Starting phenix.real_space_refine on Tue Aug 26 12:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcl_28982/08_2025/8fcl_28982.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcl_28982/08_2025/8fcl_28982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fcl_28982/08_2025/8fcl_28982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcl_28982/08_2025/8fcl_28982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fcl_28982/08_2025/8fcl_28982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcl_28982/08_2025/8fcl_28982.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 189 5.16 5 C 23162 2.51 5 N 6477 2.21 5 O 7052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 333 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36904 Number of models: 1 Model: "" Number of chains: 13 Chain: "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: "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: "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: "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: "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: "F" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "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: "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: "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: "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: "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: "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: "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: 9.17, per 1000 atoms: 0.25 Number of scatterers: 36904 At special positions: 0 Unit cell: (180.978, 194.322, 111.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 189 16.00 P 24 15.00 O 7052 8.00 N 6477 7.00 C 23162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 41 sheets defined 52.2% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... 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: 4.883A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 4.048A 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 removed outlier: 3.763A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) 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 426 through 431 removed outlier: 3.962A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) 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: 3.603A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.113A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 85 through 92 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: 4.479A 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: 3.982A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.795A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.921A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.558A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.528A 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 557 through 569 removed outlier: 3.633A 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 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 748 through 762 Processing helix chain '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: 4.557A 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: 4.084A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.796A 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 removed outlier: 3.773A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) 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: 3.625A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.546A 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: 4.145A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.508A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 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 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: 4.790A 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: 3.571A 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: 3.733A 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 removed outlier: 3.855A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 431 removed outlier: 3.650A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 3.713A 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 removed outlier: 3.523A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.021A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 612 through 615 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 705 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 762 removed outlier: 4.063A pdb=" N LYS D 754 " --> pdb=" O ASN D 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 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: 4.923A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.655A 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 removed outlier: 3.522A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) 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 removed outlier: 3.710A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.032A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 384 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 431 removed outlier: 3.568A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP E 431 " --> pdb=" O MET E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.516A 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: 3.905A 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: 4.117A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 3.843A 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 removed outlier: 3.939A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 431 removed outlier: 4.373A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.579A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 555 through 557 No H-bonds generated for 'chain 'F' and resid 555 through 557' Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 609 Processing helix chain 'F' and resid 610 through 611 No H-bonds generated for 'chain 'F' and resid 610 through 611' Processing helix chain 'F' and resid 612 through 615 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.775A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 707 Processing helix chain 'F' and resid 732 through 740 Processing helix chain 'F' and resid 748 through 763 Processing helix chain 'G' and resid 51 through 67 removed outlier: 4.209A pdb=" N ALA G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.756A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 165 removed outlier: 4.142A 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 249 through 262 removed outlier: 4.316A pdb=" N LEU G 253 " --> pdb=" O GLN G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 285 Processing helix chain 'G' and resid 289 through 294 Processing helix chain 'G' and resid 296 through 316 Processing helix chain 'G' and resid 319 through 332 removed outlier: 3.645A pdb=" N LYS G 325 " --> pdb=" O ALA G 321 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU G 326 " --> pdb=" O MET G 322 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG G 329 " --> pdb=" O LYS G 325 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY G 330 " --> pdb=" O GLU G 326 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU G 331 " --> pdb=" O GLU G 327 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG G 332 " --> pdb=" O GLN G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 368 removed outlier: 4.102A pdb=" N VAL G 362 " --> pdb=" O ARG G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 421 removed outlier: 3.627A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 435 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 removed outlier: 7.456A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.533A 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: 7.157A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.630A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.440A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.903A pdb=" N LYS A 389 " --> pdb=" O VAL A 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.451A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 29 removed outlier: 8.030A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N LYS B 81 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER B 42 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 74 