Starting phenix.real_space_refine on Tue Aug 26 12:21:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcm_28983/08_2025/8fcm_28983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcm_28983/08_2025/8fcm_28983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fcm_28983/08_2025/8fcm_28983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcm_28983/08_2025/8fcm_28983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fcm_28983/08_2025/8fcm_28983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcm_28983/08_2025/8fcm_28983.map" } resolution = 3.27 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= 0.003 sd= 0.058 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 188 5.16 5 C 23110 2.51 5 N 6466 2.21 5 O 7041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 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: 36829 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: "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: "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: "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: "F" Number of atoms: 5565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5565 Classifications: {'peptide': 712} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 2 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: "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} 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} Time building chain proxies: 7.58, per 1000 atoms: 0.21 Number of scatterers: 36829 At special positions: 0 Unit cell: (183.48, 195.156, 114.258, 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 188 16.00 P 24 15.00 O 7041 8.00 N 6466 7.00 C 23110 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: 3.13 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8714 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 39 sheets defined 52.1% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 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 139 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.396A 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: 4.160A 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 removed outlier: 3.534A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.843A 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 354 through 359 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.539A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) 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 removed outlier: 3.556A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.213A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 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 671 through 679 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.572A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 removed outlier: 3.557A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) 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 removed outlier: 3.529A pdb=" N VAL E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.722A 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: 4.001A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 334 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 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 428 removed outlier: 3.641A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (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: 3.545A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.650A 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: 4.162A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.859A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) 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: 4.642A 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: 4.129A 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: 3.783A 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 384 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 431 removed outlier: 3.691A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 3.592A 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 removed outlier: 3.509A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.269A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.659A 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 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: 4.109A 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: 4.839A 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: 4.146A 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 removed outlier: 3.516A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.775A 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: 3.615A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 431 " --> pdb=" O MET C 427 " (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 removed outlier: 3.508A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.026A 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 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' 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: 4.815A 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: 3.960A 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 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: 3.665A 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 removed outlier: 3.563A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 4.238A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 removed outlier: 3.723A pdb=" N ARG A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) 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 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 706 removed outlier: 3.798A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' 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: 3.758A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 165 removed outlier: 4.028A 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 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 280 through 285 Processing helix chain 'G' and resid 296 through 316 Processing helix chain 'G' and resid 319 through 328 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: 3.956A pdb=" N VAL G 362 " --> pdb=" O ARG G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 399 Processing helix chain 'G' and resid 411 through 421 removed outlier: 3.610A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 435 Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.548A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 removed outlier: 3.771A pdb=" N VAL F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) 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: 4.733A 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 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 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 349 through 353 removed outlier: 4.191A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 431 removed outlier: 4.416A 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 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.294A 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 Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' 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 sheet with id=AA1, first strand: chain 'B' and resid 25 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.728A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.711A 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: 6.098A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.380A 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: 6.391A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 