc_final: 0.7504 (pt0) REVERT: E 424 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8129 (ttm110) REVERT: E 550 MET cc_start: 0.9145 (mtt) cc_final: 0.8806 (mtm) REVERT: E 671 ASP cc_start: 0.8275 (t0) cc_final: 0.7946 (p0) REVERT: D 109 LYS cc_start: 0.8116 (tppt) cc_final: 0.7882 (mmmt) REVERT: D 117 LEU cc_start: 0.7636 (mp) cc_final: 0.7188 (mt) REVERT: D 244 TYR cc_start: 0.7288 (p90) cc_final: 0.6221 (p90) REVERT: D 366 GLU cc_start: 0.8315 (pp20) cc_final: 0.7782 (pp20) REVERT: D 495 TYR cc_start: 0.8165 (m-10) cc_final: 0.7901 (m-10) REVERT: D 508 MET cc_start: 0.7591 (tpp) cc_final: 0.7214 (tpt) REVERT: D 550 MET cc_start: 0.8451 (mpp) cc_final: 0.8197 (mpp) REVERT: C 275 MET cc_start: 0.8710 (mmm) cc_final: 0.8393 (mmm) REVERT: C 336 LYS cc_start: 0.9017 (pttt) cc_final: 0.8599 (mmtt) REVERT: G 270 LEU cc_start: 0.7717 (tp) cc_final: 0.6990 (mp) REVERT: G 299 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7621 (mm-30) REVERT: G 332 ARG cc_start: 0.6740 (tpm170) cc_final: 0.6527 (mmm160) REVERT: G 368 GLU cc_start: 0.8650 (mm-30) cc_final: 0.7956 (pp20) REVERT: G 406 LEU cc_start: 0.8340 (mp) cc_final: 0.8066 (mp) outliers start: 173 outliers final: 106 residues processed: 684 average time/residue: 0.2063 time to fit residues: 233.6586 Evaluate side-chains 594 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 486 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 691 CYS Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 311 VAL Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 13 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 337 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 345 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 406 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 347 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 660 ASN D 404 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.097788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.077812 restraints weight = 151135.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.079897 restraints weight = 88922.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.081250 restraints weight = 61562.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.082160 restraints weight = 47795.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.082731 restraints weight = 40164.592| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37527 Z= 0.139 Angle : 0.728 12.837 50746 Z= 0.346 Chirality : 0.047 0.311 5723 Planarity : 0.005 0.064 6650 Dihedral : 9.277 175.623 5191 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.22 % Allowed : 15.71 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 0.91 (0.12), residues: 4639 helix: 0.82 (0.11), residues: 2117 sheet: 0.56 (0.18), residues: 724 loop : 0.59 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 487 TYR 0.029 0.002 TYR B 244 PHE 0.026 0.001 PHE E 139 TRP 0.030 0.002 TRP E 476 HIS 0.008 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00314 (37527) covalent geometry : angle 0.72767 (50746) hydrogen bonds : bond 0.03915 ( 1712) hydrogen bonds : angle 4.70708 ( 4803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 592 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.7608 (tmm) cc_final: 0.7324 (tmm) REVERT: B 84 MET cc_start: 0.8407 (ppp) cc_final: 0.8013 (ppp) REVERT: B 150 ASP cc_start: 0.6870 (t0) cc_final: 0.6627 (t0) REVERT: B 212 GLN cc_start: 0.8538 (mp10) cc_final: 0.8235 (mp10) REVERT: B 332 MET cc_start: 0.8790 (mmm) cc_final: 0.8269 (mmm) REVERT: B 351 ASN cc_start: 0.8453 (p0) cc_final: 0.8203 (p0) REVERT: B 363 PHE cc_start: 0.8912 (m-10) cc_final: 0.8656 (m-10) REVERT: B 442 MET cc_start: 0.8844 (mmm) cc_final: 0.8362 (mpp) REVERT: B 458 GLN cc_start: 0.8839 (mp10) cc_final: 0.8477 (mp10) REVERT: B 491 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: B 495 TYR cc_start: 0.8602 (m-10) cc_final: 0.8149 (m-80) REVERT: B 546 GLU cc_start: 0.8717 (tp30) cc_final: 0.8339 (tp30) REVERT: B 567 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8255 (ttp80) REVERT: B 633 ILE cc_start: 0.9269 (mp) cc_final: 0.8950 (mm) REVERT: B 644 TYR cc_start: 0.8267 (t80) cc_final: 0.7917 (t80) REVERT: A 46 MET cc_start: 0.8994 (ttt) cc_final: 0.8690 (tpp) REVERT: A 143 TYR cc_start: 0.7226 (m-80) cc_final: 0.6908 (m-80) REVERT: A 388 MET cc_start: 0.5002 (mtt) cc_final: 0.4429 (mtt) REVERT: A 438 ASP cc_start: 0.8597 (t0) cc_final: 0.8136 (t70) REVERT: A 598 ASP cc_start: 0.7328 (t0) cc_final: 0.6943 (p0) REVERT: A 608 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8345 (ppp) REVERT: F 198 LEU cc_start: 0.8651 (mt) cc_final: 0.7299 (mt) REVERT: F 359 ARG cc_start: 0.7040 (mmp-170) cc_final: 0.6768 (mmp80) REVERT: F 561 GLU cc_start: 0.9252 (mp0) cc_final: 0.9010 (mp0) REVERT: F 599 ARG cc_start: 0.7686 (mpt180) cc_final: 0.7338 (mtt90) REVERT: E 244 TYR cc_start: 0.8087 (p90) cc_final: 0.7534 (p90) REVERT: E 366 GLU cc_start: 0.7768 (pt0) cc_final: 0.7564 (tt0) REVERT: E 424 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8369 (ttm110) REVERT: E 602 ASN cc_start: 0.8715 (p0) cc_final: 0.8376 (p0) REVERT: E 639 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8443 (tp) REVERT: E 671 ASP cc_start: 0.8211 (t0) cc_final: 0.7786 (p0) REVERT: D 109 LYS cc_start: 0.8080 (tppt) cc_final: 0.7844 (mmmt) REVERT: D 117 LEU cc_start: 0.7469 (mp) cc_final: 0.7118 (mt) REVERT: D 162 GLU cc_start: 0.7590 (pt0) cc_final: 0.7024 (mt-10) REVERT: D 244 TYR cc_start: 0.7200 (p90) cc_final: 0.6162 (p90) REVERT: D 366 GLU cc_start: 0.8184 (pp20) cc_final: 0.7630 (pp20) REVERT: D 476 TRP cc_start: 0.8157 (m100) cc_final: 0.7578 (m100) REVERT: D 484 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8179 (p0) REVERT: D 508 MET cc_start: 0.7648 (tpp) cc_final: 0.7430 (tpp) REVERT: C 46 MET cc_start: 0.7195 (mtt) cc_final: 0.6838 (mtt) REVERT: C 173 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8007 (p90) REVERT: C 200 GLU cc_start: 0.8298 (tp30) cc_final: 0.8064 (tp30) REVERT: C 275 MET cc_start: 0.8719 (mmm) cc_final: 0.8318 (mmm) REVERT: C 336 LYS cc_start: 0.8992 (pttt) cc_final: 0.8624 (mptt) REVERT: C 508 MET cc_start: 0.5439 (tpp) cc_final: 0.4875 (mmm) REVERT: C 517 TYR cc_start: 0.8783 (p90) cc_final: 0.8480 (p90) REVERT: G 270 LEU cc_start: 0.7612 (tp) cc_final: 0.6879 (mp) REVERT: G 299 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7541 (mm-30) REVERT: G 382 SER cc_start: 0.5546 (p) cc_final: 0.5084 (t) outliers start: 128 outliers final: 80 residues processed: 678 average time/residue: 0.2045 time to fit residues: 229.4978 Evaluate side-chains 602 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 517 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 691 CYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 239 PHE Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 409 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 chunk 399 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 395 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 382 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 GLN D 404 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN G 215 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.097478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.077600 restraints weight = 151569.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.079655 restraints weight = 89412.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.081002 restraints weight = 62031.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.081887 restraints weight = 48226.