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.663A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AB3, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.159A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 389 through 390 removed outlier: 6.777A pdb=" N LYS B 389 " --> pdb=" O VAL B 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.416A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 25 through 29 removed outlier: 7.515A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.886A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AB9, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AC1, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.058A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.473A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 25 through 30 removed outlier: 7.772A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LYS D 81 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N SER D 42 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP D 74 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU D 41 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.776A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 126 through 127 removed outlier: 3.523A pdb=" N THR D 127 " --> pdb=" O ILE D 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC7, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.213A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.431A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 25 through 29 removed outlier: 7.871A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LYS E 81 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER E 42 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ASP E 74 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU E 41 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 151 through 156 removed outlier: 5.444A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AD3, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.740A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.198A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.922A 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: 6.749A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.461A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 25 through 29 removed outlier: 6.377A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.595A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AD9, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AE1, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.084A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.575A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AE4, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AE5, first strand: chain 'G' and resid 386 through 387 removed outlier: 4.630A pdb=" N LEU G 379 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ALA G 404 " --> pdb=" O TYR G 336 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU G 338 " --> pdb=" O ALA G 404 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU G 406 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG G 340 " --> pdb=" O LEU G 406 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE G 408 " --> pdb=" O ARG G 340 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG G 342 " --> pdb=" O PHE G 408 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N TRP G 410 " --> pdb=" O ARG G 342 " (cutoff:3.500A) 1695 hydrogen bonds defined for protein. 4746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.00 Time building geometry restraints manager: 4.40 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: 7838 1.33 - 1.45: 7678 1.45 - 1.57: 21674 1.57 - 1.69: 36 1.69 - 1.82: 301 Bond restraints: 37527 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 37522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 50110 2.93 - 5.87: 553 5.87 - 8.80: 61 8.80 - 11.74: 14 11.74 - 14.67: 8 Bond angle restraints: 50746 Sorted by residual: angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 111.03 123.96 -12.93 1.11e+00 8.12e-01 1.36e+02 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 109.62 124.29 -14.67 1.50e+00 4.44e-01 9.57e+01 angle pdb=" CA GLY D 591 " pdb=" C GLY D 591 " pdb=" O GLY D 591 " ideal model delta sigma weight residual 122.23 118.60 3.63 6.90e-01 2.10e+00 2.78e+01 angle pdb=" N ARG G 137 " pdb=" CA ARG G 137 " pdb=" C ARG G 137 " ideal model delta sigma weight residual 111.02 117.26 -6.24 1.22e+00 6.72e-01 2.62e+01 angle pdb=" C HIS F 226 " pdb=" N PRO F 227 " pdb=" CA PRO F 227 " ideal model delta sigma weight residual 119.28 124.41 -5.13 1.10e+00 8.26e-01 2.18e+01 ... (remaining 50741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 22929 35.63 - 71.26: 249 71.26 - 106.88: 39 106.88 - 142.51: 10 142.51 - 178.14: 6 Dihedral angle restraints: 23233 sinusoidal: 9775 harmonic: 13458 Sorted by residual: dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 118.14 -178.14 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP C 901 " pdb=" O3A ADP C 901 " pdb=" PB ADP C 901 " pdb=" PA ADP C 901 " ideal model delta sinusoidal sigma weight residual 300.00 125.35 174.65 1 2.00e+01 2.50e-03 4.79e+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 -60.00 114.35 -174.36 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 23230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 5035 0.097 - 0.193: 667 0.193 - 0.290: 20 0.290 - 0.386: 0 0.386 - 0.483: 1 Chirality restraints: 5723 Sorted by residual: chirality pdb=" CA ARG G 332 " pdb=" N ARG G 332 " pdb=" C ARG G 332 " pdb=" CB ARG G 332 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" CA THR G 337 " pdb=" N THR G 337 " pdb=" C THR G 337 " pdb=" CB THR G 337 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA LEU G 331 " pdb=" N LEU G 331 " pdb=" C LEU G 331 " pdb=" CB LEU G 331 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5720 not shown) Planarity restraints: 6650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.094 2.00e-02 2.50e+03 5.64e-02 6.35e+01 pdb=" CG TYR A 143 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 226 " 0.046 2.00e-02 2.50e+03 3.43e-02 1.77e+01 pdb=" CG HIS F 226 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS F 226 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 HIS F 226 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS F 226 " 0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS F 226 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 331 " -0.019 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C LEU G 331 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU G 331 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG G 332 " -0.025 2.00e-02 2.50e+03 ... (remaining 6647 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10330 2.82 - 3.34: 34869 3.34 - 3.86: 60939 3.86 - 4.38: 73910 4.38 - 4.90: 120920 Nonbonded interactions: 300968 Sorted by model distance: nonbonded pdb=" NZ LYS F 211 " pdb=" O ALA F 570 " model vdw 2.300 3.120 nonbonded pdb=" OD2 ASP B 368 " pdb=" NZ LYS B 565 " model vdw 2.398 3.120 nonbonded pdb=" OD1 ASP E 35 " pdb=" N ASN E 36 " model vdw 2.407 3.120 nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.416 3.120 nonbonded pdb=" NZ LYS F 512 " pdb=" O GLY F 637 " model vdw 2.423 3.120 ... (remaining 300963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.470 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.730 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.111 37527 Z= 0.602 Angle : 0.871 14.675 50746 Z= 0.534 Chirality : 0.059 0.483 5723 Planarity : 0.004 0.084 6650 Dihedral : 12.275 178.140 14503 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.17 % Rotamer: Outliers : 0.10 % Allowed : 0.63 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.11), residues: 4639 helix: -0.23 (0.10), residues: 2063 sheet: 0.67 (0.17), residues: 774 loop : 0.95 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 323 TYR 0.096 0.002 TYR A 143 PHE 0.023 0.001 PHE G 353 TRP 0.052 0.002 TRP F 476 HIS 0.002 0.000 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.01067 (37527) covalent geometry : angle 0.87131 (50746) hydrogen bonds : bond 0.20857 ( 1695) hydrogen bonds : angle 6.48672 ( 4746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1398 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 SER cc_start: 0.7100 (m) cc_final: 0.6847 (p) REVERT: C 304 ASP cc_start: 0.6811 (t0) cc_final: 0.6593 (t0) REVERT: D 598 ASP cc_start: 0.4691 (p0) cc_final: 0.4353 (p0) REVERT: F 320 VAL cc_start: 0.7562 (t) cc_final: 0.7218 (p) outliers start: 4 outliers final: 0 residues processed: 1402 average time/residue: 0.2842 time to fit residues: 606.8444 Evaluate side-chains 697 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 697 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 0.0870 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 641 GLN B 215 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 460 ASN B 603 GLN C 90 ASN C 183 HIS C 460 ASN C 641 GLN D 90 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 404 HIS D 735 HIS E 260 ASN E 443 ASN E 602 ASN F 226 HIS F 406 HIS F 760 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.147649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.116217 restraints weight = 77648.