25 through 30 removed outlier: 8.014A pdb=" N LYS E 81 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER E 42 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASP E 74 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU E 41 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 151 through 156 removed outlier: 6.974A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.796A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.231A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AB3, 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: 7.420A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 29 removed outlier: 7.466A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LYS D 81 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER D 42 " --> pdb=" O LYS D 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.901A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB7, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AB8, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.448A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.415A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 25 through 29 Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.880A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AC4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AC5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.276A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.409A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 25 through 29 removed outlier: 7.153A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.607A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AD1, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.825A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.061A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 469 through 470 removed outlier: 6.446A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AD5, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AD6, first strand: chain 'G' and resid 386 through 387 removed outlier: 4.879A pdb=" N LEU G 379 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ALA G 404 " --> pdb=" O TYR G 336 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU G 338 " --> pdb=" O ALA G 404 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU G 406 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG G 340 " --> pdb=" O LEU G 406 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE G 408 " --> pdb=" O ARG G 340 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG G 342 " --> pdb=" O PHE G 408 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N TRP G 410 " --> pdb=" O ARG G 342 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 25 through 29 Processing sheet with id=AD8, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.677A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AE1, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AE2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.139A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.540A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) 1718 hydrogen bonds defined for protein. 4815 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: 7.79 Time building geometry restraints manager: 3.98 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: 7567 1.33 - 1.45: 7838 1.45 - 1.57: 21708 1.57 - 1.69: 36 1.69 - 1.81: 299 Bond restraints: 37448 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 3.09e+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 3.04e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 37443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 49630 2.49 - 4.98: 882 4.98 - 7.47: 86 7.47 - 9.95: 34 9.95 - 12.44: 8 Bond angle restraints: 50640 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 113.28 123.97 -10.69 1.22e+00 6.72e-01 7.68e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 112.88 122.46 -9.58 1.29e+00 6.01e-01 5.52e+01 angle pdb=" N LYS G 333 " pdb=" CA LYS G 333 " pdb=" C LYS G 333 " ideal model delta sigma weight residual 111.82 118.42 -6.60 1.16e+00 7.43e-01 3.24e+01 angle pdb=" C HIS F 226 " pdb=" N PRO F 227 " pdb=" CA PRO F 227 " ideal model delta sigma weight residual 119.28 124.46 -5.18 1.10e+00 8.26e-01 2.22e+01 angle pdb=" C GLN G 136 " pdb=" N ARG G 137 " pdb=" CA ARG G 137 " ideal model delta sigma weight residual 120.44 126.56 -6.12 1.30e+00 5.92e-01 2.22e+01 ... (remaining 50635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 22878 35.56 - 71.12: 251 71.12 - 106.69: 39 106.69 - 142.25: 8 142.25 - 177.81: 9 Dihedral angle restraints: 23185 sinusoidal: 9753 harmonic: 13432 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 300.00 122.19 177.81 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 127.80 172.19 1 2.00e+01 2.50e-03 4.78e+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 -60.00 111.81 -171.82 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 23182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4087 0.048 - 0.097: 988 0.097 - 0.145: 477 0.145 - 0.193: 150 0.193 - 0.242: 12 Chirality restraints: 5714 Sorted by residual: 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 2.68 -0.24 2.00e-01 2.50e+01 1.46e+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 1.44e+00 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 1.42e+00 ... (remaining 5711 not shown) Planarity restraints: 6636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+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 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 534 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C GLU F 534 " -0.039 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 F 360 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C PHE F 360 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE F 360 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY F 361 " -0.013 2.00e-02 2.50e+03 ... (remaining 6633 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 13371 2.88 - 3.39: 35343 3.39 - 3.89: 63025 3.89 - 4.40: 71836 4.40 - 4.90: 117350 Nonbonded interactions: 300925 Sorted by model distance: nonbonded pdb=" NZ LYS F 211 " pdb=" O ALA F 570 " model vdw 2.381 3.120 nonbonded pdb=" OD2 ASP B 368 " pdb=" NZ LYS B 565 " model vdw 2.387 3.120 nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.410 3.120 nonbonded pdb=" NZ LYS F 512 " pdb=" O GLY F 637 " model vdw 2.432 3.120 nonbonded pdb=" OD2 ASP G 176 " pdb=" NZ LYS G 180 " model vdw 2.432 3.120 ... (remaining 300920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'B' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'C' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'D' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'E' and (resid 23 through 499 or resid 509 through 902)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.550 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 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 37448 Z= 0.612 Angle : 0.852 12.442 50640 Z= 0.524 Chirality : 0.058 0.242 5714 Planarity : 0.004 0.036 6636 Dihedral : 12.277 177.812 14471 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.77 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 0.39 (0.11), residues: 4628 helix: -0.23 (0.10), residues: 2040 sheet: 0.71 (0.17), residues: 802 loop : 0.98 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 635 TYR 0.001 0.000 TYR D 143 PHE 0.002 0.000 PHE D 539 TRP 0.002 0.000 TRP C 476 HIS 0.001 0.000 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.01080 (37448) covalent geometry : angle 0.85172 (50640) hydrogen bonds : bond 0.20909 ( 