Starting phenix.real_space_refine on Tue Aug 26 12:32:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcr_28991/08_2025/8fcr_28991.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcr_28991/08_2025/8fcr_28991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fcr_28991/08_2025/8fcr_28991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcr_28991/08_2025/8fcr_28991.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcr_28991/08_2025/8fcr_28991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcr_28991/08_2025/8fcr_28991.cif" } resolution = 4.12 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 188 5.16 5 C 23170 2.51 5 N 6487 2.21 5 O 7062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.04s 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: 36931 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5637 Classifications: {'peptide': 721} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 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: 5565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5565 Classifications: {'peptide': 712} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 2 Chain: "G" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2845 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 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: 9.22, per 1000 atoms: 0.25 Number of scatterers: 36931 At special positions: 0 Unit cell: (183.48, 191.82, 115.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 188 16.00 P 24 15.00 O 7062 8.00 N 6487 7.00 C 23170 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: 3.33 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8756 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 40 sheets defined 52.2% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 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: 4.551A 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: 4.040A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 427 through 430 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.677A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.527A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.612A pdb=" N ALA A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 706 removed outlier: 3.710A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.639A 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 227 through 233 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: 3.770A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 428 removed outlier: 3.759A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.535A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.204A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 612 through 615 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 705 Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.533A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) 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: 4.788A 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: 4.041A 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: 3.819A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 334 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 431 removed outlier: 3.678A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 431 " --> pdb=" O MET C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.136A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 705 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.518A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.691A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 4.189A 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: 3.684A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 318 through 334 Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 431 removed outlier: 3.705A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP D 431 " --> pdb=" O MET D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.090A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 612 through 615 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 705 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 762 removed outlier: 3.897A 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: 4.704A 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: 3.871A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.715A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 334 Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 384 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 428 removed outlier: 3.769A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.505A 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: 3.613A 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: 4.017A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.504A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.811A 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: 3.508A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 431 removed outlier: 4.435A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.508A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.043A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 609 Processing helix chain 'F' and resid 610 through 611 No H-bonds generated for 'chain 'F' and resid 610 through 611' Processing helix chain 'F' and resid 612 through 615 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.781A 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 removed outlier: 3.516A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 Processing helix chain 'G' and resid 50 through 68 Processing helix chain 'G' and resid 75 through 94 removed outlier: 3.555A pdb=" N SER G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.771A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 165 removed outlier: 4.110A pdb=" N ASN G 165 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 188 removed outlier: 3.515A pdb=" N ILE G 185 " --> pdb=" O TYR G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 194 Processing helix chain 'G' and resid 201 through 208 Processing helix chain 'G' and resid 213 through 221 Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 250 through 262 Processing helix chain 'G' and resid 280 through 285 Processing helix chain 'G' and resid 289 through 294 removed outlier: 4.413A pdb=" N PHE G 293 " --> pdb=" O GLY G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 316 Processing helix chain 'G' and resid 319 through 328 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 358 through 370 removed outlier: 3.738A pdb=" N VAL G 362 " --> pdb=" O ARG G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 421 removed outlier: 3.577A 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 30 removed outlier: 7.259A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.382A 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: 6.466A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.567A 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: 3.674A 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: 6.076A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.509A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.940A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LYS B 81 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER B 42 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP B 74 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 41 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.599A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AB2, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.115A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.323A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 29 removed outlier: 7.484A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 151 through 156 removed outlier: 6.979A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AB7, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB8, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.203A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.460A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 29 removed outlier: 7.111A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LYS D 81 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER D 42 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP D 55 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 151 through 156 removed outlier: 6.566A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC5, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.173A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 389 through 390 removed outlier: 6.862A pdb=" N LYS D 389 " --> pdb=" O VAL D 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.401A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 25 through 30 removed outlier: 7.950A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS E 81 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER E 42 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASP E 74 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU E 41 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 151 through 156 removed outlier: 6.903A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AD2, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.743A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.220A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.534A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 25 through 29 Processing sheet with id=AD6, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.592A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AD8, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD9, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.216A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.572A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AE3, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AE4, first strand: chain 'G' and resid 386 through 387 removed outlier: 4.395A pdb=" N LEU G 379 " --> pdb=" O LEU G 387 " (cutoff:3.500A) 1713 hydrogen bonds defined for protein. 