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.119018 restraints weight = 38837.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.120658 restraints weight = 23528.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.121058 restraints weight = 19497.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.120977 restraints weight = 16897.428| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37527 Z= 0.180 Angle : 0.731 13.075 50746 Z= 0.359 Chirality : 0.047 0.220 5723 Planarity : 0.005 0.063 6650 Dihedral : 10.179 179.860 5191 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.31 % Favored : 98.66 % Rotamer: Outliers : 2.72 % Allowed : 10.80 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.12), residues: 4639 helix: 0.83 (0.11), residues: 2108 sheet: 0.67 (0.17), residues: 791 loop : 1.13 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 599 TYR 0.028 0.002 TYR B 644 PHE 0.025 0.002 PHE B 674 TRP 0.013 0.002 TRP A 454 HIS 0.006 0.001 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00416 (37527) covalent geometry : angle 0.73066 (50746) hydrogen bonds : bond 0.05226 ( 1695) hydrogen bonds : angle 4.67633 ( 4746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 793 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.6907 (p-80) cc_final: 0.6617 (p-80) REVERT: A 427 MET cc_start: 0.7541 (tmt) cc_final: 0.7142 (tmt) REVERT: A 529 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7347 (mtmt) REVERT: A 618 PHE cc_start: 0.7593 (t80) cc_final: 0.7247 (t80) REVERT: A 620 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 678 MET cc_start: 0.6872 (tpp) cc_final: 0.5165 (ptt) REVERT: A 745 ARG cc_start: 0.3867 (ptp-170) cc_final: 0.3569 (ptp90) REVERT: B 217 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8180 (mtpt) REVERT: C 35 ASP cc_start: 0.8561 (t0) cc_final: 0.8276 (t0) REVERT: C 64 ARG cc_start: 0.7528 (mmp-170) cc_final: 0.7108 (ppt170) REVERT: C 220 VAL cc_start: 0.9298 (m) cc_final: 0.9071 (p) REVERT: C 421 GLN cc_start: 0.8436 (tp40) cc_final: 0.7934 (tp40) REVERT: C 508 MET cc_start: 0.7443 (tpt) cc_final: 0.6873 (tpt) REVERT: C 560 ARG cc_start: 0.8499 (ttm170) cc_final: 0.8200 (ttm-80) REVERT: C 568 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 45 LYS cc_start: 0.6408 (mmmt) cc_final: 0.6188 (mmmt) REVERT: D 123 VAL cc_start: 0.8743 (t) cc_final: 0.8490 (m) REVERT: D 134 TYR cc_start: 0.8205 (m-10) cc_final: 0.7966 (m-10) REVERT: D 196 GLU cc_start: 0.8349 (tp30) cc_final: 0.7939 (tp30) REVERT: D 217 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8520 (mtmt) REVERT: D 278 LEU cc_start: 0.8279 (tt) cc_final: 0.8075 (tt) REVERT: D 598 ASP cc_start: 0.6896 (p0) cc_final: 0.6685 (m-30) REVERT: D 656 ILE cc_start: 0.8201 (mt) cc_final: 0.7890 (mt) REVERT: E 29 ASP cc_start: 0.8027 (t0) cc_final: 0.7814 (t70) REVERT: E 120 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7513 (p0) REVERT: E 305 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7833 (mt-10) REVERT: E 435 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7800 (pm20) REVERT: E 443 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.6966 (m-40) REVERT: E 735 HIS cc_start: 0.8230 (m170) cc_final: 0.7955 (m90) REVERT: F 603 GLN cc_start: 0.7848 (tp40) cc_final: 0.6470 (tp40) REVERT: F 607 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6743 (mm-30) REVERT: F 744 ARG cc_start: 0.4066 (mmt180) cc_final: 0.3458 (mtt180) REVERT: G 368 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8131 (pp20) outliers start: 108 outliers final: 52 residues processed: 856 average time/residue: 0.2498 time to fit residues: 343.1022 Evaluate side-chains 678 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 623 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 443 ASN Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 407 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 180 optimal weight: 8.9990 chunk 306 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 315 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 340 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 90 ASN A 115 HIS A 226 HIS A 285 ASN A 404 HIS A 406 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN A 602 ASN A 616 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS B 460 ASN C 90 ASN C 398 GLN C 641 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN E 337 GLN E 384 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.143161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112188 restraints weight = 78372.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.114279 restraints weight = 39120.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.115309 restraints weight = 25323.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115818 restraints weight = 22500.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115842 restraints weight = 19174.778| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 37527 Z= 0.222 Angle : 0.717 12.734 50746 Z= 0.349 Chirality : 0.047 0.192 5723 Planarity : 0.005 0.049 6650 Dihedral : 9.890 175.680 5191 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.35 % Allowed : 13.47 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.12), residues: 4639 helix: 0.90 (0.11), residues: 2127 sheet: 0.71 (0.17), residues: 779 loop : 0.84 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 662 TYR 0.032 0.003 TYR G 334 PHE 0.028 0.002 PHE G 353 TRP 0.014 0.002 TRP G 374 HIS 0.007 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00509 (37527) covalent geometry : angle 0.71723 (50746) hydrogen bonds : bond 0.04740 ( 1695) hydrogen bonds : angle 4.59683 ( 4746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 632 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.7082 (p-80) cc_final: 0.6812 (p-80) REVERT: A 393 ASP cc_start: 0.8087 (t0) cc_final: 0.7859 (t0) REVERT: A 427 MET cc_start: 0.7585 (tmt) cc_final: 0.7186 (tmt) REVERT: A 449 MET cc_start: 0.7687 (tpp) cc_final: 0.7307 (tpp) REVERT: A 529 LYS cc_start: 0.7451 (mtmt) cc_final: 0.7089 (mtmm) REVERT: A 575 PHE cc_start: 0.8439 (t80) cc_final: 0.7618 (t80) REVERT: A 618 PHE cc_start: 0.7777 (t80) cc_final: 0.7282 (t80) REVERT: A 620 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 674 PHE cc_start: 0.7205 (t80) cc_final: 0.6849 (t80) REVERT: A 678 MET cc_start: 0.6893 (tpp) cc_final: 0.5134 (ptt) REVERT: B 62 LYS cc_start: 0.8780 (mttt) cc_final: 0.8511 (mmtm) REVERT: B 506 PHE cc_start: 0.7473 (m-80) cc_final: 0.7141 (m-10) REVERT: B 508 MET cc_start: 0.7641 (mmm) cc_final: 0.7263 (tmm) REVERT: B 550 MET cc_start: 0.8000 (mtm) cc_final: 0.7565 (mtm) REVERT: B 568 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7001 (mm-40) REVERT: B 574 LEU cc_start: 0.8421 (tt) cc_final: 0.8143 (tt) REVERT: B 644 TYR cc_start: 0.7494 (t80) cc_final: 0.7124 (t80) REVERT: C 34 GLU cc_start: 0.6873 (pm20) cc_final: 0.6455 (tm-30) REVERT: C 35 ASP cc_start: 0.8623 (t0) cc_final: 0.8229 (t0) REVERT: C 64 ARG cc_start: 0.7684 (mmp-170) cc_final: 0.7242 (ppt170) REVERT: C 173 TYR cc_start: 0.6987 (p90) cc_final: 0.6707 (p90) REVERT: C 421 GLN cc_start: 0.8562 (tp40) cc_final: 0.8231 (tp40) REVERT: C 499 HIS cc_start: 0.7771 (m90) cc_final: 0.7496 (m90) REVERT: C 508 MET cc_start: 0.7667 (tpt) cc_final: 0.6869 (tpt) REVERT: C 568 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7892 (tm-30) REVERT: C 611 MET cc_start: 0.7998 (ttm) cc_final: 0.7419 (tpp) REVERT: C 762 LEU cc_start: 0.7615 (mt) cc_final: 0.6347 (tt) REVERT: D 123 VAL cc_start: 0.8753 (t) cc_final: 0.8504 (m) REVERT: D 124 GLU cc_start: 0.7578 (tp30) cc_final: 