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.082459 restraints weight = 40677.236| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37527 Z= 0.141 Angle : 0.724 12.252 50746 Z= 0.344 Chirality : 0.047 0.297 5723 Planarity : 0.004 0.062 6650 Dihedral : 8.899 176.958 5191 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.92 % Allowed : 17.00 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 0.95 (0.12), residues: 4639 helix: 0.89 (0.11), residues: 2120 sheet: 0.56 (0.18), residues: 724 loop : 0.58 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 700 TYR 0.026 0.002 TYR B 244 PHE 0.023 0.001 PHE E 139 TRP 0.023 0.002 TRP F 454 HIS 0.011 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00321 (37527) covalent geometry : angle 0.72429 (50746) hydrogen bonds : bond 0.03733 ( 1712) hydrogen bonds : angle 4.65321 ( 4803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 559 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.7604 (tmm) cc_final: 0.7268 (tmm) REVERT: B 84 MET cc_start: 0.8515 (ppp) cc_final: 0.8191 (ppp) REVERT: B 150 ASP cc_start: 0.6910 (t0) cc_final: 0.6669 (t0) REVERT: B 212 GLN cc_start: 0.8503 (mp10) cc_final: 0.8292 (mp10) REVERT: B 351 ASN cc_start: 0.8514 (p0) cc_final: 0.8301 (p0) REVERT: B 411 LEU cc_start: 0.8611 (mt) cc_final: 0.8051 (mt) REVERT: B 442 MET cc_start: 0.8907 (mmm) cc_final: 0.8391 (mpp) REVERT: B 458 GLN cc_start: 0.8838 (mp10) cc_final: 0.8520 (mp10) REVERT: B 508 MET cc_start: 0.8235 (tpp) cc_final: 0.7943 (tpt) REVERT: B 567 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8277 (ttp80) REVERT: B 633 ILE cc_start: 0.9189 (mp) cc_final: 0.8925 (mm) REVERT: B 644 TYR cc_start: 0.8224 (t80) cc_final: 0.7846 (t80) REVERT: A 64 ARG cc_start: 0.8103 (mmp80) cc_final: 0.7246 (tpt90) REVERT: A 143 TYR cc_start: 0.7094 (m-80) cc_final: 0.6787 (m-80) REVERT: A 388 MET cc_start: 0.5167 (mtt) cc_final: 0.4575 (mtt) REVERT: A 438 ASP cc_start: 0.8561 (t0) cc_final: 0.8113 (t70) REVERT: A 608 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8363 (ppp) REVERT: F 599 ARG cc_start: 0.7706 (mpt180) cc_final: 0.7357 (mtt90) REVERT: F 608 MET cc_start: 0.8969 (ptp) cc_final: 0.8407 (ptm) REVERT: E 238 PRO cc_start: 0.8641 (Cg_exo) cc_final: 0.7851 (Cg_endo) REVERT: E 244 TYR cc_start: 0.8051 (p90) cc_final: 0.7511 (p90) REVERT: E 424 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8302 (ttm110) REVERT: E 602 ASN cc_start: 0.8739 (p0) cc_final: 0.8358 (p0) REVERT: E 618 PHE cc_start: 0.8100 (t80) cc_final: 0.7691 (t80) REVERT: E 671 ASP cc_start: 0.8229 (t0) cc_final: 0.7704 (p0) REVERT: D 117 LEU cc_start: 0.7497 (mp) cc_final: 0.7179 (mt) REVERT: D 162 GLU cc_start: 0.7487 (pt0) cc_final: 0.6996 (mt-10) REVERT: D 366 GLU cc_start: 0.8204 (pp20) cc_final: 0.7682 (pp20) REVERT: D 380 ILE cc_start: 0.9136 (mt) cc_final: 0.8911 (tt) REVERT: D 495 TYR cc_start: 0.8028 (m-10) cc_final: 0.7822 (m-80) REVERT: D 508 MET cc_start: 0.7668 (tpp) cc_final: 0.7448 (tpp) REVERT: D 550 MET cc_start: 0.8694 (mpp) cc_final: 0.8485 (mpp) REVERT: C 46 MET cc_start: 0.7337 (mtt) cc_final: 0.6983 (mtt) REVERT: C 173 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8030 (p90) REVERT: C 275 MET cc_start: 0.8751 (mmm) cc_final: 0.8361 (mmm) REVERT: C 336 LYS cc_start: 0.9013 (pttt) cc_final: 0.8660 (mptt) REVERT: C 366 GLU cc_start: 0.7708 (pp20) cc_final: 0.7353 (pp20) REVERT: C 380 ILE cc_start: 0.9461 (mt) cc_final: 0.9219 (tt) REVERT: C 517 TYR cc_start: 0.8772 (p90) cc_final: 0.8515 (p90) REVERT: G 54 MET cc_start: 0.0472 (ptt) cc_final: 0.0073 (ptt) REVERT: G 159 MET cc_start: 0.7521 (mtt) cc_final: 0.7253 (ptp) REVERT: G 270 LEU cc_start: 0.7537 (tp) cc_final: 0.6837 (mp) REVERT: G 299 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7546 (mm-30) REVERT: G 382 SER cc_start: 0.5633 (p) cc_final: 0.5182 (t) outliers start: 116 outliers final: 86 residues processed: 