4809 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: 8.62 Time building geometry restraints manager: 4.30 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: 7600 1.33 - 1.45: 7846 1.45 - 1.57: 21768 1.57 - 1.69: 36 1.69 - 1.81: 299 Bond restraints: 37549 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.12e+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 3.08e+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 3.05e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 ... (remaining 37544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 49734 2.47 - 4.95: 916 4.95 - 7.42: 89 7.42 - 9.90: 33 9.90 - 12.37: 8 Bond angle restraints: 50780 Sorted by residual: angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 113.28 123.96 -10.68 1.22e+00 6.72e-01 7.67e+01 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 112.92 122.47 -9.55 1.23e+00 6.61e-01 6.03e+01 angle pdb=" CA ASP F 592 " pdb=" C ASP F 592 " pdb=" O ASP F 592 " ideal model delta sigma weight residual 117.94 121.86 -3.92 5.80e-01 2.97e+00 4.57e+01 angle pdb=" N LYS G 333 " pdb=" CA LYS G 333 " pdb=" C LYS G 333 " ideal model delta sigma weight residual 111.82 118.44 -6.62 1.16e+00 7.43e-01 3.26e+01 angle pdb=" C ASP F 592 " pdb=" CA ASP F 592 " pdb=" CB ASP F 592 " ideal model delta sigma weight residual 117.07 110.15 6.92 1.44e+00 4.82e-01 2.31e+01 ... (remaining 50775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 22928 34.86 - 69.71: 258 69.71 - 104.57: 42 104.57 - 139.43: 8 139.43 - 174.28: 9 Dihedral angle restraints: 23245 sinusoidal: 9751 harmonic: 13494 Sorted by residual: dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 114.28 -174.28 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual 300.00 126.06 173.93 1 2.00e+01 2.50e-03 4.79e+01 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 300.00 126.70 173.29 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 23242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4072 0.048 - 0.095: 999 0.095 - 0.143: 477 0.143 - 0.191: 173 0.191 - 0.239: 13 Chirality restraints: 5734 Sorted by residual: chirality pdb=" CA ILE E 590 " pdb=" N ILE E 590 " pdb=" C ILE E 590 " pdb=" CB ILE E 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE B 590 " pdb=" N ILE B 590 " pdb=" C ILE B 590 " pdb=" CB ILE B 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE C 590 " pdb=" N ILE C 590 " pdb=" C ILE C 590 " pdb=" CB ILE C 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 5731 not shown) Planarity restraints: 6656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 144 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C ARG E 144 " 0.044 2.00e-02 2.50e+03 pdb=" O ARG E 144 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO E 145 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 82 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C GLN G 82 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN G 82 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL G 83 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 254 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C GLU G 254 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU G 254 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG G 255 " -0.013 2.00e-02 2.50e+03 ... (remaining 6653 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 12306 2.85 - 3.36: 35039 3.36 - 3.88: 62969 3.88 - 4.39: 73724 4.39 - 4.90: 119861 Nonbonded interactions: 303899 Sorted by model distance: nonbonded pdb=" O LYS A 696 " pdb=" CG1 ILE A 699 " model vdw 2.340 3.440 nonbonded pdb=" OD2 ASP B 368 " pdb=" NZ LYS B 565 " model vdw 2.387 3.120 nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.408 3.120 nonbonded pdb=" OD2 ASP A 368 " pdb=" NZ LYS A 565 " model vdw 2.424 3.120 nonbonded pdb=" O ALA D 583 " pdb=" N GLY D 588 " model vdw 2.425 3.120 ... (remaining 303894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'B' and (resid 23 through 499 or resid 509 through 696 or (resid 697 thro \ ugh 698 and (name N or name CA or name C or name O or name CB )) or resid 699 th \ rough 902)) selection = (chain 'C' and (resid 23 through 499 or resid 509 through 696 or (resid 697 thro \ ugh 698 and (name N or name CA or name C or name O or name CB )) or resid 699 th \ rough 902)) selection = (chain 'D' and (resid 23 through 499 or resid 509 through 696 or (resid 697 thro \ ugh 698 and (name N or name CA or name C or name O or name CB )) or resid 699 th \ rough 902)) selection = (chain 'E' and (resid 23 through 499 or resid 509 through 696 or (resid 697 thro \ ugh 698 and (name N or name CA or name C or name O or name CB )) or resid 699 th \ rough 902)) selection = (chain 'F' and (resid 23 through 696 or (resid 697 through 698 and (name N or na \ me CA or name C or name O or name CB )) or resid 699 through 902)) } 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.560 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 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 0.112 37549 Z= 0.612 Angle : 0.854 12.374 50780 Z= 0.526 Chirality : 0.058 0.239 5734 Planarity : 0.004 0.035 6656 Dihedral : 12.235 174.283 14489 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.70 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.11), residues: 4647 helix: -0.15 (0.10), residues: 2068 sheet: 0.68 (0.17), residues: 802 loop : 0.88 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 89 TYR 0.001 0.000 TYR C 203 PHE 0.002 0.000 PHE D 267 TRP 0.002 0.000 TRP E 551 HIS 0.001 0.000 HIS G 215 Details of bonding type rmsd covalent geometry : bond 0.01080 (37549) covalent geometry : angle 0.85412 (50780) hydrogen bonds : bond 0.20573 ( 1713) hydrogen bonds : angle 6.43880 ( 4809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1473 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.7015 (t) cc_final: 0.5759 (t) REVERT: A 206 ILE cc_start: 0.7943 (mt) cc_final: 0.7526 (mt) REVERT: A 335 LEU cc_start: 0.7970 (mt) cc_final: 0.7405 (mt) REVERT: A 367 VAL cc_start: 0.6445 (t) cc_final: 0.6167 (t) REVERT: A 383 ILE cc_start: 0.8142 (mt) cc_final: 0.7766 (mm) REVERT: A 414 LEU cc_start: 0.8167 (mt) cc_final: 0.7859 (tp) REVERT: B 138 TYR cc_start: 0.7345 (t80) cc_final: 0.6972 (t80) REVERT: B 618 PHE cc_start: 0.6974 (t80) cc_final: 0.6518 (t80) REVERT: C 161 VAL cc_start: 0.6947 (t) cc_final: 0.6707 (t) REVERT: C 260 ASN cc_start: 0.6942 (m-40) cc_final: 0.5460 (m110) REVERT: C 373 ASP cc_start: 0.5554 (p0) cc_final: 0.5292 (p0) REVERT: C 581 SER cc_start: 0.8138 (p) cc_final: 0.7740 (t) REVERT: D 153 LEU cc_start: 0.7389 (tp) cc_final: 0.7126 (mp) REVERT: D 363 PHE cc_start: 0.6866 (m-80) cc_final: 0.6039 (m-80) REVERT: D 364 ASP cc_start: 0.6813 (p0) cc_final: 0.6370 (p0) REVERT: D 485 VAL cc_start: 0.7876 (t) cc_final: 0.7487 (t) REVERT: D 644 TYR cc_start: 0.6964 (t80) cc_final: 0.6742 (t80) REVERT: E 216 ILE cc_start: 0.8946 (mt) cc_final: 0.8735 (mt) REVERT: E 252 THR cc_start: 0.8349 (p) cc_final: 0.8090 (t) REVERT: E 268 LEU cc_start: 0.8163 (tp) cc_final: 0.7942 (tt) REVERT: E 341 VAL cc_start: 0.8234 (t) cc_final: 0.7995 (p) REVERT: E 373 ASP cc_start: 0.4585 (p0) cc_final: 0.3295 (p0) REVERT: E 456 LEU cc_start: 0.8175 (mt) cc_final: 0.7776 (mt) REVERT: E 559 VAL cc_start: 0.7183 (t) cc_final: 0.6655 (t) REVERT: E 564 ASP cc_start: 0.4591 (t70) cc_final: 0.4355 (t70) REVERT: F 335 LEU cc_start: 0.7675 (mt) cc_final: 0.6925 (mt) REVERT: F 380 ILE cc_start: 0.8583 (mt) cc_final: 0.8331 (mm) REVERT: F 432 LEU cc_start: 0.6229 (tp) cc_final: 0.5982 (tt) REVERT: G 396 ASN cc_start: 0.8239 (p0) cc_final: 0.7681 (p0) outliers start: 0 outliers final: 0 residues processed: 1473 average time/residue: 0.2512 time to fit residues: 573.1578 Evaluate side-chains 801 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 801 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.5980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 494 GLN A 538 ASN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 91 ASN C 260 ASN C 603 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN D 226 HIS ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.093504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069519 restraints weight = 151026.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.071561 restraints weight = 94164.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.072941 restraints weight = 67227.