0.7362 (tp30) REVERT: D 158 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8179 (mmt) REVERT: D 196 GLU cc_start: 0.8467 (tp30) cc_final: 0.8007 (tp30) REVERT: D 302 PHE cc_start: 0.8359 (t80) cc_final: 0.8120 (t80) REVERT: D 336 LYS cc_start: 0.7391 (mmtm) cc_final: 0.7141 (mmtm) REVERT: D 491 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: D 598 ASP cc_start: 0.7036 (p0) cc_final: 0.6651 (m-30) REVERT: E 25 ARG cc_start: 0.8033 (ttt90) cc_final: 0.6796 (mtt90) REVERT: E 47 ASP cc_start: 0.7910 (m-30) cc_final: 0.7166 (m-30) REVERT: E 305 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8001 (mt-10) REVERT: E 435 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7818 (pm20) REVERT: E 735 HIS cc_start: 0.8140 (m170) cc_final: 0.7866 (m90) REVERT: F 352 SER cc_start: 0.8486 (m) cc_final: 0.8140 (t) REVERT: F 449 MET cc_start: 0.8452 (tpt) cc_final: 0.8068 (tpp) REVERT: F 456 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8877 (mp) REVERT: F 534 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: F 744 ARG cc_start: 0.4448 (mmt180) cc_final: 0.3712 (mtp180) REVERT: G 368 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8039 (pp20) REVERT: G 374 TRP cc_start: 0.6410 (p-90) cc_final: 0.6039 (p-90) outliers start: 133 outliers final: 84 residues processed: 713 average time/residue: 0.2037 time to fit residues: 237.3708 Evaluate side-chains 636 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 547 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 236 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 628 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 412 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 80 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 316 optimal weight: 2.9990 chunk 382 optimal weight: 1.9990 chunk 420 optimal weight: 2.9990 chunk 461 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 431 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 624 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 317 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN C 199 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN D 90 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 ASN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.142413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.111220 restraints weight = 78646.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113851 restraints weight = 39741.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114639 restraints weight = 25297.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114900 restraints weight = 23644.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.115049 restraints weight = 19712.345| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37527 Z= 0.187 Angle : 0.674 9.102 50746 Z= 0.325 Chirality : 0.047 0.227 5723 Planarity : 0.005 0.054 6650 Dihedral : 9.508 176.275 5191 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.50 % Allowed : 14.68 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.12), residues: 4639 helix: 0.93 (0.11), residues: 2154 sheet: 0.70 (0.18), residues: 742 loop : 0.71 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 365 TYR 0.026 0.002 TYR B 244 PHE 0.026 0.002 PHE A 575 TRP 0.008 0.001 TRP F 551 HIS 0.009 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00431 (37527) covalent geometry : angle 0.67424 (50746) hydrogen bonds : bond 0.04175 ( 1695) hydrogen bonds : angle 4.46981 ( 4746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 616 time to evaluate : 1.479 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: A 393 ASP cc_start: 0.8033 (t0) cc_final: 0.7734 (t0) REVERT: A 449 MET cc_start: 0.7776 (tpp) cc_final: 0.7219 (tpp) REVERT: A 529 LYS cc_start: 0.7466 (mtmt) cc_final: 0.7009 (mtmm) REVERT: A 575 PHE cc_start: 0.8232 (t80) cc_final: 0.7653 (t80) REVERT: A 618 PHE cc_start: 0.7834 (t80) cc_final: 0.7319 (t80) REVERT: A 620 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8925 (mm) REVERT: A 674 PHE cc_start: 0.7302 (t80) cc_final: 0.6981 (t80) REVERT: A 678 MET cc_start: 0.7009 (tpp) cc_final: 0.5169 (ptt) REVERT: B 62 LYS cc_start: 0.8768 (mttt) cc_final: 0.8490 (mmtm) REVERT: B 273 GLU cc_start: 0.8218 (tp30) cc_final: 0.7956 (tp30) REVERT: B 449 MET cc_start: 0.7261 (tpp) cc_final: 0.7018 (tpp) REVERT: B 506 PHE cc_start: 0.7558 (m-80) cc_final: 0.7210 (m-10) REVERT: B 508 MET cc_start: 0.7724 (mmm) cc_final: 0.6666 (tmm) REVERT: B 574 LEU cc_start: 0.8531 (tt) cc_final: 0.8218 (tt) REVERT: B 644 TYR cc_start: 0.7357 (t80) cc_final: 0.7011 (t80) REVERT: C 35 ASP cc_start: 0.8593 (t0) cc_final: 0.8201 (t0) REVERT: C 36 ASN cc_start: 0.8185 (m-40) cc_final: 0.7969 (m-40) REVERT: C 64 ARG cc_start: 0.7691 (mmp-170) cc_final: 0.7282 (ppt170) REVERT: C 173 TYR cc_start: 0.6988 (p90) cc_final: 0.6696 (p90) REVERT: C 421 GLN cc_start: 0.8583 (tp40) cc_final: 0.8163 (tp40) REVERT: C 449 MET cc_start: 0.7783 (tpp) cc_final: 0.7547 (tmm) REVERT: C 495 TYR cc_start: 0.9100 (m-10) cc_final: 0.8814 (m-80) REVERT: C 499 HIS cc_start: 0.7948 (m90) cc_final: 0.7681 (m90) REVERT: C 508 MET cc_start: 0.7790 (tpt) cc_final: 0.6954 (tpt) REVERT: C 535 CYS cc_start: 0.7774 (m) cc_final: 0.7572 (m) REVERT: C 568 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7877 (tm-30) REVERT: C 611 MET cc_start: 0.8046 (ttm) cc_final: 0.7548 (tpp) REVERT: C 762 LEU cc_start: 0.7571 (mt) cc_final: 0.6270 (tt) REVERT: D 123 VAL cc_start: 0.8776 (t) cc_final: 0.8546 (m) REVERT: D 124 GLU cc_start: 0.7784 (tp30) cc_final: 0.7519 (tp30) REVERT: D 158 MET cc_start: 0.8481 (mmp) cc_final: 0.8157 (mmt) REVERT: D 196 GLU cc_start: 0.8578 (tp30) cc_final: 0.8212 (tp30) REVERT: D 302 PHE cc_start: 0.8409 (t80) cc_final: 0.8169 (t80) REVERT: D 336 LYS cc_start: 0.7457 (mmtm) cc_final: 0.7109 (mmtm) REVERT: D 491 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: D 564 ASP cc_start: 0.8616 (t70) cc_final: 0.8401 (t0) REVERT: D 598 ASP cc_start: 0.6989 (p0) cc_final: 0.6625 (m-30) REVERT: D 696 LYS cc_start: 0.8922 (ptmt) cc_final: 0.8357 (pttm) REVERT: E 305 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8051 (mt-10) REVERT: E 435 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7803 (pm20) REVERT: E 564 ASP cc_start: 0.8084 (t70) cc_final: 0.7526 (t0) REVERT: E 735 HIS cc_start: 0.8015 (m170) cc_final: 0.7754 (m90) REVERT: F 337 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7811 (tm-30) REVERT: F 352 SER cc_start: 0.8539 (m) cc_final: 0.8201 (t) REVERT: F 449 MET cc_start: 0.8387 (tpt) cc_final: 0.8083 (tpp) REVERT: F 508 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6856 (mmt) REVERT: F 744 ARG cc_start: 0.4611 (mmt180) cc_final: 0.3608 (mtp180) REVERT: G 368 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7985 (pp20) REVERT: G 374 TRP cc_start: 0.6544 (p-90) cc_final: 0.6188 (p-90) outliers start: 139 outliers final: 92 residues processed: 700 average time/residue: 0.2066 time to fit residues: 237.6247 Evaluate side-chains 647 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 552 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 628 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 412 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 13 optimal weight: 0.9980 chunk 328 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 337 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 406 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 272 optimal weight: 0.0020 chunk 347 optimal weight: 6.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN B 460 ASN C 199 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 24 ASN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.144030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.113230 restraints weight = 77957.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.115501 restraints weight = 39576.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.116557 restraints weight = 24693.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.117029 restraints weight = 23053.