1718) hydrogen bonds : angle 6.48780 ( 4815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1287 time to evaluate : 1.027 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: B 499 HIS cc_start: 0.6731 (m-70) cc_final: 0.6439 (m170) REVERT: E 244 TYR cc_start: 0.6790 (p90) cc_final: 0.6449 (p90) REVERT: D 442 MET cc_start: 0.8427 (mmm) cc_final: 0.8109 (mmt) REVERT: D 524 LYS cc_start: 0.7264 (mttt) cc_final: 0.6916 (mtmm) REVERT: C 324 ILE cc_start: 0.8692 (tp) cc_final: 0.8417 (mt) REVERT: A 243 LEU cc_start: 0.8201 (mt) cc_final: 0.7393 (mp) REVERT: G 312 GLU cc_start: 0.7215 (tp30) cc_final: 0.6682 (mm-30) REVERT: G 389 GLU cc_start: 0.5080 (tt0) cc_final: 0.4425 (pt0) outliers start: 0 outliers final: 0 residues processed: 1287 average time/residue: 0.2387 time to fit residues: 468.7712 Evaluate side-chains 645 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 432 optimal weight: 0.4980 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 568 GLN E 296 ASN E 421 GLN E 460 ASN E 490 GLN D 90 ASN D 91 ASN D 421 GLN ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN C 91 ASN C 317 HIS C 735 HIS A 90 ASN A 285 ASN A 494 GLN A 602 ASN A 603 GLN A 660 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN F 443 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.194710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.150538 restraints weight = 50353.947| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.95 r_work: 0.3656 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37448 Z= 0.160 Angle : 0.668 8.309 50640 Z= 0.332 Chirality : 0.046 0.206 5714 Planarity : 0.005 0.049 6636 Dihedral : 9.749 175.877 5181 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.12 % Favored : 98.85 % Rotamer: Outliers : 2.17 % Allowed : 9.13 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.48 (0.12), residues: 4628 helix: 1.09 (0.11), residues: 2048 sheet: 0.83 (0.17), residues: 788 loop : 1.21 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 487 TYR 0.024 0.002 TYR D 203 PHE 0.019 0.001 PHE G 408 TRP 0.028 0.002 TRP B 476 HIS 0.014 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00362 (37448) covalent geometry : angle 0.66804 (50640) hydrogen bonds : bond 0.05528 ( 1718) hydrogen bonds : angle 4.58907 ( 4815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 730 time to evaluate : 1.432 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: B 115 HIS cc_start: 0.5331 (m-70) cc_final: 0.4797 (m-70) REVERT: B 162 GLU cc_start: 0.7801 (pt0) cc_final: 0.7588 (pt0) REVERT: B 440 GLU cc_start: 0.6875 (mp0) cc_final: 0.6456 (mm-30) REVERT: E 115 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.5964 (m-70) REVERT: E 167 GLU cc_start: 0.7866 (tt0) cc_final: 0.7441 (tm-30) REVERT: E 244 TYR cc_start: 0.8349 (p90) cc_final: 0.8098 (p90) REVERT: E 556 GLU cc_start: 0.5679 (pm20) cc_final: 0.5343 (pm20) REVERT: D 140 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7150 (tt) REVERT: D 196 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8112 (mt-10) REVERT: D 383 ILE cc_start: 0.9018 (mt) cc_final: 0.8787 (mm) REVERT: C 29 ASP cc_start: 0.8088 (t0) cc_final: 0.7845 (t70) REVERT: C 46 MET cc_start: 0.5796 (mtp) cc_final: 0.5526 (mmm) REVERT: C 59 LEU cc_start: 0.8894 (mp) cc_final: 0.8624 (mt) REVERT: C 143 TYR cc_start: 0.6782 (m-80) cc_final: 0.6314 (m-80) REVERT: C 283 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7691 (mt-10) REVERT: C 324 ILE cc_start: 0.8718 (tp) cc_final: 0.8378 (mt) REVERT: C 443 ASN cc_start: 0.8479 (t0) cc_final: 0.8220 (t0) REVERT: C 508 MET cc_start: 0.7829 (tpt) cc_final: 0.7275 (tpp) REVERT: C 512 LYS cc_start: 0.7476 (mttt) cc_final: 0.7031 (tppt) REVERT: C 689 GLU cc_start: 0.7885 (tt0) cc_final: 0.7439 (tm-30) REVERT: A 135 LEU cc_start: 0.7203 (mt) cc_final: 0.6985 (mt) REVERT: A 397 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7349 (mp0) REVERT: A 449 MET cc_start: 0.6437 (tmm) cc_final: 0.6222 (tmm) REVERT: A 488 GLU cc_start: 0.6950 (tp30) cc_final: 0.6546 (mm-30) REVERT: A 633 ILE cc_start: 0.8169 (mm) cc_final: 0.7946 (tp) REVERT: A 650 GLU cc_start: 0.8225 (mp0) cc_final: 0.7854 (mp0) REVERT: G 278 GLN cc_start: 0.6223 (tp40) cc_final: 0.5771 (tt0) REVERT: G 304 GLN cc_start: 0.8022 (tp40) cc_final: 0.7465 (tm-30) REVERT: G 312 GLU cc_start: 0.8278 (tp30) cc_final: 0.7703 (tp30) REVERT: G 320 LYS cc_start: 0.7400 (ptmm) cc_final: 0.6949 (ttmt) REVERT: G 338 LEU cc_start: 0.6803 (tp) cc_final: 0.6232 (tt) REVERT: G 350 GLN cc_start: 0.6955 (tt0) cc_final: 0.6748 (tm-30) REVERT: F 52 PHE cc_start: 0.8357 (m-10) cc_final: 0.8048 (m-80) REVERT: F 239 ARG cc_start: 0.7879 (mpp-170) cc_final: 0.7356 (mpt180) REVERT: F 442 MET cc_start: 0.7953 (mmt) cc_final: 0.7536 (mmt) REVERT: F 531 ILE cc_start: 0.8206 (tp) cc_final: 0.7832 (tp) REVERT: F 536 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8063 (tp40) outliers start: 86 outliers final: 49 residues processed: 782 average time/residue: 0.2131 time to fit residues: 267.8800 Evaluate side-chains 634 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 582 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 734 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 487 ARG Chi-restraints excluded: chain F residue 536 GLN Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 751 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 2 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 325 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 133 optimal weight: 0.0970 chunk 115 optimal weight: 2.9990 chunk 363 optimal weight: 20.0000 chunk 340 optimal weight: 3.9990 chunk 345 optimal weight: 0.5980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS B 421 GLN E 384 HIS E 398 GLN D 91 ASN ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 568 GLN C 327 GLN C 384 HIS C 660 ASN A 285 ASN A 327 GLN A 603 GLN A 735 HIS ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN F 384 HIS ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.188434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143850 restraints weight = 50401.423| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.27 r_work: 0.3547 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37448 Z= 0.178 Angle : 0.647 8.895 50640 Z= 0.316 Chirality : 0.046 0.182 5714 Planarity : 0.004 0.046 6636 Dihedral : 9.169 171.603 5181 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.32 % Allowed : 10.83 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.60 (0.12), residues: 4628 helix: 1.26 (0.11), residues: 2068 sheet: 0.81 (0.17), residues: 794 loop : 1.21 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 274 TYR 0.016 0.002 TYR G 354 PHE 0.018 0.002 PHE G 377 TRP 0.020 0.002 TRP B 476 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00418 (37448) covalent geometry : angle 0.64732 (50640) hydrogen bonds : bond 0.04485 ( 1718) hydrogen bonds : angle 4.35888 ( 4815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 623 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 HIS cc_start: 0.5254 (m90) cc_final: 0.5012 (m-70) REVERT: B 185 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7305 (pt0) REVERT: B 256 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.7639 (ttp-170) REVERT: B 440 GLU cc_start: 0.7102 (mp0) cc_final: 0.6575 (mm-30) REVERT: B 490 GLN cc_start: 0.8579 (mt0) cc_final: 0.8314 (pt0) REVERT: B 644 TYR cc_start: 0.8000 (t80) cc_final: 0.7581 (t80) REVERT: B 678 MET cc_start: 0.6328 (mmt) cc_final: 0.6056 (tpp) REVERT: E 46 MET cc_start: 0.7716 (mtp) cc_final: 0.7452 (mtm) REVERT: E 115 