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.073853 restraints weight = 52839.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074442 restraints weight = 44471.737| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37549 Z= 0.187 Angle : 0.705 11.726 50780 Z= 0.352 Chirality : 0.046 0.226 5734 Planarity : 0.005 0.086 6656 Dihedral : 9.983 174.925 5201 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.27 % Favored : 98.71 % Rotamer: Outliers : 0.13 % Allowed : 2.88 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.12), residues: 4647 helix: 1.10 (0.11), residues: 2074 sheet: 0.78 (0.17), residues: 796 loop : 0.99 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 322 TYR 0.034 0.002 TYR E 495 PHE 0.029 0.002 PHE C 563 TRP 0.016 0.002 TRP B 476 HIS 0.013 0.001 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00399 (37549) covalent geometry : angle 0.70478 (50780) hydrogen bonds : bond 0.05543 ( 1713) hydrogen bonds : angle 4.75289 ( 4809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 961 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8840 (mtm) cc_final: 0.8425 (ptp) REVERT: A 88 VAL cc_start: 0.9513 (t) cc_final: 0.8926 (t) REVERT: A 135 LEU cc_start: 0.9198 (mt) cc_final: 0.8900 (mt) REVERT: A 162 GLU cc_start: 0.8487 (pt0) cc_final: 0.7915 (pt0) REVERT: A 275 MET cc_start: 0.9549 (mmm) cc_final: 0.9314 (mmm) REVERT: A 335 LEU cc_start: 0.9198 (mt) cc_final: 0.8989 (mt) REVERT: A 384 HIS cc_start: 0.8161 (m90) cc_final: 0.7789 (m90) REVERT: A 625 ARG cc_start: 0.8965 (tpp-160) cc_final: 0.8471 (tpp80) REVERT: A 730 GLU cc_start: 0.8620 (pt0) cc_final: 0.8170 (pm20) REVERT: A 752 ILE cc_start: 0.9314 (mt) cc_final: 0.8958 (mt) REVERT: B 138 TYR cc_start: 0.8317 (t80) cc_final: 0.7717 (t80) REVERT: B 139 PHE cc_start: 0.8811 (m-10) cc_final: 0.8309 (m-10) REVERT: B 212 GLN cc_start: 0.9170 (mp10) cc_final: 0.8701 (mp10) REVERT: B 236 LYS cc_start: 0.8236 (tppt) cc_final: 0.7745 (tppt) REVERT: B 242 LEU cc_start: 0.9369 (tt) cc_final: 0.9115 (tt) REVERT: B 348 ASN cc_start: 0.8790 (t0) cc_final: 0.8555 (t0) REVERT: B 386 LYS cc_start: 0.8925 (mmpt) cc_final: 0.8519 (mmmt) REVERT: B 485 VAL cc_start: 0.8259 (t) cc_final: 0.7928 (t) REVERT: B 488 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 531 ILE cc_start: 0.9067 (tt) cc_final: 0.8816 (tt) REVERT: B 538 ASN cc_start: 0.9304 (m-40) cc_final: 0.8962 (m-40) REVERT: B 574 LEU cc_start: 0.8960 (tt) cc_final: 0.8671 (tt) REVERT: B 576 PHE cc_start: 0.9056 (m-10) cc_final: 0.8812 (m-10) REVERT: B 618 PHE cc_start: 0.8702 (t80) cc_final: 0.7878 (t80) REVERT: B 633 ILE cc_start: 0.9740 (tp) cc_final: 0.9430 (mt) REVERT: C 46 MET cc_start: 0.8494 (mtp) cc_final: 0.8230 (mtp) REVERT: C 53 ARG cc_start: 0.6681 (ttt90) cc_final: 0.6052 (mpt180) REVERT: C 148 LYS cc_start: 0.7774 (tttt) cc_final: 0.7397 (mttp) REVERT: C 241 ILE cc_start: 0.9629 (mp) cc_final: 0.9330 (mp) REVERT: C 315 LYS cc_start: 0.9426 (tppt) cc_final: 0.9023 (tptt) REVERT: C 331 LEU cc_start: 0.9553 (mt) cc_final: 0.9318 (mt) REVERT: C 366 GLU cc_start: 0.8741 (pm20) cc_final: 0.8495 (pm20) REVERT: C 373 ASP cc_start: 0.8906 (p0) cc_final: 0.8482 (p0) REVERT: C 404 HIS cc_start: 0.8531 (t-90) cc_final: 0.8284 (t-90) REVERT: C 427 MET cc_start: 0.6825 (tpt) cc_final: 0.5492 (tmm) REVERT: C 432 LEU cc_start: 0.8037 (tp) cc_final: 0.7584 (tp) REVERT: C 498 GLU cc_start: 0.9119 (mp0) cc_final: 0.8862 (pt0) REVERT: C 575 PHE cc_start: 0.8254 (t80) cc_final: 0.7806 (t80) REVERT: D 153 LEU cc_start: 0.8790 (tp) cc_final: 0.8184 (mp) REVERT: D 204 ASP cc_start: 0.8693 (t70) cc_final: 0.8429 (t0) REVERT: D 305 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8834 (mm-30) REVERT: D 317 HIS cc_start: 0.7538 (p-80) cc_final: 0.7288 (p-80) REVERT: D 373 ASP cc_start: 0.8268 (p0) cc_final: 0.8064 (p0) REVERT: D 397 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8247 (tm-30) REVERT: D 401 ASN cc_start: 0.8914 (m-40) cc_final: 0.8701 (m110) REVERT: D 404 HIS cc_start: 0.8815 (m90) cc_final: 0.8471 (m90) REVERT: D 406 HIS cc_start: 0.8484 (m-70) cc_final: 0.7947 (m90) REVERT: D 495 TYR cc_start: 0.9130 (m-10) cc_final: 0.8893 (m-80) REVERT: D 508 MET cc_start: 0.7301 (tmm) cc_final: 0.7098 (tmm) REVERT: D 548 LEU cc_start: 0.9273 (mt) cc_final: 0.8979 (mt) REVERT: E 260 ASN cc_start: 0.8559 (m-40) cc_final: 0.7921 (m110) REVERT: E 268 LEU cc_start: 0.9443 (tp) cc_final: 0.9207 (tt) REVERT: E 332 MET cc_start: 0.8235 (tpt) cc_final: 0.7942 (tpp) REVERT: E 380 ILE cc_start: 0.9373 (mt) cc_final: 0.8900 (tt) REVERT: E 449 MET cc_start: 0.8600 (tpt) cc_final: 0.8380 (tmm) REVERT: E 456 LEU cc_start: 0.9607 (mt) cc_final: 0.9294 (mt) REVERT: E 474 VAL cc_start: 0.7518 (t) cc_final: 0.7283 (t) REVERT: E 541 SER cc_start: 0.9262 (p) cc_final: 0.8935 (p) REVERT: E 551 TRP cc_start: 0.3583 (t60) cc_final: 0.3013 (t-100) REVERT: E 561 GLU cc_start: 0.9570 (OUTLIER) cc_final: 0.9294 (pm20) REVERT: E 577 ASP cc_start: 0.8745 (t0) cc_final: 0.8192 (t0) REVERT: E 578 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8970 (mt-10) REVERT: E 618 PHE cc_start: 0.8360 (t80) cc_final: 0.7838 (t80) REVERT: E 620 ILE cc_start: 0.9524 (mt) cc_final: 0.8978 (mt) REVERT: E 736 PHE cc_start: 0.8805 (m-80) cc_final: 0.8397 (m-80) REVERT: F 58 LEU cc_start: 0.9318 (mt) cc_final: 0.9067 (mt) REVERT: F 203 TYR cc_start: 0.8577 (m-80) cc_final: 0.8266 (m-80) REVERT: F 261 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7749 (mm-30) REVERT: F 335 LEU cc_start: 0.8978 (mt) cc_final: 0.8536 (mt) REVERT: F 338 ARG cc_start: 0.8411 (mtt90) cc_final: 0.7531 (mmt90) REVERT: F 368 ASP cc_start: 0.9020 (t0) cc_final: 0.8392 (t70) REVERT: F 423 ILE cc_start: 0.9618 (mt) cc_final: 0.9409 (tp) REVERT: F 534 GLU cc_start: 0.8760 (tt0) cc_final: 0.8324 (tp30) REVERT: F 560 ARG cc_start: 0.9070 (ttp-110) cc_final: 0.8715 (ttm110) REVERT: F 561 GLU cc_start: 0.9162 (mp0) cc_final: 0.8944 (mp0) REVERT: F 564 ASP cc_start: 0.8492 (m-30) cc_final: 0.8281 (m-30) REVERT: F 619 ILE cc_start: 0.9709 (mp) cc_final: 0.9362 (tp) REVERT: F 625 ARG cc_start: 0.8631 (tpm170) cc_final: 0.8231 (tpm170) REVERT: F 660 ASN cc_start: 0.8407 (m110) cc_final: 0.8076 (m-40) outliers start: 5 outliers final: 2 residues processed: 965 average time/residue: 0.2349 time to fit residues: 364.4690 Evaluate side-chains 675 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 672 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 97 optimal weight: 0.9980 chunk 324 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 446 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 240 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 406 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN G 273 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.092006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.067928 restraints weight = 154111.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.069988 restraints weight = 95114.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.071397 restraints weight = 67384.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.072339 restraints weight = 52671.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.073001 restraints weight = 44244.547| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 37549 Z= 0.156 Angle : 0.667 18.213 50780 Z= 0.328 Chirality : 0.045 0.184 5734 Planarity : 0.005 0.067 6656 Dihedral : 9.535 173.114 5201 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.12), residues: 4647 helix: 1.15 (0.11), residues: 2100 sheet: 0.84 (0.17), residues: 790 loop : 0.92 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 144 TYR 0.028 0.002 TYR A 495 PHE 0.032 0.002 PHE E 563 TRP 0.012 0.002 TRP A 476 HIS 0.013 0.001 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00342 (37549) covalent geometry : angle 0.66683 (50780) hydrogen bonds : bond 0.04480 ( 1713) hydrogen bonds : angle 4.45819 ( 4809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 855 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8856 (mtm) cc_final: 0.8417 (ptp) REVERT: A 71 VAL cc_start: 0.9035 (t) cc_final: 0.8475 (p) REVERT: A 88 VAL cc_start: 0.9514 (t) cc_final: 0.8881 (t) REVERT: A 135 LEU cc_start: 0.9266 (mt) cc_final: 0.8956 (mt) REVERT: A 217 LYS cc_start: 0.9281 (ptpt) cc_final: 0.9079 (ptpp) REVERT: A 275 MET cc_start: 0.9573 (mmm) cc_final: 0.9324 (mmm) REVERT: A 335 LEU cc_start: 0.9145 (mt) cc_final: 0.8945 (mt) REVERT: A 365 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.8099 (mtm-85) REVERT: A 384 HIS cc_start: 0.8151 (m90) cc_final: 0.7795 (m90) REVERT: A 423 ILE cc_start: 0.9343 (tt) cc_final: 0.8160 (tt) REVERT: A 424 ARG cc_start: 0.8398 (mmp80) cc_final: 0.7927 (mmp80) REVERT: A 565 LYS cc_start: 0.9454 (mmmm) cc_final: 0.9191 (mmmm) REVERT: A 578 GLU cc_start: 0.8807 (mp0) cc_final: 0.8334 (mp0) REVERT: A 625 ARG cc_start: 0.8978 (tpp-160) cc_final: 0.8475 (tpp80) REVERT: A 730 GLU cc_start: 0.8703 (pt0) cc_final: 0.8257 (pm20) REVERT: B 87 VAL cc_start: 0.9346 (t) cc_final: 0.9144 (t) REVERT: B 138 TYR cc_start: 0.8296 (t80) cc_final: 0.7683 (t80) REVERT: B 139 PHE cc_start: 0.8770 (m-10) cc_final: 0.8211 (m-10) REVERT: B 212 GLN cc_start: 0.9058 (mp10) cc_final: 0.8802 (mp10) REVERT: B 236 LYS cc_start: 0.8192 (tppt) cc_final: 0.7766 (tppt) REVERT: B 242 LEU cc_start: 0.9421 (tt) cc_final: 0.9216 (tt) REVERT: B 386 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8585 (mmmt) REVERT: B 440 GLU cc_start: 0.8772 (mp0) cc_final: 0.8419 (mp0) REVERT: B 478 ASP cc_start: 0.9073 (t0) cc_final: 0.8851 (t0) REVERT: B 485 VAL cc_start: 0.8417 (t) cc_final: 0.8059 (t) REVERT: B 488 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8438 (tm-30) REVERT: B 531 ILE cc_start: 0.9090 (tt) cc_final: 0.8828 (tt) REVERT: B 538 ASN cc_start: 0.9270 (m-40) cc_final: 0.8952 (m-40) REVERT: B 563 PHE cc_start: 0.9314 (m-80) cc_final: 0.9070 (m-80) REVERT: B 574 LEU cc_start: 0.8972 (tt) cc_final: 0.8693 (tt) REVERT: B 576 PHE cc_start: 0.9105 (m-10) cc_final: 0.8792 (m-10) REVERT: B 618 PHE cc_start: 0.8698 (t80) cc_final: 0.7782 (t80) REVERT: B 740 MET cc_start: 0.8076 (mtm) cc_final: 0.7730 (mtt) REVERT: C 46 MET cc_start: 0.8560 (mtp) cc_final: 0.8259 (mtp) REVERT: C 53 ARG cc_start: 0.6669 (ttt90) cc_final: 0.6006 (mpt180) REVERT: C 315 LYS cc_start: 0.9424 (tppt) cc_final: 0.9060 (tptt) REVERT: C 326 SER cc_start: 0.8952 (m) cc_final: 0.8444 (p) REVERT: C 331 LEU cc_start: 0.9557 (mt) cc_final: 0.9334 (mt) REVERT: C 332 MET cc_start: 0.8681 (mmm) cc_final: 0.8368 (mmm) REVERT: C 349 ARG cc_start: 0.8937 (ttm170) cc_final: 0.8581 (ttm110) REVERT: C 373 ASP cc_start: 0.8874 (p0) cc_final: 0.8152 (p0) REVERT: C 375 THR cc_start: 0.9234 (m) cc_final: 0.8983 (p) REVERT: C 427 MET cc_start: 0.6766 (tpt) cc_final: 0.5716 (tmm) REVERT: C 432 LEU cc_start: 0.8108 (tp) cc_final: 0.7647 (tp) REVERT: C 492 LEU cc_start: 0.9084 (mt) cc_final: 0.8725 (mt) REVERT: C 575 PHE cc_start: 0.8489 (t80) cc_final: 0.7900 (t80) REVERT: D 153 LEU cc_start: 0.8779 (tp) cc_final: 0.8254 (mp) REVERT: D 204 ASP cc_start: 0.8686 (t70) cc_final: 0.8420 (t0) REVERT: D 305 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8909 (mm-30) REVERT: D 317 HIS cc_start: 0.7422 (p-80) cc_final: 0.6936 (p-80) REVERT: D 344 MET cc_start: 0.9296 (mtp) cc_final: 0.9026 (mpp) REVERT: D 373 ASP cc_start: 0.8218 (p0) cc_final: 0.7973 (p0) REVERT: D 404 HIS cc_start: 0.8849 (m90) cc_final: 0.8487 (m90) REVERT: D 406 HIS cc_start: 0.8377 (m-70) cc_final: 0.8025 (m90) REVERT: D 508 MET cc_start: 0.7440 (tmm) cc_final: 0.7072 (tmm) REVERT: D 548 LEU cc_start: 0.9328 (mt) cc_final: 0.9023 (mt) REVERT: D 578 GLU cc_start: 0.9167 (tp30) cc_final: 0.8728 (tp30) REVERT: D 602 ASN cc_start: 0.9129 (m-40) cc_final: 0.8911 (m-40) REVERT: D 620 ILE cc_start: 0.9313 (mt) cc_final: 0.9081 (tp) REVERT: E 241 ILE cc_start: 0.9567 (mt) cc_final: 0.9198 (tp) REVERT: E 268 LEU cc_start: 0.9430 (tp) cc_final: 0.9176 (tt) REVERT: E 332 MET cc_start: 0.8279 (tpt) cc_final: 0.7978 (tpp) REVERT: E 380 ILE cc_start: 0.9420 (mt) cc_final: 0.9101 (tt) REVERT: E 388 MET cc_start: 0.8819 (mmm) cc_final: 0.8500 (mmm) REVERT: E 449 MET cc_start: 0.8637 (tpt) cc_final: 0.8319 (tmm) REVERT: E 551 TRP cc_start: 0.3740 (t60) cc_final: 0.3057 (t-100) REVERT: E 563 PHE cc_start: 0.9080 (m-80) cc_final: 0.8804 (m-10) REVERT: E 577 ASP cc_start: 0.8657 (t0) cc_final: 0.8067 (t0) REVERT: E 578 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8890 (mt-10) REVERT: E 600 VAL cc_start: 0.9606 (t) cc_final: 0.9322 (t) REVERT: E 608 MET cc_start: 0.8790 (tmm) cc_final: 0.8447 (tmm) REVERT: E 620 ILE cc_start: 0.9574 (mt) cc_final: 0.9187 (mm) REVERT: E 736 PHE cc_start: 0.8664 (m-80) cc_final: 0.8368 (m-80) REVERT: F 58 LEU cc_start: 0.9237 (mt) cc_final: 0.9003 (mt) REVERT: F 162 GLU cc_start: 0.7638 (pt0) cc_final: 0.7400 (pt0) REVERT: F 332 MET cc_start: 0.8561 (tpt) cc_final: 0.7729 (tpp) REVERT: F 335 LEU cc_start: 0.8960 (mt) cc_final: 0.8280 (mt) REVERT: F 338 ARG cc_start: 0.8516 (mtt90) cc_final: 0.7750 (mmt90) REVERT: F 368 ASP cc_start: 0.9035 (t0) cc_final: 0.8535 (t70) REVERT: F 432 LEU cc_start: 0.8236 (pt) cc_final: 0.7570 (tp) REVERT: F 534 GLU cc_start: 0.8746 (tt0) cc_final: 0.8359 (tp30) REVERT: F 560 ARG cc_start: 0.9046 (ttp-110) cc_final: 0.8634 (ttp-110) REVERT: F 576 PHE cc_start: 0.8975 (m-10) cc_final: 0.8695 (m-10) REVERT: F 577 ASP cc_start: 0.9208 (t70) cc_final: 0.8838 (t0) REVERT: F 578 GLU cc_start: 0.9064 (mp0) cc_final: 0.8358 (mp0) REVERT: F 625 ARG cc_start: 0.8660 (tpm170) cc_final: 0.8340 (tpm170) REVERT: F 630 ASP cc_start: 0.8339 (t0) cc_final: 0.7516 (t70) REVERT: F 633 ILE cc_start: 0.9575 (mt) cc_final: 0.9285 (mt) REVERT: F 639 LEU cc_start: 0.9543 (mt) cc_final: 0.9291 (mt) REVERT: F 672 LEU cc_start: 0.9354 (mp) cc_final: 0.8967 (tt) REVERT: G 353 PHE cc_start: 0.7167 (m-80) cc_final: 0.6658 (m-80) outliers start: 3 outliers final: 1 residues processed: 858 average time/residue: 0.2307 time to fit residues: 319.6414 Evaluate side-chains 640 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 639 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 144 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 395 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 349 optimal weight: 8.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN A 603 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 421 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 GLN D 337 GLN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.088354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064581 restraints weight = 157259.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.066494 restraints weight = 98252.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067804 restraints weight = 70213.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068680 restraints weight = 55193.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.069307 restraints weight = 46765.643| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 37549 Z= 0.243 Angle : 0.726 10.723 50780 Z= 0.361 Chirality : 0.046 0.268 5734 Planarity : 0.005 0.063 6656 Dihedral : 9.350 179.234 5201 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.08 % Allowed : 2.90 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.12), residues: 4647 helix: 0.98 (0.11), residues: 2109 sheet: 0.69 (0.18), residues: 782 loop : 0.76 (0.16), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 322 TYR 0.031 0.002 TYR A 495 PHE 0.040 0.002 PHE C 563 TRP 0.018 0.002 TRP A 551 HIS 0.012 0.001 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00502 (37549) covalent geometry : angle 0.72551 (50780) hydrogen bonds : bond 0.04305 ( 1713) hydrogen bonds : angle 4.68485 ( 4809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 796 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8764 (mtm) cc_final: 0.8384 (ptp) REVERT: A 71 VAL cc_start: 0.8679 (t) cc_final: 0.8265 (p) REVERT: A 88 VAL cc_start: 0.9500 (t) cc_final: 0.8996 (t) REVERT: A 135 LEU cc_start: 0.9208 (mt) cc_final: 0.8914 (mt) REVERT: A 217 LYS cc_start: 0.9375 (ptpt) cc_final: 0.9169 (ptmm) REVERT: A 219 MET cc_start: 0.8934 (mtm) cc_final: 0.8704 (mtm) REVERT: A 275 MET cc_start: 0.9575 (mmm) cc_final: 0.9291 (mmm) REVERT: A 379 GLU cc_start: 0.8817 (mp0) cc_final: 0.8610 (mp0) REVERT: A 384 HIS cc_start: 0.8320 (m90) cc_final: 0.7884 (m90) REVERT: A 423 ILE cc_start: 0.9378 (tt) cc_final: 0.8244 (tt) REVERT: A 424 ARG cc_start: 0.8380 (mmp80) cc_final: 0.7943 (mmp80) REVERT: A 466 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7152 (tm-30) REVERT: A 543 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8598 (mmmm) REVERT: A 577 ASP cc_start: 0.9429 (t0) cc_final: 0.9135 (t0) REVERT: A 578 GLU cc_start: 0.8801 (mp0) cc_final: 0.7739 (mp0) REVERT: A 625 ARG cc_start: 0.9089 (tpp-160) cc_final: 0.8570 (tpp80) REVERT: A 678 MET cc_start: 0.5817 (mtt) cc_final: 0.5379 (mtt) REVERT: A 730 GLU cc_start: 0.8741 (pt0) cc_final: 0.8309 (pm20) REVERT: A 752 ILE cc_start: 0.9355 (mt) cc_final: 0.9103 (mt) REVERT: B 138 TYR cc_start: 0.8298 (t80) cc_final: 0.7633 (t80) REVERT: B 139 PHE cc_start: 0.8702 (m-10) cc_final: 0.7925 (m-10) REVERT: B 212 GLN cc_start: 0.9166 (mp10) cc_final: 0.8838 (mp10) REVERT: B 236 LYS cc_start: 0.8181 (tppt) cc_final: 0.7779 (tppt) REVERT: B 332 MET cc_start: 0.8882 (tpp) cc_final: 0.8651 (tpp) REVERT: B 335 LEU cc_start: 0.9122 (mt) cc_final: 0.8656 (mt) REVERT: B 386 LYS cc_start: 0.9077 (mmpt) cc_final: 0.8621 (mmmt) REVERT: B 438 ASP cc_start: 0.8261 (t70) cc_final: 0.7210 (t70) REVERT: B 440 GLU cc_start: 0.8892 (mp0) cc_final: 0.8518 (mp0) REVERT: B 488 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8626 (tm-30) REVERT: B 531 ILE cc_start: 0.9101 (tt) cc_final: 0.8825 (tt) REVERT: B 538 ASN cc_start: 0.9302 (m-40) cc_final: 0.8882 (m-40) REVERT: B 542 ILE cc_start: 0.9449 (mm) cc_final: 0.9137 (mm) REVERT: B 563 PHE cc_start: 0.9369 (m-80) cc_final: 0.9070 (m-80) REVERT: B 574 LEU cc_start: 0.9197 (tt) cc_final: 0.8749 (tt) REVERT: B 576 PHE cc_start: 0.9246 (m-10) cc_final: 0.8910 (m-10) REVERT: B 618 PHE cc_start: 0.8821 (t80) cc_final: 0.7950 (t80) REVERT: B 740 MET cc_start: 0.8097 (mtm) cc_final: 0.7854 (mtt) REVERT: C 46 MET cc_start: 0.8748 (mtp) cc_final: 0.8470 (mtt) REVERT: C 373 ASP cc_start: 0.8934 (p0) cc_final: 0.8446 (p0) REVERT: C 427 