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.117055 restraints weight = 19194.212| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37527 Z= 0.128 Angle : 0.638 10.561 50746 Z= 0.305 Chirality : 0.045 0.179 5723 Planarity : 0.004 0.051 6650 Dihedral : 9.048 177.206 5191 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.69 % Allowed : 16.32 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.12), residues: 4639 helix: 1.21 (0.11), residues: 2102 sheet: 0.64 (0.18), residues: 789 loop : 0.74 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 113 TYR 0.025 0.002 TYR B 495 PHE 0.034 0.002 PHE A 575 TRP 0.007 0.001 TRP E 551 HIS 0.010 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00291 (37527) covalent geometry : angle 0.63834 (50746) hydrogen bonds : bond 0.03736 ( 1695) hydrogen bonds : angle 4.33145 ( 4746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 614 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 ASP cc_start: 0.8022 (t0) cc_final: 0.7724 (t0) REVERT: A 449 MET cc_start: 0.7792 (tpp) cc_final: 0.7210 (tpp) REVERT: A 529 LYS cc_start: 0.7493 (mtmt) cc_final: 0.7063 (mtmm) REVERT: A 620 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8917 (mm) REVERT: A 674 PHE cc_start: 0.7365 (t80) cc_final: 0.7024 (t80) REVERT: A 678 MET cc_start: 0.7051 (tpp) cc_final: 0.5176 (ptt) REVERT: B 62 LYS cc_start: 0.8758 (mttt) cc_final: 0.8481 (mmtm) REVERT: B 322 ARG cc_start: 0.8163 (mmp80) cc_final: 0.7688 (mmp80) REVERT: B 332 MET cc_start: 0.8395 (mmm) cc_final: 0.8036 (mmm) REVERT: B 506 PHE cc_start: 0.7538 (m-80) cc_final: 0.7157 (m-10) REVERT: B 508 MET cc_start: 0.7770 (mmm) cc_final: 0.6671 (tmm) REVERT: C 35 ASP cc_start: 0.8587 (t0) cc_final: 0.8172 (t0) REVERT: C 64 ARG cc_start: 0.7687 (mmp-170) cc_final: 0.7274 (ppt170) REVERT: C 173 TYR cc_start: 0.6943 (p90) cc_final: 0.6659 (p90) REVERT: C 421 GLN cc_start: 0.8549 (tp40) cc_final: 0.8205 (tp40) REVERT: C 495 TYR cc_start: 0.9083 (m-10) cc_final: 0.8797 (m-80) REVERT: C 499 HIS cc_start: 0.7877 (m90) cc_final: 0.7632 (m90) REVERT: C 508 MET cc_start: 0.7815 (tpt) cc_final: 0.7028 (tpt) REVERT: C 568 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7790 (tm-30) REVERT: C 611 MET cc_start: 0.7916 (ttm) cc_final: 0.7493 (tpp) REVERT: C 762 LEU cc_start: 0.7479 (mt) cc_final: 0.6198 (tt) REVERT: D 123 VAL cc_start: 0.8793 (t) cc_final: 0.8569 (m) REVERT: D 124 GLU cc_start: 0.7816 (tp30) cc_final: 0.7553 (tp30) REVERT: D 158 MET cc_start: 0.8440 (mmp) cc_final: 0.8159 (mmt) REVERT: D 196 GLU cc_start: 0.8555 (tp30) cc_final: 0.8103 (tp30) REVERT: D 302 PHE cc_start: 0.8314 (t80) cc_final: 0.8054 (t80) REVERT: D 417 GLU cc_start: 0.7557 (tt0) cc_final: 0.7178 (tt0) REVERT: D 491 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: D 564 ASP cc_start: 0.8554 (t70) cc_final: 0.8311 (t0) REVERT: D 598 ASP cc_start: 0.6966 (p0) cc_final: 0.6519 (m-30) REVERT: D 696 LYS cc_start: 0.8929 (ptmt) cc_final: 0.8431 (pttm) REVERT: E 305 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7984 (mt-10) REVERT: E 331 LEU cc_start: 0.8704 (mt) cc_final: 0.8447 (mt) REVERT: E 379 GLU cc_start: 0.8325 (tt0) cc_final: 0.8003 (tt0) REVERT: E 435 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7807 (pm20) REVERT: E 564 ASP cc_start: 0.8011 (t70) cc_final: 0.7445 (t0) REVERT: E 608 MET cc_start: 0.8474 (ttm) cc_final: 0.8174 (tmm) REVERT: E 735 HIS cc_start: 0.7926 (m170) cc_final: 0.7712 (m90) REVERT: F 337 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7950 (tm-30) REVERT: F 352 SER cc_start: 0.8487 (m) cc_final: 0.8161 (t) REVERT: F 379 GLU cc_start: 0.8326 (tp30) cc_final: 0.8112 (tp30) REVERT: F 449 MET cc_start: 0.8338 (tpt) cc_final: 0.8057 (tpp) REVERT: F 508 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6745 (mmt) REVERT: F 534 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: F 619 ILE cc_start: 0.9328 (mt) cc_final: 0.9000 (tt) REVERT: F 744 ARG cc_start: 0.4667 (mmt180) cc_final: 0.4133 (mtp85) REVERT: G 368 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7999 (pp20) REVERT: G 374 TRP cc_start: 0.6514 (p-90) cc_final: 0.6174 (p-90) outliers start: 107 outliers final: 66 residues processed: 676 average time/residue: 0.1992 time to fit residues: 222.3254 Evaluate side-chains 614 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 544 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 412 MET Chi-restraints excluded: chain G residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 409 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 115 optimal weight: 0.0870 chunk 399 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 395 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 382 optimal weight: 5.9990 overall best weight: 2.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN E 680 ASN F 183 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.145004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.114333 restraints weight = 78052.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.116799 restraints weight = 38772.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.117597 restraints weight = 23836.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.118090 restraints weight = 22471.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.118160 restraints weight = 19335.316| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37527 Z= 0.165 Angle : 0.655 11.965 50746 Z= 0.314 Chirality : 0.046 0.190 5723 Planarity : 0.004 0.053 6650 Dihedral : 8.745 175.584 5191 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.15 % Allowed : 16.57 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.12), residues: 4639 helix: 1.19 (0.11), residues: 2104 sheet: 0.65 (0.18), residues: 754 loop : 0.63 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 53 TYR 0.028 0.002 TYR B 644 PHE 0.030 0.002 PHE A 575 TRP 0.006 0.001 TRP A 476 HIS 0.007 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00383 (37527) covalent geometry : angle 0.65500 (50746) hydrogen bonds : bond 0.03790 ( 1695) hydrogen bonds : angle 4.37507 ( 4746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 577 time to evaluate : 1.361 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: A 393 ASP cc_start: 0.8000 (t0) cc_final: 0.7681 (t0) REVERT: A 449 MET cc_start: 0.7875 (tpp) cc_final: 0.7190 (tpp) REVERT: A 529 LYS cc_start: 0.7630 (mtmt) cc_final: 0.7175 (mtmm) REVERT: A 618 PHE cc_start: 0.7870 (t80) cc_final: 0.7291 (t80) REVERT: A 620 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8905 (mm) REVERT: A 641 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8171 (mt0) REVERT: A 674 PHE cc_start: 0.7410 (t80) cc_final: 0.7062 (t80) REVERT: A 678 MET cc_start: 0.7048 (tpp) cc_final: 0.5133 (ptt) REVERT: B 62 LYS cc_start: 0.8732 (mttt) cc_final: 0.8493 (mmtm) REVERT: B 322 ARG cc_start: 0.8220 (mmp80) cc_final: 0.7525 (mmp80) REVERT: B 332 MET cc_start: 0.8352 (mmm) cc_final: 0.7956 (mmm) REVERT: B 506 PHE cc_start: 0.7551 (m-80) cc_final: 0.7165 (m-10) REVERT: B 508 MET cc_start: 0.7834 (mmm) cc_final: 0.6575 (tmm) REVERT: B 574 LEU cc_start: 0.8564 (tt) cc_final: 0.8298 (tt) REVERT: C 35 ASP cc_start: 0.8559 (t0) cc_final: 0.8214 (t0) REVERT: C 64 ARG cc_start: 0.7685 (mmp-170) cc_final: 0.7388 (mmp-170) REVERT: C 173 TYR cc_start: 0.7061 (p90) cc_final: 0.6744 (p90) REVERT: C 317 HIS cc_start: 0.5065 (t-90) cc_final: 0.4795 (t-90) REVERT: C 421 GLN cc_start: 0.8649 (tp40) cc_final: 0.8214 (tp40) REVERT: C 449 MET cc_start: 0.7738 (tpp) cc_final: 0.7515 (tmm) REVERT: C 465 ARG cc_start: 0.8364 (mmt180) cc_final: 0.8129 (mmt180) REVERT: C 499 HIS cc_start: 0.8082 (m90) cc_final: 0.7863 (m90) REVERT: C 508 MET cc_start: 0.7800 (tpt) cc_final: 0.7240 (tpt) REVERT: C 568 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7824 (tm-30) REVERT: C 611 MET cc_start: 0.7882 (ttm) cc_final: 0.7423 (tpp) REVERT: C 762 LEU cc_start: 0.7518 (mt) cc_final: 0.6170 (tt) REVERT: D 123 VAL cc_start: 0.8834 (t) cc_final: 0.8622 (m) REVERT: D 124 GLU cc_start: 0.7775 (tp30) cc_final: 0.7515 (tp30) REVERT: D 158 MET cc_start: 0.8451 (mmp) cc_final: 0.8165 (mmt) REVERT: D 196 GLU cc_start: 0.8522 (tp30) cc_final: 0.8187 (tp30) REVERT: D 236 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7547 (mmpt) REVERT: D 417 GLU cc_start: 0.7531 (tt0) cc_final: 0.7178 (tt0) REVERT: D 491 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: D 564 ASP cc_start: 0.8475 (t70) cc_final: 0.8213 (t0) REVERT: D 598 ASP cc_start: 0.6958 (p0) cc_final: 0.6517 (m-30) REVERT: E 25 ARG cc_start: 0.8362 (ttt90) cc_final: 0.6923 (mtt90) REVERT: E 305 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8085 (mt-10) REVERT: E 321 GLU cc_start: 0.7959 (mp0) cc_final: 0.7405 (mp0) REVERT: E 564 ASP cc_start: 0.8024 (t70) cc_final: 0.7769 (m-30) REVERT: F 337 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7973 (tm-30) REVERT: F 352 SER cc_start: 0.8487 (m) cc_final: 0.8231 (t) REVERT: F 379 GLU cc_start: 0.8342 (tp30) cc_final: 0.8130 (tp30) REVERT: F 449 MET cc_start: 0.8389 (tpt) cc_final: 0.8129 (tpp) REVERT: F 477 GLU cc_start: 0.7577 (tp30) cc_final: 0.7357 (tp30) REVERT: F 508 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6823 (mmt) REVERT: F 534 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: F 619 ILE cc_start: 0.9282 (mt) cc_final: 0.9001 (tt) REVERT: F 744 ARG cc_start: 0.4823 (mmt180) cc_final: 0.3686 (mtp180) REVERT: G 332 ARG cc_start: 0.7723 (tpp-160) cc_final: 0.7064 (mmm160) REVERT: G 374 TRP cc_start: 0.6543 (p-90) cc_final: 0.6186 (p-90) outliers start: 125 outliers final: 92 residues processed: 649 average time/residue: 0.1862 time to fit residues: 199.6374 Evaluate side-chains 627 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 530 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 236 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 602 ASN Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 412 MET Chi-restraints excluded: chain G residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 31 optimal weight: 4.9990 chunk 360 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 288 optimal weight: 10.0000 chunk 388 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 199 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN C 24 ASN C 91 ASN C 199 ASN C 226 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 641 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.144779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.113397 restraints weight = 78427.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.117321 restraints weight = 37705.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.119486 restraints weight = 21194.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.119756 restraints weight = 17763.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.119493 restraints weight = 14906.311| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37527 Z= 0.162 Angle : 0.657 12.052 50746 Z= 0.314 Chirality : 0.046 0.195 5723 Planarity : 0.004 0.053 6650 Dihedral : 8.416 162.709 5191 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.20 % Allowed : 17.02 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.12), residues: 4639 helix: 1.21 (0.11), residues: 2098 sheet: 0.59 (0.19), residues: 739 loop : 0.57 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 342 TYR 0.026 0.002 TYR B 244 PHE 0.033 0.002 PHE A 575 TRP 0.006 0.001 TRP E 551 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00377 (37527) covalent geometry : angle 0.65749 (50746) hydrogen bonds : bond 0.03724 ( 1695) hydrogen bonds : angle 4.38199 ( 4746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 558 time to evaluate : 1.058 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: A 294 GLU cc_start: 0.8065 (tp30) cc_final: 0.7814 (pp20) REVERT: A 393 ASP cc_start: 0.7981 (t0) cc_final: 0.7599 (t0) REVERT: A 449 MET cc_start: 0.7827 (tpp) cc_final: 0.7146 (tpp) REVERT: A 529 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7180 (mtmm) REVERT: A 618 PHE cc_start: 0.7879 (t80) cc_final: 0.7332 (t80) REVERT: A 620 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8949 (mm) REVERT: A 674 PHE cc_start: 0.7408 (t80) cc_final: 0.7028 (t80) REVERT: A 678 MET cc_start: 0.7117 (tpp) cc_final: 0.5240 (ptt) REVERT: B 62 LYS cc_start: 0.8736 (mttt) cc_final: 0.8496 (mmtm) REVERT: B 322 ARG cc_start: 0.8160 (mmp80) cc_final: 0.7648 (mmp80) REVERT: B 332 MET cc_start: 0.8280 (mmm) cc_final: 0.7889 (mmm) REVERT: B 506 PHE cc_start: 0.7595 (m-80) cc_final: 0.7292 (m-10) REVERT: B 508 MET cc_start: 0.7892 (tmm) cc_final: 0.6620 (tmm) REVERT: B 574 LEU cc_start: 0.8544 (tt) cc_final: 0.8247 (tt) REVERT: B 616 ASN cc_start: 0.7658 (m-40) cc_final: 0.7167 (t0) REVERT: B 635 ARG cc_start: 0.8263 (ttm110) cc_final: 0.7716 (mtm-85) REVERT: B 644 TYR cc_start: 0.7403 (t80) cc_final: 0.7005 (t80) REVERT: C 35 ASP cc_start: 0.8532 (t0) cc_final: 0.8225 (t0) REVERT: C 64 ARG cc_start: 0.7674 (mmp-170) cc_final: 0.7422 (mmp-170) REVERT: C 173 TYR cc_start: 0.7048 (p90) cc_final: 0.6735 (p90) REVERT: C 317 HIS cc_start: 0.4934 (t-90) cc_final: 0.4660 (t-90) REVERT: C 421 GLN cc_start: 0.8678 (tp40) cc_final: 0.8227 (tp40) REVERT: C 495 TYR cc_start: 0.9013 (m-10) cc_final: 0.8783 (m-80) REVERT: C 508 MET cc_start: 0.7810 (tpt) cc_final: 0.7286 (tpt) REVERT: C 568 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7794 (tm-30) REVERT: C 611 MET cc_start: 0.7859 (ttm) cc_final: 0.7454 (tpp) REVERT: C 762 LEU cc_start: 0.7466 (mt) cc_final: 0.6098 (tt) REVERT: D 84 MET cc_start: 0.5404 (tpp) cc_final: 0.4540 (tpp) REVERT: D 123 VAL cc_start: 0.8808 (t) cc_final: 0.8594 (m) REVERT: D 124 GLU cc_start: 0.7761 (tp30) cc_final: 0.7534 (tp30) REVERT: D 158 MET cc_start: 0.8535 (mmp) cc_final: 0.8278 (mmt) REVERT: D 196 GLU cc_start: 0.8525 (tp30) cc_final: 0.8221 (tp30) REVERT: D 302 PHE cc_start: 0.8345 (t80) cc_final: 0.8020 (t80) REVERT: D 417 GLU cc_start: 0.7623 (tt0) cc_final: 0.7200 (tt0) REVERT: D 487 ARG cc_start: 0.8430 (tpp80) cc_final: 0.7690 (ptp-170) REVERT: D 491 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: D 564 ASP cc_start: 0.8466 (t70) cc_final: 0.8184 (t0) REVERT: D 598 ASP cc_start: 0.6956 (p0) cc_final: 0.6531 (m-30) REVERT: E 25 ARG cc_start: 0.8375 (ttt90) cc_final: 0.6902 (mtt90) REVERT: E 305 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8085 (mt-10) REVERT: E 321 GLU cc_start: 0.7970 (mp0) cc_final: 0.7435 (mp0) REVERT: E 534 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7050 (tm-30) REVERT: E 564 ASP cc_start: 0.8085 (t70) cc_final: 0.7819 (m-30) REVERT: E 608 MET cc_start: 0.8484 (ttm) cc_final: 0.8223 (tmm) REVERT: E 678 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7269 (mtt) REVERT: F 352 SER cc_start: 0.8463 (m) cc_final: 0.8232 (t) REVERT: F 508 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6831 (mmt) REVERT: F 619 ILE cc_start: 0.9241 (mt) cc_final: 0.8987 (tt) REVERT: F 744 ARG cc_start: 0.4883 (mmt180) cc_final: 0.4232 (mtp85) REVERT: G 332 ARG cc_start: 0.7477 (tpp-160) cc_final: 0.6975 (mmm160) REVERT: G 374 TRP cc_start: 0.6544 (p-90) cc_final: 0.6226 (p-90) REVERT: G 386 LYS cc_start: 0.8886 (mttt) cc_final: 0.8669 (ptmt) outliers start: 127 outliers final: 96 residues processed: 636 average time/residue: 0.1999 time to fit residues: 208.6285 Evaluate side-chains 634 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 534 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 412 MET Chi-restraints excluded: chain G residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 112 optimal weight: 2.9990 chunk 451 optimal weight: 4.9990 chunk 296 optimal weight: 0.2980 chunk 416 optimal weight: 10.0000 chunk 345 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 164 optimal weight: 0.6980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 296 ASN B 460 ASN C 91 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 115 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.145328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.113772 restraints weight = 77944.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.118165 restraints weight = 38181.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.118983 restraints weight = 21978.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119416 restraints weight = 18856.