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5663 (m-70) REVERT: E 397 GLU cc_start: 0.8162 (tt0) cc_final: 0.7809 (tm-30) REVERT: E 556 GLU cc_start: 0.5626 (pm20) cc_final: 0.5346 (pm20) REVERT: E 560 ARG cc_start: 0.8272 (ptm160) cc_final: 0.7820 (ttt180) REVERT: D 140 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7233 (tt) REVERT: D 196 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8269 (mt-10) REVERT: D 560 ARG cc_start: 0.8343 (ptp-110) cc_final: 0.7844 (ttm110) REVERT: D 645 ILE cc_start: 0.8354 (mm) cc_final: 0.8133 (mt) REVERT: D 744 ARG cc_start: 0.5986 (mmt90) cc_final: 0.5715 (mmt90) REVERT: C 29 ASP cc_start: 0.8192 (t0) cc_final: 0.7875 (t70) REVERT: C 46 MET cc_start: 0.5840 (mtp) cc_final: 0.5602 (mmm) REVERT: C 143 TYR cc_start: 0.6834 (m-80) cc_final: 0.6378 (m-80) REVERT: C 292 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7547 (mm-30) REVERT: C 324 ILE cc_start: 0.8753 (tp) cc_final: 0.8419 (mt) REVERT: C 442 MET cc_start: 0.8111 (mmm) cc_final: 0.7902 (mmt) REVERT: C 512 LYS cc_start: 0.7610 (mttt) cc_final: 0.6883 (tppt) REVERT: C 689 GLU cc_start: 0.7997 (tt0) cc_final: 0.7525 (tm-30) REVERT: C 744 ARG cc_start: 0.6797 (ttt180) cc_final: 0.6527 (ttm170) REVERT: A 66 GLU cc_start: 0.7884 (tt0) cc_final: 0.7506 (tp30) REVERT: A 322 ARG cc_start: 0.7435 (mtt90) cc_final: 0.7075 (mtt90) REVERT: A 397 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7379 (mp0) REVERT: A 427 MET cc_start: 0.6598 (ttm) cc_final: 0.6276 (tmm) REVERT: A 449 MET cc_start: 0.6582 (tmm) cc_final: 0.6314 (tmm) REVERT: A 488 GLU cc_start: 0.7035 (tp30) cc_final: 0.6462 (mm-30) REVERT: G 54 MET cc_start: 0.2562 (tpt) cc_final: 0.2273 (tpt) REVERT: G 273 GLN cc_start: 0.7829 (tm-30) cc_final: 0.6088 (mm110) REVERT: G 278 GLN cc_start: 0.6351 (tp40) cc_final: 0.5997 (tt0) REVERT: G 370 LEU cc_start: 0.7849 (mt) cc_final: 0.7643 (mm) REVERT: F 33 ASN cc_start: 0.7613 (t0) cc_final: 0.7399 (t0) REVERT: F 80 GLU cc_start: 0.7946 (tp30) cc_final: 0.7322 (tp30) REVERT: F 167 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7408 (mm-30) REVERT: F 239 ARG cc_start: 0.7995 (mpp-170) cc_final: 0.7267 (mpt180) REVERT: F 442 MET cc_start: 0.8138 (mmt) cc_final: 0.7889 (mmt) REVERT: F 536 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8196 (tp40) REVERT: F 563 PHE cc_start: 0.8710 (m-80) cc_final: 0.8470 (m-80) outliers start: 92 outliers final: 60 residues processed: 676 average time/residue: 0.2081 time to fit residues: 226.3438 Evaluate side-chains 601 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 538 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 69 CYS Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 487 ARG Chi-restraints excluded: chain F residue 536 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 294 optimal weight: 0.4980 chunk 197 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 291 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 chunk 439 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 443 ASN D 460 ASN D 568 GLN A 90 ASN A 735 HIS ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.188457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143741 restraints weight = 50723.861| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.47 r_work: 0.3520 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37448 Z= 0.142 Angle : 0.607 8.291 50640 Z= 0.294 Chirality : 0.045 0.195 5714 Planarity : 0.004 0.050 6636 Dihedral : 8.701 169.507 5181 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.04 % Allowed : 11.86 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.68 (0.12), residues: 4628 helix: 1.43 (0.11), residues: 2049 sheet: 0.81 (0.18), residues: 781 loop : 1.13 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 567 TYR 0.024 0.002 TYR A 203 PHE 0.028 0.002 PHE G 377 TRP 0.027 0.001 TRP B 476 HIS 0.013 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00328 (37448) covalent geometry : angle 0.60698 (50640) hydrogen bonds : bond 0.03921 ( 1718) hydrogen bonds : angle 4.17850 ( 4815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 607 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7269 (pt0) REVERT: B 440 GLU cc_start: 0.7226 (mp0) cc_final: 0.6593 (mm-30) REVERT: B 491 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7374 (tm-30) REVERT: B 577 ASP cc_start: 0.9371 (t0) cc_final: 0.9077 (t0) REVERT: B 644 TYR cc_start: 0.7932 (t80) cc_final: 0.7565 (t80) REVERT: E 46 MET cc_start: 0.7661 (mtp) cc_final: 0.7384 (mtm) REVERT: E 115 HIS cc_start: 0.6216 (OUTLIER) cc_final: 0.5638 (m-70) REVERT: E 273 GLU cc_start: 0.8212 (tp30) cc_final: 0.7760 (tp30) REVERT: E 397 GLU cc_start: 0.8254 (tt0) cc_final: 0.7747 (tm-30) REVERT: E 508 MET cc_start: 0.8193 (tpt) cc_final: 0.7525 (tpt) REVERT: E 560 ARG cc_start: 0.8243 (ptm160) cc_final: 0.7784 (ttt180) REVERT: E 693 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7825 (ttt90) REVERT: E 731 ILE cc_start: 0.8088 (mt) cc_final: 0.7833 (mp) REVERT: D 60 LYS cc_start: 0.8070 (mttm) cc_final: 0.7858 (mttp) REVERT: D 140 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7214 (tt) REVERT: D 560 ARG cc_start: 0.8297 (ptp-110) cc_final: 0.7800 (ttm110) REVERT: D 645 ILE cc_start: 0.8315 (mm) cc_final: 0.8070 (mt) REVERT: D 650 GLU cc_start: 0.8486 (mp0) cc_final: 0.8284 (mp0) REVERT: C 29 ASP cc_start: 0.8146 (t0) cc_final: 0.7845 (t70) REVERT: C 46 MET cc_start: 0.5944 (mtp) cc_final: 0.5668 (mmm) REVERT: C 143 TYR cc_start: 0.6841 (m-80) cc_final: 0.6330 (m-80) REVERT: C 283 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7717 (mt-10) REVERT: C 512 LYS cc_start: 0.7599 (mttt) cc_final: 0.6772 (tppt) REVERT: C 689 GLU cc_start: 0.8039 (tt0) cc_final: 0.7531 (tm-30) REVERT: C 744 ARG cc_start: 0.6726 (ttt180) cc_final: 0.6512 (ttm170) REVERT: A 66 GLU cc_start: 0.7882 (tt0) cc_final: 0.7428 (tp30) REVERT: A 322 ARG cc_start: 0.7276 (mtt90) cc_final: 0.6847 (mtt90) REVERT: A 397 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7427 (mp0) REVERT: A 427 MET cc_start: 0.6667 (ttm) cc_final: 0.6424 (tmm) REVERT: A 449 MET cc_start: 0.6468 (tmm) cc_final: 0.6176 (tmm) REVERT: A 488 GLU cc_start: 0.6994 (tp30) cc_final: 0.6224 (mt-10) REVERT: A 508 MET cc_start: 0.6992 (tpt) cc_final: 0.6620 (tpt) REVERT: G 54 MET cc_start: 0.2549 (tpt) cc_final: 0.2306 (tpt) REVERT: G 273 GLN cc_start: 0.7789 (tm-30) cc_final: 0.6012 (mm110) REVERT: G 278 GLN cc_start: 0.6386 (tp40) cc_final: 0.6073 (tt0) REVERT: G 338 LEU cc_start: 0.7024 (tp) cc_final: 0.6346 (tt) REVERT: F 33 ASN cc_start: 0.7779 (t0) cc_final: 0.7498 (t0) REVERT: F 80 GLU cc_start: 0.8170 (tp30) cc_final: 0.7553 (tp30) REVERT: F 167 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7489 (mm-30) REVERT: F 239 ARG cc_start: 0.7898 (mpp-170) cc_final: 0.7295 (mtp85) REVERT: F 565 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8689 (mtmm) outliers start: 81 outliers final: 56 residues processed: 653 average time/residue: 0.2116 time to fit residues: 223.7208 Evaluate side-chains 611 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 553 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 649 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 274 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 chunk 254 optimal weight: 1.9990 chunk 461 optimal weight: 0.3980 chunk 418 optimal weight: 0.1980 chunk 133 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 457 optimal weight: 0.0670 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 285 ASN D 568 GLN C 91 ASN A 90 ASN ** G 