641 average time/residue: 0.1872 time to fit residues: 199.2498 Evaluate side-chains 599 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 511 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 494 GLN Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 691 CYS Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 239 PHE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 31 optimal weight: 1.9990 chunk 360 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 214 optimal weight: 0.0000 chunk 37 optimal weight: 0.0020 chunk 288 optimal weight: 9.9990 chunk 388 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS F 43 GLN F 90 ASN ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.098518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.078656 restraints weight = 151547.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.080750 restraints weight = 89130.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.082113 restraints weight = 61736.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.083022 restraints weight = 47954.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.083595 restraints weight = 40305.902| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37527 Z= 0.127 Angle : 0.729 12.563 50746 Z= 0.345 Chirality : 0.047 0.303 5723 Planarity : 0.005 0.072 6650 Dihedral : 8.597 179.932 5191 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.37 % Allowed : 18.06 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 0.99 (0.12), residues: 4639 helix: 0.89 (0.11), residues: 2134 sheet: 0.70 (0.19), residues: 714 loop : 0.60 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 700 TYR 0.027 0.002 TYR D 244 PHE 0.030 0.001 PHE C 563 TRP 0.043 0.002 TRP A 454 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00289 (37527) covalent geometry : angle 0.72912 (50746) hydrogen bonds : bond 0.03564 ( 1712) hydrogen bonds : angle 4.59380 ( 4803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 572 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.7624 (tmm) cc_final: 0.7210 (tmm) REVERT: B 84 MET cc_start: 0.8539 (ppp) cc_final: 0.8302 (ppp) REVERT: B 150 ASP cc_start: 0.6826 (t0) cc_final: 0.6624 (t0) REVERT: B 351 ASN cc_start: 0.8400 (p0) cc_final: 0.8189 (p0) REVERT: B 442 MET cc_start: 0.8819 (mmm) cc_final: 0.8375 (mpp) REVERT: B 458 GLN cc_start: 0.8795 (mp10) cc_final: 0.8477 (mp10) REVERT: B 567 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8340 (ttm110) REVERT: B 611 MET cc_start: 0.7659 (mmm) cc_final: 0.6958 (tpt) REVERT: B 633 ILE cc_start: 0.9063 (mp) cc_final: 0.8853 (mm) REVERT: B 644 TYR cc_start: 0.8082 (t80) cc_final: 0.7637 (t80) REVERT: A 64 ARG cc_start: 0.8137 (mmp80) cc_final: 0.7333 (tpt90) REVERT: A 143 TYR cc_start: 0.7178 (m-80) cc_final: 0.6877 (m-80) REVERT: A 200 GLU cc_start: 0.8660 (tp30) cc_final: 0.8395 (tp30) REVERT: A 319 GLU cc_start: 0.8381 (tp30) cc_final: 0.7923 (tm-30) REVERT: A 388 MET cc_start: 0.5154 (mtt) cc_final: 0.4555 (mtt) REVERT: A 438 ASP cc_start: 0.8545 (t0) cc_final: 0.8102 (t70) REVERT: F 26 LEU cc_start: 0.8369 (mt) cc_final: 0.8122 (mp) REVERT: F 561 GLU cc_start: 0.9140 (mp0) cc_final: 0.8710 (mm-30) REVERT: F 564 ASP cc_start: 0.8599 (t0) cc_final: 0.8298 (t0) REVERT: F 599 ARG cc_start: 0.7671 (mpt180) cc_final: 0.7351 (mtt90) REVERT: F 608 MET cc_start: 0.8828 (ptp) cc_final: 0.8611 (ptm) REVERT: F 619 ILE cc_start: 0.9435 (mm) cc_final: 0.9220 (mm) REVERT: E 162 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7619 (mm-30) REVERT: E 424 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8209 (ttm110) REVERT: E 602 ASN cc_start: 0.8653 (p0) cc_final: 0.8369 (p0) REVERT: E 618 PHE cc_start: 0.8067 (t80) cc_final: 0.7801 (t80) REVERT: E 671 ASP cc_start: 0.8197 (t0) cc_final: 0.7800 (p0) REVERT: D 117 LEU cc_start: 0.7523 (mp) cc_final: 