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.119545 restraints weight = 16594.592| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37527 Z= 0.151 Angle : 0.657 13.090 50746 Z= 0.314 Chirality : 0.046 0.206 5723 Planarity : 0.005 0.053 6650 Dihedral : 7.963 141.243 5191 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.92 % Allowed : 17.53 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.12), residues: 4639 helix: 1.27 (0.11), residues: 2107 sheet: 0.62 (0.19), residues: 737 loop : 0.57 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 93 TYR 0.029 0.002 TYR B 244 PHE 0.032 0.001 PHE A 575 TRP 0.007 0.001 TRP F 551 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00346 (37527) covalent geometry : angle 0.65734 (50746) hydrogen bonds : bond 0.03633 ( 1695) hydrogen bonds : angle 4.33325 ( 4746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 576 time to evaluate : 1.444 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: A 294 GLU cc_start: 0.8023 (tp30) cc_final: 0.7814 (pp20) REVERT: A 393 ASP cc_start: 0.7974 (t0) cc_final: 0.7568 (t0) REVERT: A 449 MET cc_start: 0.7795 (tpp) cc_final: 0.7115 (tpp) REVERT: A 529 LYS cc_start: 0.7546 (mtmt) cc_final: 0.7104 (mtmm) REVERT: A 618 PHE cc_start: 0.7856 (t80) cc_final: 0.7278 (t80) REVERT: A 620 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8907 (mm) REVERT: A 674 PHE cc_start: 0.7403 (t80) cc_final: 0.7061 (t80) REVERT: A 678 MET cc_start: 0.7154 (tpp) cc_final: 0.5218 (ptt) REVERT: B 62 LYS cc_start: 0.8745 (mttt) cc_final: 0.8507 (mmtm) REVERT: B 322 ARG cc_start: 0.8152 (mmp80) cc_final: 0.7668 (mmp80) REVERT: B 506 PHE cc_start: 0.7562 (m-80) cc_final: 0.7270 (m-10) REVERT: B 508 MET cc_start: 0.7881 (tmm) cc_final: 0.6640 (tmm) REVERT: B 568 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8284 (mm-40) REVERT: B 574 LEU cc_start: 0.8593 (tt) cc_final: 0.8300 (tt) REVERT: B 616 ASN cc_start: 0.7598 (m-40) cc_final: 0.7211 (t0) REVERT: B 635 ARG cc_start: 0.8338 (ttm110) cc_final: 0.7766 (mtm-85) REVERT: B 644 TYR cc_start: 0.7344 (t80) cc_final: 0.6985 (t80) REVERT: C 35 ASP cc_start: 0.8525 (t0) cc_final: 0.8214 (t0) REVERT: C 55 ASP cc_start: 0.8323 (t70) cc_final: 0.6984 (m-30) REVERT: C 64 ARG cc_start: 0.7699 (mmp-170) cc_final: 0.7457 (mmp-170) REVERT: C 173 TYR cc_start: 0.6997 (p90) cc_final: 0.6528 (p90) REVERT: C 317 HIS cc_start: 0.4886 (t-90) cc_final: 0.4629 (t-90) REVERT: C 421 GLN cc_start: 0.8684 (tp40) cc_final: 0.8210 (tp40) REVERT: C 508 MET cc_start: 0.7811 (tpt) cc_final: 0.7110 (tpt) REVERT: C 568 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 611 MET cc_start: 0.7814 (ttm) cc_final: 0.7406 (tpp) REVERT: C 762 LEU cc_start: 0.7409 (mt) cc_final: 0.6070 (tt) REVERT: D 123 VAL cc_start: 0.8810 (t) cc_final: 0.8593 (m) REVERT: D 124 GLU cc_start: 0.7792 (tp30) cc_final: 0.7576 (tp30) REVERT: D 196 GLU cc_start: 0.8547 (tp30) cc_final: 0.8285 (tp30) REVERT: D 302 PHE cc_start: 0.8322 (t80) cc_final: 0.8008 (t80) REVERT: D 417 GLU cc_start: 0.7608 (tt0) cc_final: 0.7201 (tt0) REVERT: D 487 ARG cc_start: 0.8437 (tpp80) cc_final: 0.7666 (ptp-170) REVERT: D 491 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: D 564 ASP cc_start: 0.8463 (t70) cc_final: 0.8164 (t0) REVERT: D 598 ASP cc_start: 0.6976 (p0) cc_final: 0.6535 (m-30) REVERT: E 25 ARG cc_start: 0.8386 (ttt90) cc_final: 0.6925 (mtt90) REVERT: E 132 GLU cc_start: 0.8529 (tp30) cc_final: 0.8266 (tt0) REVERT: E 158 MET cc_start: 0.8272 (mtt) cc_final: 0.8059 (mtt) REVERT: E 305 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8074 (mt-10) REVERT: E 534 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7057 (tm-30) REVERT: E 564 ASP cc_start: 0.8074 (t70) cc_final: 0.7805 (m-30) REVERT: E 608 MET cc_start: 0.8466 (ttm) cc_final: 0.8201 (tmm) REVERT: E 678 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7322 (mtt) REVERT: E 735 HIS cc_start: 0.8007 (m90) cc_final: 0.7741 (m90) REVERT: F 337 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7866 (tm-30) REVERT: F 352 SER cc_start: 0.8484 (m) cc_final: 0.8245 (t) REVERT: F 449 MET cc_start: 0.7954 (tpp) cc_final: 0.7617 (tpp) REVERT: F 508 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6830 (mmt) REVERT: F 619 ILE cc_start: 0.9222 (mt) cc_final: 0.9006 (tt) REVERT: F 744 ARG cc_start: 0.4924 (mmt180) cc_final: 0.4266 (mtp85) REVERT: G 332 ARG cc_start: 0.7569 (tpp-160) cc_final: 0.7054 (mmm160) REVERT: G 368 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7988 (pp20) REVERT: G 374 TRP cc_start: 0.6539 (p-90) cc_final: 0.6218 (p-90) REVERT: G 386 LYS cc_start: 0.8875 (mttt) cc_final: 0.8675 (ptmt) outliers start: 116 outliers final: 92 residues processed: 646 average time/residue: 0.2030 time to fit residues: 213.4887 Evaluate side-chains 635 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 539 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 533 ASN Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 412 MET Chi-restraints excluded: chain G residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 212 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 334 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 383 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN C 199 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 641 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.144498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.113190 restraints weight = 78411.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.117192 restraints weight = 38245.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.118429 restraints weight = 22297.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.118940 restraints weight = 18264.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.118884 restraints weight = 16839.488| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37527 Z= 0.165 Angle : 0.681 13.918 50746 Z= 0.324 Chirality : 0.046 0.232 5723 Planarity : 0.005 0.082 6650 Dihedral : 7.711 159.815 5191 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.87 % Allowed : 17.75 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.12), residues: 4639 helix: 1.26 (0.11), residues: 2101 sheet: 0.58 (0.19), residues: 737 loop : 0.51 (0.15), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 342 TYR 0.026 0.002 TYR B 244 PHE 0.032 0.002 PHE A 575 TRP 0.007 0.001 TRP F 551 HIS 0.014 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00382 (37527) covalent geometry : angle 0.68127 (50746) hydrogen bonds : bond 0.03695 ( 1695) hydrogen bonds : angle 4.37570 ( 4746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 548 time to evaluate : 1.352 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: A 294 GLU cc_start: 0.8042 (tp30) cc_final: 0.7829 (pp20) REVERT: A 393 ASP cc_start: 0.7950 (t0) cc_final: 0.7555 (t0) REVERT: A 449 MET cc_start: 0.7821 (tpp) cc_final: 0.7107 (tpp) REVERT: A 529 LYS cc_start: 0.7563 (mtmt) cc_final: 0.7156 (mtmm) REVERT: A 618 PHE cc_start: 0.7865 (t80) cc_final: 0.7328 (t80) REVERT: A 620 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8939 (mm) REVERT: A 674 PHE cc_start: 0.7426 (t80) cc_final: 0.7122 (t80) REVERT: A 678 MET cc_start: 0.7125 (tpp) cc_final: 0.5106 (ptt) REVERT: B 62 LYS cc_start: 0.8748 (mttt) cc_final: 0.8510 (mmtm) REVERT: B 322 ARG cc_start: 0.8175 (mmp80) cc_final: 0.7704 (mmp80) REVERT: B 506 PHE cc_start: 0.7602 (m-80) cc_final: 0.7313 (m-10) REVERT: B 508 MET cc_start: 0.7861 (tmm) cc_final: 0.6617 (tmm) REVERT: B 568 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8282 (mm-40) REVERT: B 574 LEU cc_start: 0.8621 (tt) cc_final: 0.8318 (tt) REVERT: B 616 ASN cc_start: 0.7646 (m-40) cc_final: 0.7274 (t0) REVERT: B 635 ARG cc_start: 0.8365 (ttm110) cc_final: 0.7775 (mtm-85) REVERT: C 26 LEU cc_start: 0.6057 (mt) cc_final: 0.5692 (mt) REVERT: C 35 ASP cc_start: 0.8559 (t0) cc_final: 0.8253 (t0) REVERT: C 55 ASP cc_start: 0.8320 (t70) cc_final: 0.6966 (m-30) REVERT: C 64 ARG cc_start: 0.7724 (mmp-170) cc_final: 0.7417 (mmp-170) REVERT: C 173 TYR cc_start: 0.7009 (p90) cc_final: 0.6695 (p90) REVERT: C 317 HIS cc_start: 0.5020 (t-90) cc_final: 0.4740 (t-90) REVERT: C 421 GLN cc_start: 0.8696 (tp40) cc_final: 0.8202 (tp40) REVERT: C 495 TYR cc_start: 0.9035 (m-10) cc_final: 0.8773 (m-80) REVERT: C 508 MET cc_start: 0.7790 (tpt) cc_final: 0.7112 (tpt) REVERT: C 568 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7792 (tm-30) REVERT: C 611 MET cc_start: 0.7864 (ttm) cc_final: 0.7462 (tpp) REVERT: D 123 VAL cc_start: 0.8814 (t) cc_final: 0.8597 (m) REVERT: D 124 GLU cc_start: 0.7801 (tp30) cc_final: 0.7593 (tp30) REVERT: D 147 ARG cc_start: 0.6159 (ttt180) cc_final: 0.5911 (ttt180) REVERT: D 196 GLU cc_start: 0.8521 (tp30) cc_final: 0.8278 (tp30) REVERT: D 302 PHE cc_start: 0.8340 (t80) cc_final: 0.8020 (t80) REVERT: D 417 GLU cc_start: 0.7573 (tt0) cc_final: 0.7175 (tt0) REVERT: D 491 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: D 522 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8650 (t) REVERT: D 598 ASP cc_start: 0.7000 (p0) cc_final: 0.6575 (m-30) REVERT: E 25 ARG cc_start: 0.8409 (ttt90) cc_final: 0.6922 (mtt90) REVERT: E 132 