MET cc_start: 0.6960 (tpt) cc_final: 0.6393 (tmm) REVERT: C 550 MET cc_start: 0.9295 (mtm) cc_final: 0.9039 (mtp) REVERT: C 574 LEU cc_start: 0.9355 (tp) cc_final: 0.8869 (tp) REVERT: C 608 MET cc_start: 0.9139 (ptp) cc_final: 0.8939 (ptp) REVERT: D 204 ASP cc_start: 0.8684 (t70) cc_final: 0.8378 (t0) REVERT: D 213 LEU cc_start: 0.9311 (tt) cc_final: 0.8873 (tp) REVERT: D 305 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8754 (mm-30) REVERT: D 344 MET cc_start: 0.9289 (mtp) cc_final: 0.9065 (mtt) REVERT: D 373 ASP cc_start: 0.8313 (p0) cc_final: 0.8055 (p0) REVERT: D 404 HIS cc_start: 0.8837 (m90) cc_final: 0.8443 (m90) REVERT: D 466 GLU cc_start: 0.8540 (tp30) cc_final: 0.8271 (tp30) REVERT: D 508 MET cc_start: 0.7616 (tmm) cc_final: 0.7258 (tmm) REVERT: D 548 LEU cc_start: 0.9307 (mt) cc_final: 0.9004 (mt) REVERT: D 578 GLU cc_start: 0.9141 (tp30) cc_final: 0.8626 (tp30) REVERT: D 620 ILE cc_start: 0.9366 (mt) cc_final: 0.9127 (tp) REVERT: E 332 MET cc_start: 0.8547 (tpt) cc_final: 0.8115 (tpp) REVERT: E 380 ILE cc_start: 0.9593 (mt) cc_final: 0.9274 (tt) REVERT: E 420 LEU cc_start: 0.9569 (mt) cc_final: 0.9295 (mt) REVERT: E 449 MET cc_start: 0.8685 (tpt) cc_final: 0.8342 (tmm) REVERT: E 561 GLU cc_start: 0.9567 (OUTLIER) cc_final: 0.9155 (pm20) REVERT: E 574 LEU cc_start: 0.9499 (tp) cc_final: 0.9229 (tp) REVERT: E 575 PHE cc_start: 0.9326 (t80) cc_final: 0.9041 (t80) REVERT: E 576 PHE cc_start: 0.9556 (m-80) cc_final: 0.9118 (m-80) REVERT: E 577 ASP cc_start: 0.8882 (t0) cc_final: 0.8317 (t0) REVERT: E 578 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9047 (mt-10) REVERT: E 608 MET cc_start: 0.8685 (tmm) cc_final: 0.8206 (tmm) REVERT: E 620 ILE cc_start: 0.9589 (mt) cc_final: 0.9147 (mm) REVERT: F 41 LEU cc_start: 0.9372 (mt) cc_final: 0.9166 (mt) REVERT: F 58 LEU cc_start: 0.9280 (mt) cc_final: 0.8998 (mt) REVERT: F 162 GLU cc_start: 0.7624 (pt0) cc_final: 0.7349 (pt0) REVERT: F 219 MET cc_start: 0.8782 (mtt) cc_final: 0.8396 (mtt) REVERT: F 261 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7638 (mm-30) REVERT: F 305 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8927 (mp0) REVERT: F 332 MET cc_start: 0.8736 (tpt) cc_final: 0.8030 (tpp) REVERT: F 335 LEU cc_start: 0.9090 (mt) cc_final: 0.8297 (mt) REVERT: F 368 ASP cc_start: 0.9060 (t0) cc_final: 0.8515 (t70) REVERT: F 388 MET cc_start: 0.8800 (mmm) cc_final: 0.8573 (mmm) REVERT: F 560 ARG cc_start: 0.9184 (ttp-110) cc_final: 0.8758 (ttp-110) REVERT: F 564 ASP cc_start: 0.8688 (m-30) cc_final: 0.8435 (m-30) REVERT: F 605 LEU cc_start: 0.9410 (mt) cc_final: 0.9196 (mt) REVERT: F 614 LYS cc_start: 0.9320 (tppt) cc_final: 0.9031 (ttpp) REVERT: F 618 PHE cc_start: 0.9294 (t80) cc_final: 0.8974 (t80) REVERT: F 625 ARG cc_start: 0.8752 (tpm170) cc_final: 0.8547 (tpm170) REVERT: F 630 ASP cc_start: 0.8509 (t0) cc_final: 0.7612 (t0) REVERT: F 633 ILE cc_start: 0.9543 (mt) cc_final: 0.9088 (mm) REVERT: F 639 LEU cc_start: 0.9605 (mt) cc_final: 0.9341 (mt) REVERT: F 660 ASN cc_start: 0.8615 (m110) cc_final: 0.8411 (m-40) REVERT: F 672 LEU cc_start: 0.9372 (mp) cc_final: 0.9021 (tt) REVERT: G 339 LEU cc_start: 0.9563 (mt) cc_final: 0.9289 (mt) outliers start: 3 outliers final: 1 residues processed: 799 average time/residue: 0.2351 time to fit residues: 305.0422 Evaluate side-chains 583 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 581 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 39 optimal weight: 9.9990 chunk 354 optimal weight: 10.0000 chunk 405 optimal weight: 7.9990 chunk 456 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 393 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 91 ASN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 536 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS F 602 ASN F 760 GLN G 65 GLN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.085853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062135 restraints weight = 159744.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.063950 restraints weight = 101298.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065150 restraints weight = 73409.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065916 restraints weight = 58570.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.066534 restraints weight = 50349.988| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 37549 Z= 0.290 Angle : 0.790 10.455 50780 Z= 0.394 Chirality : 0.048 0.281 5734 Planarity : 0.006 0.067 6656 Dihedral : 9.346 178.966 5201 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.12), residues: 4647 helix: 0.58 (0.11), residues: 2096 sheet: 0.43 (0.18), residues: 785 loop : 0.34 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 322 TYR 0.028 0.002 TYR G 334 PHE 0.049 0.003 PHE F 131 TRP 0.041 0.002 TRP A 476 HIS 0.014 0.002 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00613 (37549) covalent geometry : angle 0.79019 (50780) hydrogen bonds : bond 0.04447 ( 1713) hydrogen bonds : angle 5.01001 ( 4809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 724 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8742 (mtm) cc_final: 0.8391 (ptp) REVERT: A 88 VAL cc_start: 0.9475 (t) cc_final: 0.8832 (t) REVERT: A 135 LEU cc_start: 0.9163 (mt) cc_final: 0.8903 (mt) REVERT: A 217 LYS cc_start: 0.9395 (ptpt) cc_final: 0.9140 (ptpp) REVERT: A 242 LEU cc_start: 0.8762 (tp) cc_final: 0.8524 (tp) REVERT: A 275 MET cc_start: 0.9566 (mmm) cc_final: 0.9273 (mmm) REVERT: A 380 ILE cc_start: 0.9447 (mt) cc_final: 0.8799 (tt) REVERT: A 384 HIS cc_start: 0.8461 (m90) cc_final: 0.7909 (m90) REVERT: A 423 ILE cc_start: 0.9398 (tt) cc_final: 0.8373 (tt) REVERT: A 424 ARG cc_start: 0.8381 (mmp80) cc_final: 0.8014 (mmp80) REVERT: A 476 TRP cc_start: 0.8391 (m100) cc_final: 0.8043 (m100) REVERT: A 477 GLU cc_start: 0.9441 (mt-10) cc_final: 0.9161 (mp0) REVERT: A 495 TYR cc_start: 0.9114 (m-80) cc_final: 0.8839 (m-80) REVERT: A 542 ILE cc_start: 0.9531 (mp) cc_final: 0.9309 (mp) REVERT: A 577 ASP cc_start: 0.9552 (t0) cc_final: 0.9299 (t0) REVERT: A 578 GLU cc_start: 0.8788 (mp0) cc_final: 0.8034 (mp0) REVERT: A 625 ARG cc_start: 0.9150 (tpp-160) cc_final: 0.8682 (tpp80) REVERT: A 730 GLU cc_start: 0.8810 (pt0) cc_final: 0.8485 (pm20) REVERT: B 150 ASP cc_start: 0.7695 (m-30) cc_final: 0.6548 (t70) REVERT: B 212 GLN cc_start: 0.9167 (mp10) cc_final: 0.8902 (mp10) REVERT: B 236 LYS cc_start: 0.8287 (tppt) cc_final: 0.7876 (tppt) REVERT: B 348 ASN cc_start: 0.8849 (t0) cc_final: 0.7472 (t0) REVERT: B 386 LYS cc_start: 0.9093 (mmpt) cc_final: 0.8631 (mmmt) REVERT: B 440 GLU cc_start: 0.8928 (mp0) cc_final: 0.8554 (mp0) REVERT: B 485 VAL cc_start: 0.8645 (t) cc_final: 0.8369 (t) REVERT: B 488 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8800 (tm-30) REVERT: B 565 LYS cc_start: 0.9588 (tptp) cc_final: 0.9372 (tptp) REVERT: B 574 LEU cc_start: 0.9196 (tt) cc_final: 0.8902 (tt) REVERT: B 576 PHE cc_start: 0.9330 (m-10) cc_final: 0.9025 (m-10) REVERT: B 618 PHE cc_start: 0.8807 (t80) cc_final: 0.7891 (t80) REVERT: B 740 MET cc_start: 0.8342 (mtm) cc_final: 0.8056 (mtt) REVERT: C 46 MET cc_start: 0.8884 (mtp) cc_final: 0.8568 (mtt) REVERT: C 275 MET cc_start: 0.8872 (mmt) cc_final: 0.8601 (mmm) REVERT: C 373 ASP cc_start: 0.8958 (p0) cc_final: 0.8348 (p0) REVERT: C 427 MET cc_start: 0.6915 (tpt) cc_final: 0.6135 (tmm) REVERT: C 432 LEU cc_start: 0.8374 (pt) cc_final: 0.7733 (pt) REVERT: C 470 GLU cc_start: 0.9304 (pm20) cc_final: 0.8880 (pm20) REVERT: C 550 MET cc_start: 0.9404 (mtm) cc_final: 0.8935 (mpp) REVERT: C 608 MET cc_start: 0.9296 (ptp) cc_final: 0.9078 (ptp) REVERT: C 740 MET cc_start: 0.8455 (mmp) cc_final: 0.8222 (mmm) REVERT: D 204 ASP cc_start: 0.8712 (t70) cc_final: 0.8460 (t0) REVERT: D 261 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8922 (mm-30) REVERT: D 373 ASP cc_start: 0.8478 (p0) cc_final: 0.8148 (p0) REVERT: D 404 HIS cc_start: 0.8706 (m90) cc_final: 0.8393 (m90) REVERT: D 508 MET cc_start: 0.7761 (tmm) cc_final: 0.7343 (tmm) REVERT: D 548 LEU cc_start: 0.9302 (mt) cc_final: 0.8993 (mt) REVERT: E 222 LEU cc_start: 0.9283 (tp) cc_final: 0.9017 (tt) REVERT: E 332 MET cc_start: 0.8677 (tpt) cc_final: 0.8245 (tpp) REVERT: E 380 ILE cc_start: 0.9642 (mt) cc_final: 0.9309 (tt) REVERT: E 427 MET cc_start: 0.9241 (tmm) cc_final: 0.8932 (tpp) REVERT: E 449 MET cc_start: 0.8611 (tpt) cc_final: 0.8396 (tpt) REVERT: E 577 ASP cc_start: 0.8938 (t0) cc_final: 0.8432 (t0) REVERT: E 578 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8958 (mt-10) REVERT: E 608 MET cc_start: 0.8899 (tmm) cc_final: 0.8485 (tmm) REVERT: E 618 PHE cc_start: 0.8378 (t80) cc_final: 0.8139 (t80) REVERT: E 620 ILE cc_start: 0.9664 (mt) cc_final: 0.9323 (mm) REVERT: F 58 LEU cc_start: 0.9319 (mt) cc_final: 0.9031 (mt) REVERT: F 162 GLU cc_start: 0.7839 (pt0) cc_final: 0.7475 (pt0) REVERT: F 203 TYR cc_start: 0.8873 (m-80) cc_final: 0.8603 (m-10) REVERT: F 332 MET cc_start: 0.8839 (tpt) cc_final: 0.8311 (tpp) REVERT: F 335 LEU cc_start: 0.9268 (mt) cc_final: 0.8367 (mt) REVERT: F 344 MET cc_start: 0.7987 (mpp) cc_final: 0.7657 (mpp) REVERT: F 368 ASP cc_start: 0.9032 (t0) cc_final: 0.8666 (t70) REVERT: F 388 MET cc_start: 0.8894 (mmm) cc_final: 0.8669 (mmm) REVERT: F 432 LEU cc_start: 0.8226 (pt) cc_final: 0.7454 (tp) REVERT: F 614 LYS cc_start: 0.9331 (tppt) cc_final: 0.9083 (ttpp) REVERT: F 625 ARG cc_start: 0.8871 (tpm170) cc_final: 0.8663 (tpm170) REVERT: F 630 ASP cc_start: 0.8595 (t0) cc_final: 0.7770 (t0) REVERT: F 633 ILE cc_start: 0.9552 (mt) cc_final: 0.9208 (mm) REVERT: F 639 LEU cc_start: 0.9732 (mt) cc_final: 0.9510 (mt) REVERT: F 660 ASN cc_start: 0.8662 (m110) cc_final: 0.8458 (m-40) REVERT: F 672 LEU cc_start: 0.9363 (mp) cc_final: 0.9037 (tt) REVERT: G 339 LEU cc_start: 0.9530 (mt) cc_final: 0.9242 (mt) outliers start: 0 outliers final: 0 residues processed: 724 average time/residue: 0.2387 time to fit residues: 283.5546 Evaluate side-chains 551 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 58 optimal weight: 8.9990 chunk 333 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 chunk 393 optimal weight: 0.0670 chunk 94 optimal weight: 0.9980 chunk 233 optimal weight: 8.9990 chunk 372 optimal weight: 5.9990 chunk 310 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 overall best weight: 3.