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.190193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.144372 restraints weight = 50612.486| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.41 r_work: 0.3557 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 37448 Z= 0.108 Angle : 0.588 12.448 50640 Z= 0.281 Chirality : 0.044 0.384 5714 Planarity : 0.004 0.047 6636 Dihedral : 8.243 170.259 5181 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.74 % Allowed : 12.62 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.73 (0.12), residues: 4628 helix: 1.52 (0.11), residues: 2074 sheet: 0.80 (0.18), residues: 781 loop : 1.10 (0.16), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 599 TYR 0.026 0.001 TYR E 244 PHE 0.027 0.001 PHE G 377 TRP 0.022 0.001 TRP B 476 HIS 0.004 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00236 (37448) covalent geometry : angle 0.58839 (50640) hydrogen bonds : bond 0.03488 ( 1718) hydrogen bonds : angle 4.03926 ( 4815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 619 time to evaluate : 1.438 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: B 58 LEU cc_start: 0.7128 (mt) cc_final: 0.6805 (tt) REVERT: B 115 HIS cc_start: 0.5569 (m-70) cc_final: 0.5136 (t70) REVERT: B 256 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.7598 (ttp-170) REVERT: B 491 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7389 (tm-30) REVERT: B 644 TYR cc_start: 0.7884 (t80) cc_final: 0.7573 (t80) REVERT: E 273 GLU cc_start: 0.8185 (tp30) cc_final: 0.7766 (tp30) REVERT: E 397 GLU cc_start: 0.8188 (tt0) cc_final: 0.7740 (tm-30) REVERT: E 508 MET cc_start: 0.8191 (tpt) cc_final: 0.7557 (tpt) REVERT: E 560 ARG cc_start: 0.8261 (ptm160) cc_final: 0.7415 (ttt180) REVERT: E 693 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7825 (ttm-80) REVERT: E 731 ILE cc_start: 0.8112 (mt) cc_final: 0.7887 (mp) REVERT: D 560 ARG cc_start: 0.8293 (ptp-110) cc_final: 0.7823 (ttm110) REVERT: D 645 ILE cc_start: 0.8318 (mm) cc_final: 0.8046 (mt) REVERT: C 29 ASP cc_start: 0.8181 (t0) cc_final: 0.7920 (t70) REVERT: C 46 MET cc_start: 0.5875 (mtp) cc_final: 0.5616 (mmm) REVERT: C 143 TYR cc_start: 0.6835 (m-80) cc_final: 0.6336 (m-80) REVERT: C 244 TYR cc_start: 0.8447 (p90) cc_final: 0.8235 (p90) REVERT: C 324 ILE cc_start: 0.8552 (tt) cc_final: 0.8303 (tp) REVERT: C 440 GLU cc_start: 0.8392 (tp30) cc_final: 0.7856 (mp0) REVERT: C 689 GLU cc_start: 0.7943 (tt0) cc_final: 0.7425 (tm-30) REVERT: A 66 GLU cc_start: 0.7808 (tt0) cc_final: 0.7254 (tp30) REVERT: A 322 ARG cc_start: 0.7312 (mtt90) cc_final: 0.6712 (mtm110) REVERT: A 397 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7458 (mp0) REVERT: A 427 MET cc_start: 0.6594 (ttm) cc_final: 0.6340 (tmm) REVERT: A 449 MET cc_start: 0.6597 (tmm) cc_final: 0.6297 (tmm) REVERT: A 488 GLU cc_start: 0.7002 (tp30) cc_final: 0.6230 (mt-10) REVERT: A 508 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6739 (tpt) REVERT: A 732 ARG cc_start: 0.7386 (mtp-110) cc_final: 0.7067 (mtm110) REVERT: G 54 MET cc_start: 0.2571 (tpt) cc_final: 0.2337 (tpt) REVERT: G 277 PHE cc_start: 0.5786 (m-80) cc_final: 0.5559 (m-80) REVERT: G 278 GLN cc_start: 0.6457 (tp40) cc_final: 0.6148 (tt0) REVERT: G 391 GLU cc_start: 0.7652 (pt0) cc_final: 0.7390 (mp0) REVERT: F 33 ASN cc_start: 0.7735 (t0) cc_final: 0.7531 (t0) REVERT: F 52 PHE cc_start: 0.8062 (m-10) cc_final: 0.7818 (m-80) REVERT: F 80 GLU cc_start: 0.8124 (tp30) cc_final: 0.7571 (tp30) REVERT: F 167 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7543 (mm-30) REVERT: F 239 ARG cc_start: 0.7881 (mpp-170) cc_final: 0.7279 (mtp180) REVERT: F 565 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8673 (mtmm) REVERT: F 599 ARG cc_start: 0.7666 (mmm160) cc_final: 0.6781 (mtm-85) outliers start: 69 outliers final: 44 residues processed: 659 average time/residue: 0.2124 time to fit residues: 226.3884 Evaluate side-chains 594 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 549 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 649 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 128 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 430 optimal weight: 4.9990 chunk 330 optimal weight: 3.9990 chunk 449 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 452 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 351 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 384 HIS B 460 ASN B 490 GLN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS D 90 ASN D 226 HIS D 460 ASN D 533 ASN D 568 GLN A 90 ASN A 568 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.179842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134919 restraints weight = 51368.336| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.16 r_work: 0.3387 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 37448 Z= 0.312 Angle : 0.795 9.741 50640 Z= 0.387 Chirality : 0.051 0.259 5714 Planarity : 0.006 0.054 6636 Dihedral : 8.348 172.236 5181 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.95 % Allowed : 12.84 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.06 (0.12), residues: 4628 helix: 0.92 (0.11), residues: 2086 sheet: 0.73 (0.18), residues: 743 loop : 0.66 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 567 TYR 0.026 0.003 TYR E 244 PHE 0.029 0.003 PHE D 516 TRP 0.027 0.002 TRP B 476 HIS 0.008 0.001 HIS E 384 Details of bonding type rmsd covalent geometry : bond 0.00757 (37448) covalent geometry : angle 0.79479 (50640) hydrogen bonds : bond 0.04674 ( 1718) hydrogen bonds : angle 4.55602 ( 4815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 596 time to evaluate : 1.249 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: B 256 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.7688 (ttp-170) REVERT: B 338 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7310 (mtm-85) REVERT: B 490 GLN cc_start: 0.8526 (pt0) cc_final: 0.8152 (pt0) REVERT: B 491 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7463 (tm-30) REVERT: E 46 MET cc_start: 0.7740 (mtp) cc_final: 0.7440 (mtm) REVERT: E 109 LYS cc_start: 0.6752 (mmtt) cc_final: 0.6534 (mtpt) REVERT: E 115 HIS cc_start: 0.6266 (OUTLIER) cc_final: 0.5693 (m-70) REVERT: E 287 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.6902 (ptp90) REVERT: E 397 GLU cc_start: 0.8412 (tt0) cc_final: 0.7936 (tm-30) REVERT: E 508 MET cc_start: 0.8241 (tpt) cc_final: 0.7526 (tpt) REVERT: E 693 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7957 (ttm-80) REVERT: E 731 ILE cc_start: 0.8290 (mt) cc_final: 0.8071 (mp) REVERT: E 740 MET cc_start: 0.8450 (mmm) cc_final: 0.8246 (tpp) REVERT: D 33 ASN cc_start: 0.7675 (t0) cc_final: 0.7413 (t0) REVERT: D 100 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7378 (pp) REVERT: D 140 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7486 (tt) REVERT: D 143 TYR cc_start: 0.9007 (m-80) cc_final: 0.8780 (m-80) REVERT: D 183 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.7381 (t70) REVERT: D 560 ARG cc_start: 0.8463 (ptp-110) cc_final: 0.8147 (ptp90) REVERT: D 564 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8842 (t70) REVERT: D 568 GLN cc_start: 0.8578 (mt0) cc_final: 0.8216 (mt0) REVERT: C 512 LYS cc_start: 0.7643 (mttt) cc_final: 0.6822 (tppt) REVERT: C 689 GLU cc_start: 0.8099 (tt0) cc_final: 0.7692 (tm-30) REVERT: A 397 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7591 (mp0) REVERT: A 427 MET cc_start: 0.6803 (ttm) cc_final: 0.6571 (tmm) REVERT: A 449 MET cc_start: 0.6282 (tmm) cc_final: 0.5806 (tmm) REVERT: A 484 ASP cc_start: 0.8464 (m-30) cc_final: 0.7911 (t0) REVERT: A 488 GLU cc_start: 0.7175 (tp30) cc_final: 0.6299 (mt-10) REVERT: A 508 MET cc_start: 0.7475 (tpt) cc_final: 0.7267 (tpp) REVERT: A 561 GLU cc_start: 0.7981 (mp0) cc_final: 0.7482 (mp0) REVERT: G 54 MET cc_start: 0.2474 (tpt) cc_final: 0.2191 (tpt) REVERT: G 370 LEU cc_start: 0.7588 (mm) cc_final: 0.7366 (mt) REVERT: F 33 ASN cc_start: 0.8190 (t0) cc_final: 0.7895 (t0) REVERT: F 167 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7835 (tp30) REVERT: F 239 ARG cc_start: 0.7866 (mpp-170) cc_final: 0.7232 (mtp85) REVERT: F 273 GLU cc_start: 0.8720 (tp30) cc_final: 0.8215 (tp30) REVERT: F 582 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6267 (mp) REVERT: F 644 TYR cc_start: 0.8627 (t80) cc_final: 0.8227 (t80) outliers start: 117 outliers final: 79 residues processed: 667 average time/residue: 0.2098 time to fit residues: 224.5063 Evaluate side-chains 605 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 520 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 642 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 344 optimal weight: 30.0000 chunk 419 optimal weight: 0.1980 chunk 201 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 chunk 279 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 411 optimal weight: 0.9990 chunk 384 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 294 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 460 ASN E 285 ASN E 404 HIS D 460 ASN D 533 ASN C 340 HIS C 568 GLN A 90 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.179309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125333 restraints weight = 51332.337| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.37 r_work: 0.3473 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 37448 Z= 0.124 Angle : 0.623 8.747 50640 Z= 0.300 Chirality : 0.044 0.206 5714 Planarity : 0.004 0.053 6636 Dihedral : 7.583 162.979 5181 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.79 % Allowed : 15.14 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.38 (0.12), residues: 4628 helix: 1.29 (0.11), residues: 2088 sheet: 0.68 (0.18), residues: 769 loop : 0.78 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 560 TYR 0.023 0.002 TYR E 244 PHE 0.020 0.001 PHE G 377 TRP 0.015 0.001 TRP B 476 HIS 0.003 0.001 HIS E 384 Details of bonding type rmsd covalent geometry : bond 0.00285 (37448) covalent geometry : angle 0.62291 (50640) hydrogen bonds : bond 0.03482 ( 1718) hydrogen bonds : angle 4.12625 ( 4815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 586 time to evaluate : 1.250 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: B 58 LEU cc_start: 0.7017 (mt) cc_final: 0.6659 (tt) REVERT: B 256 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7563 (ttp-170) REVERT: B 358 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8206 (mtm-85) REVERT: B 449 MET cc_start: 0.7947 (tpt) cc_final: 0.7089 (tpt) REVERT: B 476 TRP cc_start: 0.4575 (m100) cc_final: 0.4185 (m100) REVERT: B 491 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7804 (tm-30) REVERT: E 46 MET cc_start: 0.7665 (mtp) cc_final: 0.7441 (mtm) REVERT: E 273 GLU cc_start: 0.8112 (tp30) cc_final: 0.7664 (tp30) REVERT: E 287 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6788 (ptp90) REVERT: E 397 GLU cc_start: 0.8295 (tt0) cc_final: 0.7727 (tm-30) REVERT: E 508 MET cc_start: 0.8235 (tpt) cc_final: 0.7426 (tpt) REVERT: E 560 ARG cc_start: 0.8501 (ptm160) cc_final: 0.8116 (ttt180) REVERT: E 693 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7950 (ttt90) REVERT: E 731 ILE cc_start: 0.8337 (mt) cc_final: 0.8077 (mp) REVERT: D 33 ASN cc_start: 0.7659 (t0) cc_final: 0.7367 (t0) REVERT: D 143 TYR cc_start: 0.9022 (m-80) cc_final: 0.8813 (m-80) REVERT: D 560 ARG cc_start: 0.8367 (ptp-110) cc_final: 0.8025 (ptp90) REVERT: D 564 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8746 (t70) REVERT: C 187 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7964 (mm-30) REVERT: C 221 GLU cc_start: 0.8788 (pp20) cc_final: 0.8308 (pt0) REVERT: C 442 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7424 (mtp) REVERT: C 504 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8940 (mp) REVERT: C 509 THR cc_start: 0.8922 (m) cc_final: 0.8672 (p) REVERT: C 512 LYS cc_start: 0.7603 (mttt) cc_final: 0.6783 (tppt) REVERT: C 689 GLU cc_start: 0.8037 (tt0) cc_final: 0.7612 (tm-30) REVERT: C 740 MET cc_start: 0.7408 (tpp) cc_final: 0.6340 (mmm) REVERT: A 332 MET cc_start: 0.8180 (mmm) cc_final: 0.7702 (mmm) REVERT: A 359 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7716 (ttp80) REVERT: A 397 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7551 (mp0) REVERT: A 449 MET cc_start: 0.6516 (tmm) cc_final: 0.6106 (tmm) REVERT: A 484 ASP cc_start: 0.8452 (m-30) cc_final: 0.7895 (t0) REVERT: A 488 GLU cc_start: 0.7025 (tp30) cc_final: 0.6237 (mt-10) REVERT: A 508 MET cc_start: 0.7164 (tpt) cc_final: 0.6181 (tpp) REVERT: A 561 GLU cc_start: 0.7992 (mp0) cc_final: 0.7487 (mp0) REVERT: A 616 ASN cc_start: 0.8275 (m-40) cc_final: 0.7266 (p0) REVERT: G 54 MET cc_start: 0.2504 (tpt) cc_final: 0.2240 (tpt) REVERT: G 275 ARG cc_start: 0.7488 (ttm170) cc_final: 0.7276 (ttt90) REVERT: G 370 LEU cc_start: 0.7659 (mm) cc_final: 0.7406 (mt) REVERT: G 391 GLU cc_start: 0.7549 (pt0) cc_final: 0.7201 (mp0) REVERT: F 33 ASN cc_start: 0.8203 (t0) cc_final: 0.7922 (t0) REVERT: F 80 GLU cc_start: 0.8415 (tp30) cc_final: 0.8196 (tp30) REVERT: F 167 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7870 (mm-30) REVERT: F 239 ARG cc_start: 0.7912 (mpp-170) cc_final: 0.7341 (mtp85) REVERT: F 550 MET cc_start: 0.7869 (mmt) cc_final: 0.7041 (mmt) REVERT: F 567 ARG cc_start: 0.8662 (mtt-85) cc_final: 0.7467 (mmt180) REVERT: F 582 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6086 (mp) REVERT: F 644 TYR cc_start: 0.8491 (t80) cc_final: 0.8165 (t80) outliers start: 71 outliers final: 46 residues processed: 625 average time/residue: 0.2130 time to fit residues: 212.5574 Evaluate side-chains 586 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 535 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain G residue 311 VAL Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 649 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 411 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 408 optimal weight: 0.5980 chunk 415 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 383 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 HIS B 460 ASN B 763 GLN E 404 HIS ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 568 GLN A 90 ASN A 285 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 568 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.179741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126756 restraints weight = 50917.525| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.26 r_work: 0.3432 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 37448 Z= 0.205 Angle : 0.674 12.926 50640 Z= 0.324 Chirality : 0.047 0.205 5714 Planarity : 0.005 0.053 6636 Dihedral : 7.477 149.130 5181 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.27 % Allowed : 14.81 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.24 (0.12), residues: 4628 helix: 1.19 (0.11), residues: 2086 sheet: 0.61 (0.18), residues: 753 loop : 0.69 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 753 TYR 0.026 0.002 TYR A 495 PHE 0.024 0.002 PHE G 292 TRP 0.020 0.002 TRP B 551 HIS 0.008 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00496 (37448) covalent geometry : angle 0.67361 (50640) hydrogen bonds : bond 0.03788 ( 1718) hydrogen bonds : angle 4.24549 ( 4815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 