0.7273 (mt) REVERT: D 162 GLU cc_start: 0.7359 (pt0) cc_final: 0.6901 (mt-10) REVERT: D 219 MET cc_start: 0.7863 (mtm) cc_final: 0.7640 (mtm) REVERT: D 404 HIS cc_start: 0.8118 (t70) cc_final: 0.7586 (t-170) REVERT: D 508 MET cc_start: 0.7648 (tpp) cc_final: 0.7397 (tpp) REVERT: C 173 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8073 (p90) REVERT: C 244 TYR cc_start: 0.8310 (p90) cc_final: 0.7622 (p90) REVERT: C 275 MET cc_start: 0.8678 (mmm) cc_final: 0.8231 (mmm) REVERT: C 332 MET cc_start: 0.8587 (ttm) cc_final: 0.8300 (ttt) REVERT: C 336 LYS cc_start: 0.8978 (pttt) cc_final: 0.8641 (mptt) REVERT: C 366 GLU cc_start: 0.7555 (pp20) cc_final: 0.7332 (pp20) REVERT: C 380 ILE cc_start: 0.9436 (mt) cc_final: 0.9184 (tt) REVERT: C 517 TYR cc_start: 0.8737 (p90) cc_final: 0.8470 (p90) REVERT: C 609 ASP cc_start: 0.7985 (m-30) cc_final: 0.7744 (m-30) REVERT: G 54 MET cc_start: 0.0474 (ptt) cc_final: 0.0098 (ptt) REVERT: G 159 MET cc_start: 0.7627 (mtt) cc_final: 0.7261 (ptp) REVERT: G 270 LEU cc_start: 0.7478 (tp) cc_final: 0.6823 (mp) REVERT: G 299 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7510 (mm-30) REVERT: G 382 SER cc_start: 0.5528 (p) cc_final: 0.5082 (t) outliers start: 94 outliers final: 64 residues processed: 636 average time/residue: 0.1923 time to fit residues: 202.7825 Evaluate side-chains 588 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 523 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 239 PHE Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 112 optimal weight: 6.9990 chunk 451 optimal weight: 9.9990 chunk 296 optimal weight: 7.9990 chunk 416 optimal weight: 9.9990 chunk 345 optimal weight: 7.9990 chunk 239 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 226 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 GLN ** G 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.094229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.074450 restraints weight = 154388.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.076407 restraints weight = 91632.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.077684 restraints weight = 64022.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.078510 restraints weight = 49987.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.079085 restraints weight = 42384.726| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 37527 Z= 0.263 Angle : 0.821 15.310 50746 Z= 0.400 Chirality : 0.049 0.329 5723 Planarity : 0.005 0.065 6650 Dihedral : 8.672 177.490 5191 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.74 % Allowed : 18.38 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 0.61 (0.12), residues: 4639 helix: 0.62 (0.11), residues: 2144 sheet: 0.40 (0.18), residues: 720 loop : 0.38 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG E 635 TYR 0.025 0.002 TYR B 244 PHE 0.027 0.002 PHE B 682 TRP 0.034 0.002 TRP A 454 HIS 0.008 0.001 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00582 (37527) covalent geometry : angle 0.82146 (50746) hydrogen bonds : bond 0.04062 ( 1712) hydrogen bonds : angle 4.99724 ( 4803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 508 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.7652 (tmm) cc_final: 0.7150 (tmm) REVERT: B 84 MET cc_start: 0.8559 (ppp) cc_final: 0.8106 (ppp) REVERT: B 150 ASP cc_start: 0.6960 (t0) cc_final: 0.6703 (t0) REVERT: B 379 GLU cc_start: 0.8049 (tt0) cc_final: 0.7807 (tt0) REVERT: B 458 GLN cc_start: 0.8949 (mp10) cc_final: 0.8535 (mp10) REVERT: B 508 MET cc_start: 0.8268 (tpp) cc_final: 0.7859 (tpt) REVERT: B 644 TYR cc_start: 0.8202 (t80) cc_final: 0.7805 (t80) REVERT: A 143 TYR cc_start: 0.7110 (m-80) cc_final: 0.6860 (m-80) REVERT: A 388 MET cc_start: 0.5149 (mtt) cc_final: 0.4553 (mtt) REVERT: A 438 ASP cc_start: 0.8544 (t0) cc_final: 0.8079 (t70) REVERT: A 576 PHE cc_start: 0.8444 (m-80) cc_final: 0.8183 (m-10) REVERT: F 608 MET cc_start: 0.8912 (ptp) cc_final: 0.8620 (ptm) REVERT: E 162 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7738 (mm-30) REVERT: E 424 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8186 (ttm110) REVERT: E 602 ASN cc_start: 0.8883 (p0) cc_final: 0.8664 (p0) REVERT: E 618 PHE cc_start: 0.8308 (t80) cc_final: 0.7993 (t80) REVERT: E 751 ASP cc_start: 0.8788 (m-30) cc_final: 0.8254 (t0) REVERT: D 117 LEU cc_start: 0.7637 (mp) cc_final: 0.7273 (mt) REVERT: D 162 GLU cc_start: 0.7468 (pt0) cc_final: 0.6909 (mt-10) REVERT: D 404 HIS cc_start: 0.8328 (t70) cc_final: 0.8027 (t70) REVERT: D 495 TYR cc_start: 0.8313 (m-10) cc_final: 0.8102 (m-80) REVERT: D 508 MET cc_start: 0.7696 (tpp) cc_final: 0.7428 (tpp) REVERT: C 173 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8080 (p90) REVERT: C 275 MET cc_start: 0.8793 (mmm) cc_final: 0.8531 (mmm) REVERT: C 332 MET cc_start: 0.8709 (ttm) cc_final: 0.8444 (ttt) REVERT: C 336 LYS cc_start: 0.9077 (pttt) cc_final: 0.8681 (mptt) REVERT: C 508 MET cc_start: 0.5268 (mmm) cc_final: 0.4211 (mmm) REVERT: C 517 TYR cc_start: 0.8772 (p90) cc_final: 0.8469 (p90) REVERT: G 270 LEU cc_start: 0.7757 (tp) cc_final: 0.6948 (mp) REVERT: G 299 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7676 (mm-30) REVERT: G 368 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8135 (pp20) REVERT: G 382 SER cc_start: 0.5842 (p) cc_final: 0.5351 (t) outliers start: 109 outliers final: 87 residues processed: 590 average time/residue: 0.1989 time to fit residues: 195.2443 Evaluate side-chains 567 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 479 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 212 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 334 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 383 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN F 763 GLN D 90 ASN D 760 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.092829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.074633 restraints weight = 156471.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.075643 restraints weight = 100510.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.076648 restraints weight = 70404.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.076948 restraints weight = 56707.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.077529 restraints weight = 51062.978| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.6910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 37527 Z= 0.257 Angle : 0.848 21.319 50746 Z= 0.410 Chirality : 0.050 0.353 5723 Planarity : 0.005 0.068 6650 Dihedral : 8.707 179.357 5191 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.77 % Allowed : 19.04 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 0.23 (0.12), residues: 4639 helix: 0.37 (0.11), residues: 2141 sheet: 0.12 (0.18), residues: 729 loop : 0.15 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 89 TYR 0.029 0.002 TYR B 244 PHE 0.028 0.002 PHE C 576 TRP 0.051 0.003 TRP E 476 HIS 0.007 0.002 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00567 (37527) covalent geometry : angle 0.84838 (50746) hydrogen bonds : bond 0.04225 ( 1712) hydrogen bonds : angle 5.16269 ( 4803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 503 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.7835 (tmm) cc_final: 0.7356 (tmm) REVERT: B 84 MET cc_start: 0.8621 (ppp) cc_final: 0.8196 (ppp) REVERT: B 150 ASP cc_start: 0.7027 (t0) cc_final: 0.6786 (t0) REVERT: B 442 MET cc_start: 0.8869 (mmm) cc_final: 0.8560 (mpp) REVERT: B 495 TYR cc_start: 0.8444 (m-80) cc_final: 0.8226 (m-80) REVERT: B 508 MET cc_start: 0.8329 (tpp) cc_final: 0.8070 (tpt) REVERT: B 567 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8291 (ttp80) REVERT: B 644 TYR cc_start: 0.8195 (t80) cc_final: 0.7801 (t80) REVERT: A 132 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8584 (tp30) REVERT: A 143 TYR cc_start: 0.7287 (m-80) cc_final: 0.7058 (m-80) REVERT: A 388 MET cc_start: 0.5207 (mtt) cc_final: 0.4622 (mtt) REVERT: A 438 ASP cc_start: 0.8654 (t0) cc_final: 0.8161 (t70) REVERT: A 576 PHE cc_start: 0.8505 (m-80) cc_final: 0.8244 (m-80) REVERT: A 678 MET cc_start: 0.6680 (mtt) cc_final: 0.6427 (mtt) REVERT: F 599 ARG cc_start: 0.7807 (mpt180) cc_final: 0.7339 (mtt90) REVERT: F 608 MET cc_start: 0.8876 (ptp) cc_final: 0.8326 (ptm) REVERT: E 424 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.8227 (ttm110) REVERT: D 162 GLU cc_start: 0.7693 (pt0) cc_final: 0.7151 (mt-10) REVERT: D 244 TYR cc_start: 0.7233 (p90) cc_final: 0.6659 (p90) REVERT: D 256 ARG cc_start: 0.8528 (tpp-160) cc_final: 0.8307 (tpt170) REVERT: D 404 HIS cc_start: 0.8258 (t70) cc_final: 0.7903 (t70) REVERT: D 508 MET cc_start: 0.7670 (tpp) cc_final: 0.7463 (tpp) REVERT: C 275 MET cc_start: 0.8774 (mmm) cc_final: 0.8528 (mmm) REVERT: C 336 LYS cc_start: 0.9053 (pttt) cc_final: 0.8677 (mptt) REVERT: C 508 MET cc_start: 0.5706 (mmm) cc_final: 0.4616 (mmm) REVERT: C 517 TYR cc_start: 0.8765 (p90) cc_final: 0.8520 (p90) REVERT: C 558 ASN cc_start: 0.8813 (m-40) cc_final: 0.7681 (p0) REVERT: G 270 LEU cc_start: 0.7774 (tp) cc_final: 0.6852 (mp) REVERT: G 368 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8177 (pp20) REVERT: G 382 SER cc_start: 0.6307 (p) cc_final: 0.5882 (t) outliers start: 110 outliers final: 88 residues processed: 578 average time/residue: 0.2138 time to fit residues: 207.0243 Evaluate side-chains 560 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 472 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 87 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 344 optimal weight: 6.9990 chunk 202 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 293 optimal weight: 20.0000 chunk 378 optimal weight: 2.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.093585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075140 restraints weight = 154777.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.077004 restraints weight = 89784.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.077983 restraints weight = 57339.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.078145 restraints weight = 50756.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.078148 restraints weight = 43932.397| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 37527 Z= 0.219 Angle : 0.839 19.747 50746 Z= 0.405 Chirality : 0.049 0.382 5723 Planarity : 0.005 0.068 6650 Dihedral : 8.625 175.193 5191 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.22 % Allowed : 19.72 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 0.18 (0.12), residues: 4639 helix: 0.34 (0.11), residues: 2138 sheet: 0.07 (0.19), residues: 718 loop : 0.11 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 635 TYR 0.041 0.002 TYR D 495 PHE 0.025 0.002 PHE C 576 TRP 0.039 0.003 TRP F 454 HIS 0.005 0.001 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00492 (37527) covalent geometry : angle 0.83931 (50746) hydrogen bonds : bond 0.04086 ( 1712) hydrogen bonds : angle 5.13974 ( 4803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 503 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.7877 (tmm) cc_final: 0.7406 (tmm) REVERT: B 84 MET cc_start: 0.8649 (ppp) cc_final: 0.8167 (ppp) REVERT: B 150 ASP cc_start: 0.6999 (t0) cc_final: 0.6736 (t0) REVERT: B 442 MET cc_start: 0.8931 (mmm) cc_final: 0.8554 (mpp) REVERT: B 495 TYR cc_start: 0.8438 (m-80) cc_final: 0.8026 (m-80) REVERT: B 508 MET cc_start: 0.8352 (tpp) cc_final: 0.8112 (tpt) REVERT: B 567 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8347 (ttp80) REVERT: B 644 TYR cc_start: 0.8237 (t80) cc_final: 0.7828 (t80) REVERT: A 64 ARG cc_start: 0.8147 (mmp80) cc_final: 0.7838 (tmm160) REVERT: A 132 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8595 (tp30) REVERT: A 143 TYR cc_start: 0.7374 (m-80) cc_final: 0.7115 (m-80) REVERT: A 388 MET cc_start: 0.5307 (mtt) cc_final: 0.4717 (mtt) REVERT: A 438 ASP cc_start: 0.8657 (t0) cc_final: 0.8158 (t70) REVERT: A 576 PHE cc_start: 0.8574 (m-80) cc_final: 0.8371 (m-80) REVERT: A 678 MET cc_start: 0.6662 (mtt) cc_final: 0.6416 (mtt) REVERT: F 599 ARG cc_start: 0.7934 (mpt180) cc_final: 0.7477 (mtt90) REVERT: E 424 ARG cc_start: 0.8937 (mtm-85) cc_final: 0.8306 (ttm110) REVERT: D 117 LEU cc_start: 0.7902 (mp) cc_final: 0.7382 (mt) REVERT: D 162 GLU cc_start: 0.7770 (pt0) cc_final: 0.7219 (mt-10) REVERT: D 336 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7595 (mmtt) REVERT: D 508 MET cc_start: 0.7816 (tpp) cc_final: 0.7526 (tpp) REVERT: C 275 MET cc_start: 0.8909 (mmm) cc_final: 0.8689 (mmm) REVERT: C 336 LYS cc_start: 0.9127 (pttt) cc_final: 0.8704 (mptt) REVERT: C 508 MET cc_start: 0.5121 (mmm) cc_final: 0.4153 (mmm) REVERT: C 517 TYR cc_start: 0.8821 (p90) cc_final: 0.8568 (p90) REVERT: C 558 ASN cc_start: 0.8616 (m-40) cc_final: 0.7515 (p0) REVERT: C 608 MET cc_start: 0.8746 (ptp) cc_final: 0.8188 (ptp) REVERT: G 54 MET cc_start: 0.0371 (ptt) cc_final: -0.0136 (ptt) REVERT: G 270 LEU cc_start: 0.7791 (tp) cc_final: 0.6841 (mp) REVERT: G 368 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8294 (pp20) REVERT: G 382 SER cc_start: 0.6528 (p) cc_final: 0.6111 (t) outliers start: 88 outliers final: 81 residues processed: 567 average time/residue: 0.2168 time to fit residues: 202.9165 Evaluate side-chains 556 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 475 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 674 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 159 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 chunk 378 optimal weight: 0.8980 chunk 400 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 193 optimal weight: 0.0980 chunk 442 optimal weight: 8.9990 chunk 126 optimal weight: 0.0870 chunk 367 optimal weight: 9.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN F 406 HIS E 603 GLN D 327 GLN D 421 GLN D 458 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.097112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.079002 restraints weight = 151502.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.080325 restraints weight = 91703.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.081094 restraints weight = 61453.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.081269 restraints weight = 58975.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.081345 restraints weight = 50978.584| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37527 Z= 0.141 Angle : 0.831 15.817 50746 Z= 0.395 Chirality : 0.049 0.378 5723 Planarity : 0.005 0.069 6650 Dihedral : 8.312 168.488 5191 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.79 % Allowed : 20.55 % Favored : 77.66 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.82 % 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 aren not related in a simple way. whole: 0.50 (0.12), residues: 4639 helix: 0.56 (0.11), residues: 2131 sheet: 0.33 (0.19), residues: 702 loop : 0.29 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 342 TYR 0.046 0.002 TYR D 495 PHE 0.027 0.002 PHE F 618 TRP 0.048 0.003 TRP F 454 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00318 (37527) covalent geometry : angle 0.83088 (50746) hydrogen bonds : bond 0.03810 ( 1712) hydrogen bonds : angle 4.82919 ( 4803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7634.46 seconds wall clock time: 132 minutes 4.76 seconds (7924.76 seconds total)