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 538 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 285 ASN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN G 165 ASN ** G 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.086447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062403 restraints weight = 158357.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.064286 restraints weight = 99022.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065490 restraints weight = 70975.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.066325 restraints weight = 56504.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.066841 restraints weight = 48014.710| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 37549 Z= 0.188 Angle : 0.685 9.552 50780 Z= 0.337 Chirality : 0.046 0.305 5734 Planarity : 0.005 0.067 6656 Dihedral : 8.924 167.124 5201 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.12), residues: 4647 helix: 0.86 (0.11), residues: 2107 sheet: 0.50 (0.18), residues: 777 loop : 0.35 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 625 TYR 0.028 0.002 TYR D 134 PHE 0.020 0.002 PHE C 563 TRP 0.013 0.001 TRP B 551 HIS 0.011 0.001 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00408 (37549) covalent geometry : angle 0.68546 (50780) hydrogen bonds : bond 0.03955 ( 1713) hydrogen bonds : angle 4.70895 ( 4809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 742 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8711 (mtm) cc_final: 0.8328 (ptp) REVERT: A 135 LEU cc_start: 0.9232 (mt) cc_final: 0.8952 (mt) REVERT: A 162 GLU cc_start: 0.7983 (pp20) cc_final: 0.7749 (pp20) REVERT: A 217 LYS cc_start: 0.9406 (ptpt) cc_final: 0.9164 (ptpp) REVERT: A 380 ILE cc_start: 0.9374 (mt) cc_final: 0.8912 (tt) REVERT: A 384 HIS cc_start: 0.8393 (m90) cc_final: 0.7858 (m90) REVERT: A 476 TRP cc_start: 0.8531 (m100) cc_final: 0.8159 (m100) REVERT: A 477 GLU cc_start: 0.9389 (mt-10) cc_final: 0.9179 (mp0) REVERT: A 543 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8308 (mmmm) REVERT: A 546 GLU cc_start: 0.8981 (tp30) cc_final: 0.8717 (tp30) REVERT: A 577 ASP cc_start: 0.9540 (t0) cc_final: 0.8953 (t0) REVERT: A 578 GLU cc_start: 0.8902 (mp0) cc_final: 0.7750 (mp0) REVERT: A 625 ARG cc_start: 0.9078 (tpp-160) cc_final: 0.8621 (tpp80) REVERT: A 638 ARG cc_start: 0.8399 (mmt180) cc_final: 0.7825 (mmt-90) REVERT: A 730 GLU cc_start: 0.8781 (pt0) cc_final: 0.8502 (pm20) REVERT: B 88 VAL cc_start: 0.9464 (t) cc_final: 0.9253 (t) REVERT: B 150 ASP cc_start: 0.7443 (m-30) cc_final: 0.6700 (t70) REVERT: B 212 GLN cc_start: 0.9113 (mp10) cc_final: 0.8902 (mp10) REVERT: B 236 LYS cc_start: 0.8280 (tppt) cc_final: 0.7916 (tppt) REVERT: B 332 MET cc_start: 0.9320 (tpp) cc_final: 0.8799 (tpp) REVERT: B 386 LYS cc_start: 0.9080 (mmpt) cc_final: 0.8616 (mmmt) REVERT: B 440 GLU cc_start: 0.8913 (mp0) cc_final: 0.8580 (mp0) REVERT: B 485 VAL cc_start: 0.8682 (t) cc_final: 0.8410 (t) REVERT: B 488 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8802 (tm-30) REVERT: B 608 MET cc_start: 0.8905 (ptp) cc_final: 0.8466 (tpt) REVERT: B 618 PHE cc_start: 0.8777 (t80) cc_final: 0.7884 (t80) REVERT: B 740 MET cc_start: 0.8397 (mtm) cc_final: 0.8078 (mtt) REVERT: C 46 MET cc_start: 0.8916 (mtp) cc_final: 0.8514 (mtt) REVERT: C 242 LEU cc_start: 0.9635 (mt) cc_final: 0.9396 (mp) REVERT: C 275 MET cc_start: 0.8996 (mmt) cc_final: 0.8778 (mmm) REVERT: C 331 LEU cc_start: 0.9599 (mm) cc_final: 0.9335 (mp) REVERT: C 373 ASP cc_start: 0.8880 (p0) cc_final: 0.8337 (p0) REVERT: C 427 MET cc_start: 0.6843 (tpt) cc_final: 0.5714 (tmm) REVERT: C 432 LEU cc_start: 0.8493 (pt) cc_final: 0.7760 (pt) REVERT: C 470 GLU cc_start: 0.9245 (pm20) cc_final: 0.8954 (pm20) REVERT: C 492 LEU cc_start: 0.8981 (mt) cc_final: 0.8482 (mt) REVERT: C 550 MET cc_start: 0.9078 (mtm) cc_final: 0.8787 (mtp) REVERT: C 574 LEU cc_start: 0.9369 (tp) cc_final: 0.9086 (tp) REVERT: C 608 MET cc_start: 0.9231 (ptp) cc_final: 0.9002 (ptp) REVERT: D 46 MET cc_start: 0.9201 (ptp) cc_final: 0.8800 (ppp) REVERT: D 158 MET cc_start: 0.8820 (mtt) cc_final: 0.8296 (tmm) REVERT: D 204 ASP cc_start: 0.8679 (t70) cc_final: 0.8443 (t0) REVERT: D 261 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8606 (mm-30) REVERT: D 305 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8736 (mm-30) REVERT: D 312 LYS cc_start: 0.8475 (mppt) cc_final: 0.8132 (mppt) REVERT: D 332 MET cc_start: 0.9199 (tpp) cc_final: 0.8967 (tpp) REVERT: D 344 MET cc_start: 0.9256 (mtp) cc_final: 0.9028 (mtt) REVERT: D 373 ASP cc_start: 0.8404 (p0) cc_final: 0.8128 (p0) REVERT: D 404 HIS cc_start: 0.8591 (m90) cc_final: 0.8226 (m90) REVERT: D 508 MET cc_start: 0.7703 (tmm) cc_final: 0.7337 (tmm) REVERT: D 548 LEU cc_start: 0.9354 (mt) cc_final: 0.9070 (mt) REVERT: D 678 MET cc_start: 0.9285 (mmp) cc_final: 0.9072 (mmm) REVERT: E 221 GLU cc_start: 0.8535 (pp20) cc_final: 0.8166 (pp20) REVERT: E 332 MET cc_start: 0.8642 (tpt) cc_final: 0.8190 (tpp) REVERT: E 380 ILE cc_start: 0.9584 (mt) cc_final: 0.9281 (tt) REVERT: E 420 LEU cc_start: 0.9590 (mt) cc_final: 0.9344 (mt) REVERT: E 543 LYS cc_start: 0.9009 (tppt) cc_final: 0.8201 (tppp) REVERT: E 577 ASP cc_start: 0.8886 (t0) cc_final: 0.8025 (t0) REVERT: E 578 GLU cc_start: 0.9406 (mt-10) cc_final: 0.8819 (mt-10) REVERT: E 608 MET cc_start: 0.8776 (tmm) cc_final: 0.8343 (tmm) REVERT: E 678 MET cc_start: 0.9273 (mmp) cc_final: 0.9041 (mmp) REVERT: F 41 LEU cc_start: 0.9342 (mt) cc_final: 0.9135 (mt) REVERT: F 58 LEU cc_start: 0.9299 (mt) cc_final: 0.9067 (mt) REVERT: F 203 TYR cc_start: 0.8825 (m-80) cc_final: 0.8611 (m-10) REVERT: F 305 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8854 (mp0) REVERT: F 326 SER cc_start: 0.9401 (m) cc_final: 0.9179 (p) REVERT: F 329 LEU cc_start: 0.9606 (mp) cc_final: 0.9335 (mp) REVERT: F 332 MET cc_start: 0.8872 (tpt) cc_final: 0.8247 (tpp) REVERT: F 335 LEU cc_start: 0.9265 (mt) cc_final: 0.8422 (mt) REVERT: F 368 ASP cc_start: 0.8961 (t0) cc_final: 0.8566 (t70) REVERT: F 560 ARG cc_start: 0.9005 (ttp-110) cc_final: 0.8640 (ttm110) REVERT: F 564 ASP cc_start: 0.8767 (m-30) cc_final: 0.8488 (m-30) REVERT: F 578 GLU cc_start: 0.8815 (mp0) cc_final: 0.8282 (mp0) REVERT: F 614 LYS cc_start: 0.9320 (tppt) cc_final: 0.9068 (ttpp) REVERT: F 625 ARG cc_start: 0.8892 (tpm170) cc_final: 0.8636 (tpm170) REVERT: F 630 ASP cc_start: 0.8646 (t0) cc_final: 0.7845 (t0) REVERT: F 633 ILE cc_start: 0.9471 (mt) cc_final: 0.9184 (mm) REVERT: F 660 ASN cc_start: 0.8606 (m110) cc_final: 0.8404 (m-40) REVERT: F 672 LEU cc_start: 0.9334 (mp) cc_final: 0.9012 (tt) REVERT: G 63 LEU cc_start: 0.8262 (mt) cc_final: 0.8017 (mt) REVERT: G 339 LEU cc_start: 0.9517 (mt) cc_final: 0.9227 (mt) outliers start: 0 outliers final: 0 residues processed: 742 average time/residue: 0.2384 time to fit residues: 290.3920 Evaluate side-chains 554 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 331 optimal weight: 0.9990 chunk 121 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 463 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 268 optimal weight: 0.0870 chunk 321 optimal weight: 2.9990 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 406 HIS ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 103 GLN B 215 GLN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 340 HIS C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.088248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064290 restraints weight = 158526.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066221 restraints weight = 98666.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.067557 restraints weight = 70541.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.068423 restraints weight = 55522.