562 time to evaluate : 1.413 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: B 256 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.7628 (ttp-170) REVERT: B 368 ASP cc_start: 0.8503 (t70) cc_final: 0.8295 (t0) REVERT: B 449 MET cc_start: 0.7988 (tpt) cc_final: 0.7106 (tpt) REVERT: B 490 GLN cc_start: 0.8428 (pt0) cc_final: 0.8107 (pt0) REVERT: E 46 MET cc_start: 0.7701 (mtp) cc_final: 0.7420 (mtm) REVERT: E 109 LYS cc_start: 0.6750 (mmtt) cc_final: 0.6517 (mtpt) REVERT: E 273 GLU cc_start: 0.8157 (tp30) cc_final: 0.7702 (tp30) REVERT: E 287 ARG cc_start: 0.7252 (mtm-85) cc_final: 0.6802 (ptp90) REVERT: E 397 GLU cc_start: 0.8364 (tt0) cc_final: 0.7842 (tm-30) REVERT: E 508 MET cc_start: 0.8249 (tpt) cc_final: 0.7481 (tpt) REVERT: E 560 ARG cc_start: 0.8636 (ptm160) cc_final: 0.8309 (ttt180) REVERT: E 616 ASN cc_start: 0.7719 (t0) cc_final: 0.6702 (p0) REVERT: E 693 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7879 (ttm-80) REVERT: E 731 ILE cc_start: 0.8388 (mt) cc_final: 0.8117 (mp) REVERT: D 33 ASN cc_start: 0.7736 (t0) cc_final: 0.7472 (t0) REVERT: D 100 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7283 (pp) REVERT: D 560 ARG cc_start: 0.8419 (ptp-110) cc_final: 0.8114 (ptp90) REVERT: D 564 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8778 (t70) REVERT: C 187 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7976 (mm-30) REVERT: C 221 GLU cc_start: 0.8794 (pp20) cc_final: 0.8350 (pt0) REVERT: C 440 GLU cc_start: 0.8510 (tp30) cc_final: 0.7880 (mp0) REVERT: C 442 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7649 (mtp) REVERT: C 504 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8928 (mp) REVERT: C 509 THR cc_start: 0.8900 (m) cc_final: 0.8664 (p) REVERT: C 512 LYS cc_start: 0.7603 (mttt) cc_final: 0.6752 (tppt) REVERT: C 689 GLU cc_start: 0.8064 (tt0) cc_final: 0.7636 (tm-30) REVERT: C 740 MET cc_start: 0.7397 (tpp) cc_final: 0.6395 (mmm) REVERT: A 359 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7682 (ttt-90) REVERT: A 397 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7528 (mp0) REVERT: A 484 ASP cc_start: 0.8454 (m-30) cc_final: 0.7925 (t0) REVERT: A 488 GLU cc_start: 0.7086 (tp30) cc_final: 0.6298 (mt-10) REVERT: A 508 MET cc_start: 0.7280 (tpt) cc_final: 0.6310 (tpp) REVERT: A 561 GLU cc_start: 0.8014 (mp0) cc_final: 0.7480 (mp0) REVERT: G 54 MET cc_start: 0.2540 (tpt) cc_final: 0.2282 (tpt) REVERT: G 275 ARG cc_start: 0.7429 (ttm170) cc_final: 0.7129 (ttt90) REVERT: G 278 GLN cc_start: 0.6399 (tm-30) cc_final: 0.6114 (tt0) REVERT: G 370 LEU cc_start: 0.7710 (mm) cc_final: 0.7414 (mt) REVERT: G 391 GLU cc_start: 0.7588 (pt0) cc_final: 0.7195 (mp0) REVERT: F 33 ASN cc_start: 0.8231 (t0) cc_final: 0.7930 (t0) REVERT: F 167 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7870 (tp30) REVERT: F 239 ARG cc_start: 0.7933 (mpp-170) cc_final: 0.7336 (mtp85) REVERT: F 567 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.8105 (mmt-90) REVERT: F 582 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6294 (mp) outliers start: 90 outliers final: 67 residues processed: 609 average time/residue: 0.2212 time to fit residues: 215.7769 Evaluate side-chains 599 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 526 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 275 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 383 optimal weight: 0.0670 chunk 165 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 413 optimal weight: 1.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN E 404 HIS E 616 ASN D 460 ASN D 568 GLN C 558 ASN A 90 ASN A 103 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.181262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128379 restraints weight = 51078.206| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.29 r_work: 0.3450 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 37448 Z= 0.154 Angle : 0.651 14.514 50640 Z= 0.311 Chirality : 0.045 0.212 5714 Planarity : 0.004 0.055 6636 Dihedral : 7.144 135.935 5181 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.89 % Allowed : 15.27 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.29 (0.12), residues: 4628 helix: 1.25 (0.11), residues: 2087 sheet: 0.60 (0.19), residues: 752 loop : 0.71 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 732 TYR 0.029 0.002 TYR A 495 PHE 0.021 0.002 PHE G 377 TRP 0.020 0.001 TRP F 551 HIS 0.007 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00367 (37448) covalent geometry : angle 0.65091 (50640) hydrogen bonds : bond 0.03548 ( 1718) hydrogen bonds : angle 4.15664 ( 4815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 548 time to evaluate : 1.034 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: B 256 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.7627 (ttp-170) REVERT: B 352 SER cc_start: 0.9214 (m) cc_final: 0.8969 (p) REVERT: B 358 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8361 (mtt-85) REVERT: B 368 ASP cc_start: 0.8500 (t70) cc_final: 0.8279 (t0) REVERT: B 427 MET cc_start: 0.6083 (tpp) cc_final: 0.5294 (tpp) REVERT: B 449 MET cc_start: 0.7991 (tpt) cc_final: 0.7116 (tpt) REVERT: B 476 TRP cc_start: 0.4771 (m100) cc_final: 0.4429 (m100) REVERT: B 490 GLN cc_start: 0.8384 (pt0) cc_final: 0.8038 (pt0) REVERT: E 46 MET cc_start: 0.7649 (mtp) cc_final: 0.7378 (mtm) REVERT: E 273 GLU cc_start: 0.8145 (tp30) cc_final: 0.7702 (tp30) REVERT: E 287 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6763 (ptp90) REVERT: E 397 GLU cc_start: 0.8323 (tt0) cc_final: 0.7820 (tm-30) REVERT: E 508 MET cc_start: 0.8235 (tpt) cc_final: 0.7457 (tpt) REVERT: E 560 ARG cc_start: 0.8571 (ptm160) cc_final: 0.8256 (ttt180) REVERT: E 693 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.7900 (ttm-80) REVERT: D 24 ASN cc_start: 0.6715 (m-40) cc_final: 0.6097 (p0) REVERT: D 33 ASN cc_start: 0.7772 (t0) cc_final: 0.7503 (t0) REVERT: D 100 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7217 (pp) REVERT: D 560 ARG cc_start: 0.8411 (ptp-110) cc_final: 0.8105 (ptp90) REVERT: D 564 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8751 (t70) REVERT: C 187 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7959 (mm-30) REVERT: C 221 GLU cc_start: 0.8793 (pp20) cc_final: 0.8360 (pt0) REVERT: C 438 ASP cc_start: 0.8919 (t0) cc_final: 0.8602 (t0) REVERT: C 440 GLU cc_start: 0.8539 (tp30) cc_final: 0.7840 (mp0) REVERT: C 442 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7542 (mtp) REVERT: C 504 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8960 (mp) REVERT: C 512 LYS cc_start: 0.7580 (mttt) cc_final: 0.6754 (tppt) REVERT: C 689 GLU cc_start: 0.8074 (tt0) cc_final: 0.7633 (tm-30) REVERT: C 740 MET cc_start: 0.7438 (tpp) cc_final: 0.6518 (mmm) REVERT: A 344 MET cc_start: 0.8238 (mtm) cc_final: 0.7713 (mtm) REVERT: A 359 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7759 (ttp80) REVERT: A 387 ASN cc_start: 0.8470 (m-40) cc_final: 0.7934 (t0) REVERT: A 397 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7561 (mp0) REVERT: A 449 MET cc_start: 0.6512 (tmm) cc_final: 0.6199 (tmm) REVERT: A 484 ASP cc_start: 0.8474 (m-30) cc_final: 0.8045 (t0) REVERT: A 488 GLU cc_start: 0.7014 (tp30) cc_final: 0.6265 (mt-10) REVERT: A 508 MET cc_start: 0.7206 (tpt) cc_final: 0.6200 (tpp) REVERT: A 561 GLU cc_start: 0.8009 (mp0) cc_final: 0.7485 (mp0) REVERT: G 273 GLN cc_start: 0.7531 (tp40) cc_final: 0.5788 (mp10) REVERT: G 278 GLN cc_start: 0.6398 (tm-30) cc_final: 0.6108 (tt0) REVERT: G 370 LEU cc_start: 0.7894 (mm) cc_final: 0.7547 (mt) REVERT: G 378 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6287 (pm20) REVERT: F 33 ASN cc_start: 0.8236 (t0) cc_final: 0.7938 (t0) REVERT: F 167 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7864 (tp30) REVERT: F 239 ARG cc_start: 0.7931 (mpp-170) cc_final: 0.7387 (mtm180) REVERT: F 550 MET cc_start: 0.7936 (mmt) cc_final: 0.7136 (mmt) REVERT: F 567 ARG cc_start: 0.8716 (mtt-85) cc_final: 0.8240 (mmt-90) REVERT: F 582 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6408 (mp) outliers start: 75 outliers final: 63 residues processed: 593 average time/residue: 0.2160 time to fit residues: 205.3637 Evaluate side-chains 585 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 516 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 chunk 249 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 316 optimal weight: 0.7980 chunk 443 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN E 404 HIS D 460 ASN A 90 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.180782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127775 restraints weight = 50766.909| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.29 r_work: 0.3447 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 37448 Z= 0.162 Angle : 0.736 59.163 50640 Z= 0.377 Chirality : 0.046 0.554 5714 Planarity : 0.004 0.062 6636 Dihedral : 7.147 135.617 5181 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.42 % Favored : 97.56 % Rotamer: Outliers : 1.89 % Allowed : 15.34 % Favored : 82.77 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.30 (0.12), residues: 4628 helix: 1.26 (0.11), residues: 2087 sheet: 0.59 (0.19), residues: 752 loop : 0.72 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 732 TYR 0.041 0.002 TYR A 495 PHE 0.023 0.001 PHE G 377 TRP 0.018 0.001 TRP F 551 HIS 0.008 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00378 (37448) covalent geometry : angle 0.73642 (50640) hydrogen bonds : bond 0.03578 ( 1718) hydrogen bonds : angle 4.15883 ( 4815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9256 Ramachandran restraints generated. 4628 Oldfield, 0 Emsley, 4628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 518 time to evaluate : 1.135 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: B 131 PHE cc_start: 0.6926 (t80) cc_final: 0.6303 (t80) REVERT: B 256 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.7595 (ttp-170) REVERT: B 352 SER cc_start: 0.9215 (m) cc_final: 0.8968 (p) REVERT: B 358 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8356 (mtt-85) REVERT: B 368 ASP cc_start: 0.8485 (t70) cc_final: 0.8275 (t0) REVERT: B 427 MET cc_start: 0.6093 (tpp) cc_final: 0.5340 (tpp) REVERT: B 449 MET cc_start: 0.7965 (tpt) cc_final: 0.7085 (tpt) REVERT: B 476 TRP cc_start: 0.4730 (m100) cc_final: 0.4397 (m100) REVERT: B 490 GLN cc_start: 0.8391 (pt0) cc_final: 0.8056 (pt0) REVERT: E 46 MET cc_start: 0.7618 (mtp) cc_final: 0.7345 (mtm) REVERT: E 273 GLU cc_start: 0.8151 (tp30) cc_final: 0.7704 (tp30) REVERT: E 287 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6754 (ptp90) REVERT: E 397 GLU cc_start: 0.8308 (tt0) cc_final: 0.7800 (tm-30) REVERT: E 508 MET cc_start: 0.8221 (tpt) cc_final: 0.7442 (tpt) REVERT: E 560 ARG cc_start: 0.8574 (ptm160) cc_final: 0.8256 (ttt180) REVERT: E 693 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.7881 (ttm-80) REVERT: D 33 ASN cc_start: 0.7776 (t0) cc_final: 0.7503 (t0) REVERT: D 100 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7209 (pp) REVERT: D 560 ARG cc_start: 0.8417 (ptp-110) cc_final: 0.8113 (ptp90) REVERT: D 564 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8757 (t70) REVERT: C 187 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7992 (mm-30) REVERT: C 221 GLU cc_start: 0.8804 (pp20) cc_final: 0.8367 (pt0) REVERT: C 438 ASP cc_start: 0.8919 (t0) cc_final: 0.8559 (t0) REVERT: C 440 GLU cc_start: 0.8541 (tp30) cc_final: 0.7831 (mp0) REVERT: C 442 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7551 (mtp) REVERT: C 504 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8967 (mp) REVERT: C 512 LYS cc_start: 0.7565 (mttt) cc_final: 0.6743 (tppt) REVERT: C 689 GLU cc_start: 0.8069 (tt0) cc_final: 0.7624 (tm-30) REVERT: C 740 MET cc_start: 0.7432 (tpp) cc_final: 0.6512 (mmm) REVERT: A 344 MET cc_start: 0.8233 (mtm) cc_final: 0.7693 (mtm) REVERT: A 359 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7749 (ttp80) REVERT: A 387 ASN cc_start: 0.8467 (m-40) cc_final: 0.8051 (m-40) REVERT: A 397 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7567 (mp0) REVERT: A 449 MET cc_start: 0.6476 (tmm) cc_final: 0.6160 (tmm) REVERT: A 484 ASP cc_start: 0.8472 (m-30) cc_final: 0.8036 (t0) REVERT: A 488 GLU cc_start: 0.7064 (tp30) cc_final: 0.6289 (mt-10) REVERT: A 508 MET cc_start: 0.7171 (tpt) cc_final: 0.6175 (tpp) REVERT: A 561 GLU cc_start: 0.8003 (mp0) cc_final: 0.7479 (mp0) REVERT: G 275 ARG cc_start: 0.7308 (ttm170) cc_final: 0.6993 (ttt90) REVERT: G 370 LEU cc_start: 0.7904 (mm) cc_final: 0.7563 (mt) REVERT: G 378 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6223 (pm20) REVERT: G 391 GLU cc_start: 0.7614 (pt0) cc_final: 0.7303 (mp0) REVERT: F 33 ASN cc_start: 0.8241 (t0) cc_final: 0.7939 (t0) REVERT: F 140 LEU cc_start: 0.7782 (mm) cc_final: 0.7552 (mm) REVERT: F 167 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7857 (tp30) REVERT: F 239 ARG cc_start: 0.7929 (mpp-170) cc_final: 0.7383 (mtm180) REVERT: F 550 MET cc_start: 0.7907 (mmt) cc_final: 0.7096 (mmt) REVERT: F 567 ARG cc_start: 0.8731 (mtt-85) cc_final: 0.8254 (mmt-90) REVERT: F 582 ILE cc_start: 0.6535 (OUTLIER) cc_final: 0.6312 (mp) outliers start: 75 outliers final: 64 residues processed: 564 average time/residue: 0.2158 time to fit residues: 195.9028 Evaluate side-chains 586 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 516 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 325 LYS Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 42 optimal weight: 8.9990 chunk 409 optimal weight: 0.0270 chunk 420 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 365 optimal weight: 40.0000 chunk 391 optimal weight: 0.4980 chunk 458 optimal weight: 2.9990 chunk 206 optimal weight: 0.5980 chunk 199 optimal weight: 0.0980 chunk 324 optimal weight: 0.9990 overall best weight: 0.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN E 327 GLN E 404 HIS D 460 ASN C 421 GLN C 660 ASN ** G 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 404 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.179950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125990 restraints weight = 51067.775| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.36 r_work: 0.3478 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 37448 Z= 0.119 Angle : 0.634 13.753 50640 Z= 0.301 Chirality : 0.044 0.258 5714 Planarity : 0.004 0.054 6636 Dihedral : 6.632 122.494 5181 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.64 % Allowed : 15.70 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % 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: 1.45 (0.13), residues: 4628 helix: 1.41 (0.12), residues: 2086 sheet: 0.60 (0.18), residues: 751 loop : 0.79 (0.16), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 732 TYR 0.038 0.002 TYR A 495 PHE 0.024 0.001 PHE G 377 TRP 0.017 0.001 TRP F 551 HIS 0.008 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00273 (37448) covalent geometry : angle 0.63382 (50640) hydrogen bonds : bond 0.03263 ( 1718) hydrogen bonds : angle 4.04239 ( 4815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10149.65 seconds wall clock time: 173 minutes 34.38 seconds (10414.38 seconds total)