GLU cc_start: 0.8548 (tp30) cc_final: 0.8274 (tt0) REVERT: E 158 MET cc_start: 0.8292 (mtt) cc_final: 0.8080 (mtt) REVERT: E 305 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8094 (mt-10) REVERT: E 534 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7088 (tm-30) REVERT: E 564 ASP cc_start: 0.8059 (t70) cc_final: 0.7810 (m-30) REVERT: E 608 MET cc_start: 0.8474 (ttm) cc_final: 0.8209 (tmm) REVERT: F 352 SER cc_start: 0.8487 (m) cc_final: 0.8265 (t) REVERT: F 449 MET cc_start: 0.8030 (tpp) cc_final: 0.7813 (tpp) REVERT: F 477 GLU cc_start: 0.7653 (tp30) cc_final: 0.7391 (tp30) REVERT: F 508 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6877 (mmt) REVERT: F 619 ILE cc_start: 0.9240 (mt) cc_final: 0.9021 (tt) REVERT: G 332 ARG cc_start: 0.7617 (tpp-160) cc_final: 0.7145 (mmm160) REVERT: G 374 TRP cc_start: 0.6576 (p-90) cc_final: 0.6241 (p-90) REVERT: G 386 LYS cc_start: 0.8875 (mttt) cc_final: 0.8665 (ptmt) outliers start: 114 outliers final: 96 residues processed: 621 average time/residue: 0.2207 time to fit residues: 225.5853 Evaluate side-chains 634 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 534 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 236 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 533 ASN Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 412 MET Chi-restraints excluded: chain G residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 87 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 344 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 302 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 378 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN C 199 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 641 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN G 294 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.112217 restraints weight = 78634.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116190 restraints weight = 38334.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.118410 restraints weight = 21708.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.118409 restraints weight = 18868.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.118282 restraints weight = 15924.865| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37527 Z= 0.185 Angle : 0.700 14.384 50746 Z= 0.335 Chirality : 0.046 0.237 5723 Planarity : 0.005 0.078 6650 Dihedral : 7.639 174.148 5191 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.74 % Allowed : 18.01 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.12), residues: 4639 helix: 1.22 (0.11), residues: 2100 sheet: 0.51 (0.19), residues: 752 loop : 0.46 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 342 TYR 0.026 0.002 TYR B 244 PHE 0.031 0.002 PHE E 682 TRP 0.007 0.001 TRP E 551 HIS 0.011 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00429 (37527) covalent geometry : angle 0.69979 (50746) hydrogen bonds : bond 0.03778 ( 1695) hydrogen bonds : angle 4.43008 ( 4746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 549 time to evaluate : 1.571 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: A 393 ASP cc_start: 0.7880 (t0) cc_final: 0.7493 (t0) REVERT: A 449 MET cc_start: 0.7864 (tpp) cc_final: 0.7111 (tpp) REVERT: A 529 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7143 (mtmm) REVERT: A 618 PHE cc_start: 0.7866 (t80) cc_final: 0.7310 (t80) REVERT: A 620 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8913 (mm) REVERT: A 674 PHE cc_start: 0.7432 (t80) cc_final: 0.7075 (t80) REVERT: A 678 MET cc_start: 0.7097 (tpp) cc_final: 0.5099 (ptt) REVERT: B 62 LYS cc_start: 0.8746 (mttt) cc_final: 0.8515 (mmtm) REVERT: B 322 ARG cc_start: 0.8172 (mmp80) cc_final: 0.7447 (mmp80) REVERT: B 506 PHE cc_start: 0.7683 (m-80) cc_final: 0.7400 (m-10) REVERT: B 508 MET cc_start: 0.7873 (tmm) cc_final: 0.6636 (tmm) REVERT: B 616 ASN cc_start: 0.7672 (m-40) cc_final: 0.7302 (t0) REVERT: B 635 ARG cc_start: 0.8402 (ttm110) cc_final: 0.7787 (mtm-85) REVERT: C 35 ASP cc_start: 0.8530 (t0) cc_final: 0.8258 (t0) REVERT: C 55 ASP cc_start: 0.8357 (t70) cc_final: 0.7015 (m-30) REVERT: C 173 TYR cc_start: 0.7108 (p90) cc_final: 0.6781 (p90) REVERT: C 317 HIS cc_start: 0.4989 (t-90) cc_final: 0.4708 (t-90) REVERT: C 421 GLN cc_start: 0.8720 (tp40) cc_final: 0.8202 (tp40) REVERT: C 495 TYR cc_start: 0.9019 (m-10) cc_final: 0.8774 (m-80) REVERT: C 508 MET cc_start: 0.7798 (tpt) cc_final: 0.7146 (tpt) REVERT: C 568 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 611 MET cc_start: 0.7830 (ttm) cc_final: 0.7440 (tpp) REVERT: C 762 LEU cc_start: 0.7424 (mt) cc_final: 0.6036 (tt) REVERT: D 123 VAL cc_start: 0.8826 (t) cc_final: 0.8621 (m) REVERT: D 124 GLU cc_start: 0.7762 (tp30) cc_final: 0.7546 (tp30) REVERT: D 417 GLU cc_start: 0.7660 (tt0) cc_final: 0.7230 (tt0) REVERT: D 491 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: D 522 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8604 (t) REVERT: D 598 ASP cc_start: 0.7020 (p0) cc_final: 0.6610 (m-30) REVERT: E 25 ARG cc_start: 0.8428 (ttt90) cc_final: 0.6961 (mtt90) REVERT: E 132 GLU cc_start: 0.8531 (tp30) cc_final: 0.8259 (tt0) REVERT: E 158 MET cc_start: 0.8278 (mtt) cc_final: 0.8063 (mtt) REVERT: E 231 LYS cc_start: 0.8865 (tttm) cc_final: 0.8586 (ttpp) REVERT: E 305 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8087 (mt-10) REVERT: E 534 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7029 (tm-30) REVERT: E 564 ASP cc_start: 0.8053 (t70) cc_final: 0.7817 (m-30) REVERT: E 608 MET cc_start: 0.8466 (ttm) cc_final: 0.8215 (tmm) REVERT: F 352 SER cc_start: 0.8494 (m) cc_final: 0.8282 (t) REVERT: F 449 MET cc_start: 0.8021 (tpp) cc_final: 0.7813 (tpp) REVERT: F 477 GLU cc_start: 0.7694 (tp30) cc_final: 0.7428 (tp30) REVERT: F 508 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6928 (mmt) REVERT: F 619 ILE cc_start: 0.9259 (mt) cc_final: 0.9030 (tt) REVERT: G 332 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.7135 (mmm160) REVERT: G 368 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8038 (pp20) REVERT: G 374 TRP cc_start: 0.6590 (p-90) cc_final: 0.6242 (p-90) REVERT: G 386 LYS cc_start: 0.8871 (mttt) cc_final: 0.8661 (ptmt) outliers start: 109 outliers final: 91 residues processed: 612 average time/residue: 0.2094 time to fit residues: 210.9096 Evaluate side-chains 623 residues out of total 3971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 528 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 735 HIS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 412 MET Chi-restraints excluded: chain G residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 159 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 258 optimal weight: 10.0000 chunk 378 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 193 optimal weight: 0.2980 chunk 442 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 367 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN C 199 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 641 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.146217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115922 restraints weight = 77845.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.118212 restraints weight = 38468.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.119164 restraints weight = 23808.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.119647 restraints weight = 22065.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.119724 restraints weight = 19341.225| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37527 Z= 0.123 Angle : 0.676 14.781 50746 Z= 0.322 Chirality : 0.045 0.229 5723 Planarity : 0.005 0.110 6650 Dihedral : 7.390 179.872 5191 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.91 % Allowed : 19.04 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.13), residues: 4639 helix: 1.35 (0.12), residues: 2092 sheet: 0.52 (0.19), residues: 752 loop : 0.59 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 342 TYR 0.027 0.002 TYR B 244 PHE 0.027 0.001 PHE A 575 TRP 0.007 0.001 TRP E 454 HIS 0.011 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00282 (37527) covalent geometry : angle 0.67649 (50746) hydrogen bonds : bond 0.03498 ( 1695) hydrogen bonds : angle 4.29316 ( 4746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7565.10 seconds wall clock time: 130 minutes 39.51 seconds (7839.51 seconds total)