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.068992 restraints weight = 47030.073| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37549 Z= 0.139 Angle : 0.658 9.011 50780 Z= 0.322 Chirality : 0.046 0.249 5734 Planarity : 0.004 0.065 6656 Dihedral : 8.411 157.696 5201 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.03 % Allowed : 0.98 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.12), residues: 4647 helix: 0.99 (0.11), residues: 2106 sheet: 0.40 (0.17), residues: 818 loop : 0.35 (0.16), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 693 TYR 0.030 0.002 TYR G 334 PHE 0.025 0.001 PHE A 363 TRP 0.046 0.002 TRP F 476 HIS 0.008 0.001 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00312 (37549) covalent geometry : angle 0.65816 (50780) hydrogen bonds : bond 0.03763 ( 1713) hydrogen bonds : angle 4.55438 ( 4809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 753 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8818 (mtm) cc_final: 0.8350 (ptp) REVERT: A 135 LEU cc_start: 0.9238 (mt) cc_final: 0.8957 (mt) REVERT: A 217 LYS cc_start: 0.9408 (ptpt) cc_final: 0.9104 (ptpp) REVERT: A 384 HIS cc_start: 0.8288 (m90) cc_final: 0.7850 (m90) REVERT: A 423 ILE cc_start: 0.9345 (tt) cc_final: 0.8203 (tt) REVERT: A 424 ARG cc_start: 0.8386 (mmp80) cc_final: 0.8029 (mmp80) REVERT: A 476 TRP cc_start: 0.8586 (m100) cc_final: 0.8327 (m100) REVERT: A 546 GLU cc_start: 0.8964 (tp30) cc_final: 0.8689 (tp30) REVERT: A 625 ARG cc_start: 0.9048 (tpp-160) cc_final: 0.8601 (tpp80) REVERT: A 638 ARG cc_start: 0.8219 (mmt180) cc_final: 0.7735 (mmt-90) REVERT: A 751 ASP cc_start: 0.9461 (m-30) cc_final: 0.8826 (t70) REVERT: B 150 ASP cc_start: 0.7415 (m-30) cc_final: 0.6903 (t70) REVERT: B 236 LYS cc_start: 0.8174 (tppt) cc_final: 0.7870 (tppt) REVERT: B 386 LYS cc_start: 0.9092 (mmpt) cc_final: 0.8616 (mmmt) REVERT: B 440 GLU cc_start: 0.8933 (mp0) cc_final: 0.8654 (mp0) REVERT: B 608 MET cc_start: 0.8944 (ptp) cc_final: 0.8622 (tpt) REVERT: B 618 PHE cc_start: 0.8724 (t80) cc_final: 0.7818 (t80) REVERT: B 650 GLU cc_start: 0.9017 (mp0) cc_final: 0.8501 (mm-30) REVERT: B 740 MET cc_start: 0.8200 (mtm) cc_final: 0.7960 (mtt) REVERT: C 46 MET cc_start: 0.8929 (mtp) cc_final: 0.8516 (mtt) REVERT: C 275 MET cc_start: 0.8969 (mmt) cc_final: 0.8750 (mmm) REVERT: C 373 ASP cc_start: 0.8781 (p0) cc_final: 0.8235 (p0) REVERT: C 427 MET cc_start: 0.6883 (tpt) cc_final: 0.5792 (tmm) REVERT: C 432 LEU cc_start: 0.8468 (pt) cc_final: 0.7711 (pt) REVERT: C 550 MET cc_start: 0.8997 (mtm) cc_final: 0.8707 (mtp) REVERT: C 608 MET cc_start: 0.9247 (ptp) cc_final: 0.8993 (ptp) REVERT: C 740 MET cc_start: 0.8466 (mmp) cc_final: 0.8214 (mmm) REVERT: D 158 MET cc_start: 0.8704 (mtt) cc_final: 0.8220 (tmm) REVERT: D 204 ASP cc_start: 0.8626 (t70) cc_final: 0.8416 (t0) REVERT: D 261 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8564 (mm-30) REVERT: D 305 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8628 (mm-30) REVERT: D 312 LYS cc_start: 0.8460 (mppt) cc_final: 0.8091 (mppt) REVERT: D 344 MET cc_start: 0.9180 (mtp) cc_final: 0.8929 (mtp) REVERT: D 373 ASP cc_start: 0.8363 (p0) cc_final: 0.8103 (p0) REVERT: D 404 HIS cc_start: 0.8673 (m90) cc_final: 0.8174 (m90) REVERT: D 508 MET cc_start: 0.7699 (tmm) cc_final: 0.7323 (tmm) REVERT: D 535 CYS cc_start: 0.8655 (t) cc_final: 0.8438 (t) REVERT: D 548 LEU cc_start: 0.9367 (mt) cc_final: 0.9103 (mt) REVERT: D 629 ILE cc_start: 0.8777 (mm) cc_final: 0.8576 (mm) REVERT: D 678 MET cc_start: 0.9289 (mmp) cc_final: 0.9072 (mmm) REVERT: E 37 SER cc_start: 0.8060 (m) cc_final: 0.7688 (p) REVERT: E 47 ASP cc_start: 0.9206 (m-30) cc_final: 0.8972 (m-30) REVERT: E 221 GLU cc_start: 0.8540 (pp20) cc_final: 0.8183 (pp20) REVERT: E 231 LYS cc_start: 0.9313 (pttm) cc_final: 0.8811 (tptt) REVERT: E 321 GLU cc_start: 0.8664 (pt0) cc_final: 0.8325 (pt0) REVERT: E 332 MET cc_start: 0.8554 (tpt) cc_final: 0.8135 (tpp) REVERT: E 380 ILE cc_start: 0.9552 (mt) cc_final: 0.9229 (tt) REVERT: E 420 LEU cc_start: 0.9630 (mt) cc_final: 0.9371 (mt) REVERT: E 543 LYS cc_start: 0.9036 (tppt) cc_final: 0.8194 (tppp) REVERT: E 577 ASP cc_start: 0.8852 (t0) cc_final: 0.7927 (t0) REVERT: E 578 GLU cc_start: 0.9381 (mt-10) cc_final: 0.8658 (mt-10) REVERT: E 608 MET cc_start: 0.8771 (tmm) cc_final: 0.8323 (tmm) REVERT: E 671 ASP cc_start: 0.9120 (t0) cc_final: 0.8548 (p0) REVERT: E 678 MET cc_start: 0.9233 (mmp) cc_final: 0.8976 (mmp) REVERT: E 736 PHE cc_start: 0.8866 (m-10) cc_final: 0.8643 (m-80) REVERT: F 41 LEU cc_start: 0.9317 (mt) cc_final: 0.9114 (mt) REVERT: F 58 LEU cc_start: 0.9261 (mt) cc_final: 0.8898 (tp) REVERT: F 219 MET cc_start: 0.8920 (mtp) cc_final: 0.8656 (mtt) REVERT: F 305 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8872 (mp0) REVERT: F 326 SER cc_start: 0.9395 (m) cc_final: 0.9146 (p) REVERT: F 332 MET cc_start: 0.8802 (tpt) cc_final: 0.8191 (tpp) REVERT: F 335 LEU cc_start: 0.9261 (mt) cc_final: 0.8386 (mt) REVERT: F 368 ASP cc_start: 0.8930 (t0) cc_final: 0.8439 (t70) REVERT: F 388 MET cc_start: 0.8630 (mmm) cc_final: 0.8368 (mmm) REVERT: F 543 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8706 (mtpt) REVERT: F 578 GLU cc_start: 0.8747 (mp0) cc_final: 0.8297 (mp0) REVERT: F 614 LYS cc_start: 0.9338 (tppt) cc_final: 0.9080 (ttpp) REVERT: F 625 ARG cc_start: 0.8889 (tpm170) cc_final: 0.8610 (tpm170) REVERT: F 630 ASP cc_start: 0.8686 (t0) cc_final: 0.7883 (t0) REVERT: F 633 ILE cc_start: 0.9371 (mt) cc_final: 0.8984 (mm) REVERT: F 660 ASN cc_start: 0.8544 (m110) cc_final: 0.8323 (m-40) REVERT: F 672 LEU cc_start: 0.9315 (mp) cc_final: 0.9004 (tt) REVERT: G 339 LEU cc_start: 0.9521 (mt) cc_final: 0.9225 (mt) outliers start: 1 outliers final: 0 residues processed: 754 average time/residue: 0.2427 time to fit residues: 298.7625 Evaluate side-chains 573 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 53 optimal weight: 8.9990 chunk 293 optimal weight: 0.7980 chunk 316 optimal weight: 5.9990 chunk 325 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 446 optimal weight: 9.9990 chunk 350 optimal weight: 0.0270 chunk 315 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 466 optimal weight: 3.9990 overall best weight: 2.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 602 ASN C 616 ASN D 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.087320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.062625 restraints weight = 157242.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064484 restraints weight = 98811.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065707 restraints weight = 71252.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.066567 restraints weight = 56919.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.067119 restraints weight = 48435.459| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37549 Z= 0.151 Angle : 0.671 10.845 50780 Z= 0.329 Chirality : 0.047 0.229 5734 Planarity : 0.004 0.064 6656 Dihedral : 8.052 150.809 5201 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.03 % Allowed : 1.11 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.12), residues: 4647 helix: 1.00 (0.11), residues: 2104 sheet: 0.38 (0.17), residues: 823 loop : 0.32 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 753 TYR 0.031 0.002 TYR G 334 PHE 0.028 0.002 PHE D 360 TRP 0.023 0.001 TRP F 476 HIS 0.010 0.001 HIS C 340 Details of bonding type rmsd covalent geometry : bond 0.00336 (37549) covalent geometry : angle 0.67118 (50780) hydrogen bonds : bond 0.03719 ( 1713) hydrogen bonds : angle 4.57830 ( 4809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 730 time to evaluate : 1.368 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 46 MET cc_start: 0.8771 (mtm) cc_final: 0.8396 (ptp) REVERT: A 71 VAL cc_start: 0.8677 (m) cc_final: 0.8472 (p) REVERT: A 135 LEU cc_start: 0.9236 (mt) cc_final: 0.8943 (mt) REVERT: A 217 LYS cc_start: 0.9435 (ptpt) cc_final: 0.9122 (ptpp) REVERT: A 332 MET cc_start: 0.8864 (ttm) cc_final: 0.8487 (ttt) REVERT: A 384 HIS cc_start: 0.8235 (m90) cc_final: 0.7880 (m90) REVERT: A 477 GLU cc_start: 0.9204 (pm20) cc_final: 0.8888 (pm20) REVERT: A 529 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8837 (mmmm) REVERT: A 546 GLU cc_start: 0.8986 (tp30) cc_final: 0.8729 (tp30) REVERT: A 577 ASP cc_start: 0.9384 (t70) cc_final: 0.9097 (t0) REVERT: A 578 GLU cc_start: 0.8676 (mp0) cc_final: 0.8164 (mp0) REVERT: A 607 GLU cc_start: 0.8042 (mp0) cc_final: 0.7757 (mp0) REVERT: A 625 ARG cc_start: 0.9045 (tpp-160) cc_final: 0.8599 (tpp80) REVERT: A 751 ASP cc_start: 0.9454 (m-30) cc_final: 0.8860 (t70) REVERT: B 139 PHE cc_start: 0.8671 (m-80) cc_final: 0.8458 (m-80) REVERT: B 150 ASP cc_start: 0.7528 (m-30) cc_final: 0.6924 (t70) REVERT: B 236 LYS cc_start: 0.8177 (tppt) cc_final: 0.7880 (tppt) REVERT: B 332 MET cc_start: 0.9240 (tpp) cc_final: 0.8752 (tpp) REVERT: B 386 LYS cc_start: 0.9118 (mmpt) cc_final: 0.8662 (mmmt) REVERT: B 440 GLU cc_start: 0.8981 (mp0) cc_final: 0.8686 (mp0) REVERT: B 509 THR cc_start: 0.8852 (m) cc_final: 0.8535 (t) REVERT: B 576 PHE cc_start: 0.9342 (m-10) cc_final: 0.9074 (m-10) REVERT: B 578 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8521 (mm-30) REVERT: B 608 MET cc_start: 0.9006 (ptp) cc_final: 0.8785 (tpt) REVERT: B 618 PHE cc_start: 0.8733 (t80) cc_final: 0.7802 (t80) REVERT: B 731 ILE cc_start: 0.8051 (mt) cc_final: 0.7785 (tt) REVERT: C 46 MET cc_start: 0.8930 (mtp) cc_final: 0.8531 (mtt) REVERT: C 275 MET cc_start: 0.8984 (mmt) cc_final: 0.8772 (mmm) REVERT: C 305 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9039 (mm-30) REVERT: C 326 SER cc_start: 0.8843 (m) cc_final: 0.8366 (p) REVERT: C 373 ASP cc_start: 0.8802 (p0) cc_final: 0.8259 (p0) REVERT: C 427 MET cc_start: 0.6864 (tpt) cc_final: 0.5769 (tmm) REVERT: C 432 LEU cc_start: 0.8468 (pt) cc_final: 0.7823 (pt) REVERT: C 550 MET cc_start: 0.9021 (mtm) cc_final: 0.8707 (mtp) REVERT: C 608 MET cc_start: 0.9242 (ptp) cc_final: 0.8937 (ptp) REVERT: C 616 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8295 (t0) REVERT: C 740 MET cc_start: 0.8514 (mmp) cc_final: 0.8258 (mmm) REVERT: D 158 MET cc_start: 0.8619 (mtt) cc_final: 0.8214 (tmm) REVERT: D 204 ASP cc_start: 0.8680 (t70) cc_final: 0.8462 (t0) REVERT: D 261 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8580 (mm-30) REVERT: D 305 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8675 (mm-30) REVERT: D 312 LYS cc_start: 0.8461 (mppt) cc_final: 0.8116 (mppt) REVERT: D 344 MET cc_start: 0.9214 (mtp) cc_final: 0.8918 (mpp) REVERT: D 373 ASP cc_start: 0.8318 (p0) cc_final: 0.8075 (p0) REVERT: D 404 HIS cc_start: 0.8532 (m90) cc_final: 0.8025 (m90) REVERT: D 508 MET cc_start: 0.7746 (tmm) cc_final: 0.7372 (tmm) REVERT: D 535 CYS cc_start: 0.8640 (t) cc_final: 0.8434 (t) REVERT: D 548 LEU cc_start: 0.9372 (mt) cc_final: 0.9122 (mt) REVERT: D 678 MET cc_start: 0.9285 (mmp) cc_final: 0.9046 (mmm) REVERT: E 37 SER cc_start: 0.8120 (m) cc_final: 0.7742 (p) REVERT: E 47 ASP cc_start: 0.9240 (m-30) cc_final: 0.9018 (m-30) REVERT: E 221 GLU cc_start: 0.8667 (pp20) cc_final: 0.8233 (pp20) REVERT: E 231 LYS cc_start: 0.9290 (pttm) cc_final: 0.8804 (tptt) REVERT: E 288 LYS cc_start: 0.9636 (mttt) cc_final: 0.9281 (mtmm) REVERT: E 321 GLU cc_start: 0.8672 (pt0) cc_final: 0.8359 (pt0) REVERT: E 332 MET cc_start: 0.8552 (tpt) cc_final: 0.8174 (tpp) REVERT: E 380 ILE cc_start: 0.9555 (mt) cc_final: 0.9231 (tt) REVERT: E 420 LEU cc_start: 0.9640 (mt) cc_final: 0.9382 (mt) REVERT: E 543 LYS cc_start: 0.9019 (tppt) cc_final: 0.8199 (tppp) REVERT: E 577 ASP cc_start: 0.8872 (t0) cc_final: 0.7961 (t0) REVERT: E 578 GLU cc_start: 0.9404 (mt-10) cc_final: 0.8743 (mt-10) REVERT: E 608 MET cc_start: 0.8802 (tmm) cc_final: 0.8301 (tmm) REVERT: E 671 ASP cc_start: 0.9133 (t0) cc_final: 0.8831 (p0) REVERT: E 736 PHE cc_start: 0.8891 (m-10) cc_final: 0.8657 (m-80) REVERT: E 749 ASP cc_start: 0.8443 (t70) cc_final: 0.8178 (t0) REVERT: F 41 LEU cc_start: 0.9351 (mt) cc_final: 0.9136 (mt) REVERT: F 58 LEU cc_start: 0.9204 (mt) cc_final: 0.8876 (tp) REVERT: F 59 LEU cc_start: 0.9405 (mt) cc_final: 0.9153 (mt) REVERT: F 158 MET cc_start: 0.7783 (mmp) cc_final: 0.6215 (mmp) REVERT: F 162 GLU cc_start: 0.7641 (pt0) cc_final: 0.7424 (pt0) REVERT: F 219 MET cc_start: 0.8939 (mtp) cc_final: 0.8670 (mtt) REVERT: F 305 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8911 (mp0) REVERT: F 326 SER cc_start: 0.9385 (m) cc_final: 0.9128 (p) REVERT: F 335 LEU cc_start: 0.9301 (mt) cc_final: 0.8729 (mt) REVERT: F 368 ASP cc_start: 0.8951 (t0) cc_final: 0.8453 (t70) REVERT: F 388 MET cc_start: 0.8606 (mmm) cc_final: 0.7608 (mmp) REVERT: F 543 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8749 (mtpt) REVERT: F 575 PHE cc_start: 0.8947 (t80) cc_final: 0.8718 (t80) REVERT: F 578 GLU cc_start: 0.8731 (mp0) cc_final: 0.8307 (mp0) REVERT: F 614 LYS cc_start: 0.9339 (tppt) cc_final: 0.9087 (ttpp) REVERT: F 630 ASP cc_start: 0.8753 (t0) cc_final: 0.7980 (t0) REVERT: F 633 ILE cc_start: 0.9377 (mt) cc_final: 0.8959 (mm) REVERT: F 660 ASN cc_start: 0.8557 (m110) cc_final: 0.8344 (m-40) REVERT: F 672 LEU cc_start: 0.9346 (mp) cc_final: 0.9017 (tt) REVERT: G 339 LEU cc_start: 0.9537 (mt) cc_final: 0.9248 (mt) outliers start: 1 outliers final: 0 residues processed: 731 average time/residue: 0.2064 time to fit residues: 249.6280 Evaluate side-chains 564 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 563 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 310 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 290 optimal weight: 1.9990 chunk 268 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 413 optimal weight: 6.9990 chunk 146 optimal weight: 0.0770 chunk 418 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 280 optimal weight: 0.0970 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 215 GLN B 340 HIS B 404 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 602 ASN D 421 GLN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.088470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064489 restraints weight = 158888.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.066362 restraints weight = 98881.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.067628 restraints weight = 70940.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.068523 restraints weight = 56286.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.069093 restraints weight = 47750.726| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37549 Z= 0.124 Angle : 0.675 8.779 50780 Z= 0.328 Chirality : 0.046 0.226 5734 Planarity : 0.004 0.060 6656 Dihedral : 7.681 140.883 5201 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.12), residues: 4647 helix: 1.06 (0.11), residues: 2101 sheet: 0.48 (0.18), residues: 789 loop : 0.39 (0.16), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 560 TYR 0.030 0.002 TYR G 334 PHE 0.044 0.001 PHE B 552 TRP 0.017 0.001 TRP A 476 HIS 0.009 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00276 (37549) covalent geometry : angle 0.67511 (50780) hydrogen bonds : bond 0.03629 ( 1713) hydrogen bonds : angle 4.44461 ( 4809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 752 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8864 (mtm) cc_final: 0.8180 (ptp) REVERT: A 71 VAL cc_start: 0.8600 (m) cc_final: 0.8398 (p) REVERT: A 135 LEU cc_start: 0.9244 (mt) cc_final: 0.8962 (mt) REVERT: A 162 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6866 (tm-30) REVERT: A 217 LYS cc_start: 0.9412 (ptpt) cc_final: 0.9129 (ptpp) REVERT: A 332 MET cc_start: 0.8844 (ttm) cc_final: 0.8396 (ttt) REVERT: A 384 HIS cc_start: 0.8156 (m90) cc_final: 0.7820 (m90) REVERT: A 420 LEU cc_start: 0.9323 (tp) cc_final: 0.9092 (tp) REVERT: A 423 ILE cc_start: 0.9315 (tt) cc_final: 0.8078 (tt) REVERT: A 424 ARG cc_start: 0.8416 (mmp80) cc_final: 0.8064 (mmp80) REVERT: A 477 GLU cc_start: 0.9151 (pm20) cc_final: 0.8943 (pm20) REVERT: A 540 ILE cc_start: 0.9638 (mp) cc_final: 0.9422 (pt) REVERT: A 546 GLU cc_start: 0.8993 (tp30) cc_final: 0.8744 (tp30) REVERT: A 577 ASP cc_start: 0.9373 (t70) cc_final: 0.9106 (t0) REVERT: A 578 GLU cc_start: 0.8727 (mp0) cc_final: 0.8168 (mp0) REVERT: A 608 MET cc_start: 0.8318 (ppp) cc_final: 0.7932 (ppp) REVERT: A 625 ARG cc_start: 0.9040 (tpp-160) cc_final: 0.8613 (tpp80) REVERT: A 638 ARG cc_start: 0.8105 (mmt180) cc_final: 0.7552 (mmt-90) REVERT: A 695 CYS cc_start: 0.9381 (m) cc_final: 0.9130 (t) REVERT: A 751 ASP cc_start: 0.9435 (m-30) cc_final: 0.8786 (t70) REVERT: B 139 PHE cc_start: 0.8657 (m-80) cc_final: 0.8453 (m-80) REVERT: B 150 ASP cc_start: 0.7541 (m-30) cc_final: 0.6886 (t70) REVERT: B 236 LYS cc_start: 0.8119 (tppt) cc_final: 0.7771 (tppt) REVERT: B 386 LYS cc_start: 0.9124 (mmpt) cc_final: 0.8661 (mmmt) REVERT: B 402 GLU cc_start: 0.8665 (pm20) cc_final: 0.8298 (pm20) REVERT: B 440 GLU cc_start: 0.8979 (mp0) cc_final: 0.8682 (mp0) REVERT: B 578 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8469 (mm-30) REVERT: B 618 PHE cc_start: 0.8732 (t80) cc_final: 0.7815 (t80) REVERT: B 650 GLU cc_start: 0.9030 (mp0) cc_final: 0.8493 (mm-30) REVERT: B 731 ILE cc_start: 0.8076 (mt) cc_final: 0.7834 (tt) REVERT: B 740 MET cc_start: 0.8428 (mtm) cc_final: 0.8106 (mtt) REVERT: C 46 MET cc_start: 0.8888 (mtp) cc_final: 0.8503 (mtt) REVERT: C 327 GLN cc_start: 0.9021 (tp40) cc_final: 0.8765 (tp40) REVERT: C 331 LEU cc_start: 0.9492 (mt) cc_final: 0.9269 (mt) REVERT: C 332 MET cc_start: 0.9165 (tpp) cc_final: 0.8955 (tpp) REVERT: C 373 ASP cc_start: 0.8783 (p0) cc_final: 0.8254 (p0) REVERT: C 550 MET cc_start: 0.8997 (mtm) cc_final: 0.8665 (mtp) REVERT: C 608 MET cc_start: 0.9191 (ptp) cc_final: 0.8927 (ptp) REVERT: C 616 ASN cc_start: 0.9111 (t0) cc_final: 0.8711 (t0) REVERT: C 740 MET cc_start: 0.8447 (mmp) cc_final: 0.8223 (mmm) REVERT: C 757 MET cc_start: 0.8650 (ptt) cc_final: 0.7656 (tpp) REVERT: D 158 MET cc_start: 0.8508 (mtt) cc_final: 0.8220 (tmm) REVERT: D 204 ASP cc_start: 0.8660 (t70) cc_final: 0.8434 (t0) REVERT: D 217 LYS cc_start: 0.9320 (mtmm) cc_final: 0.9083 (mttm) REVERT: D 261 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8591 (mm-30) REVERT: D 305 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8623 (mm-30) REVERT: D 312 LYS cc_start: 0.8459 (mppt) cc_final: 0.8115 (mppt) REVERT: D 344 MET cc_start: 0.9216 (mtp) cc_final: 0.8942 (mtp) REVERT: D 373 ASP cc_start: 0.8243 (p0) cc_final: 0.7994 (p0) REVERT: D 404 HIS cc_start: 0.8478 (m90) cc_final: 0.7943 (m90) REVERT: D 508 MET cc_start: 0.7690 (tmm) cc_final: 0.7254 (tmm) REVERT: D 678 MET cc_start: 0.9313 (mmp) cc_final: 0.9051 (mmm) REVERT: E 37 SER cc_start: 0.8096 (m) cc_final: 0.7713 (p) REVERT: E 47 ASP cc_start: 0.9253 (m-30) cc_final: 0.9004 (m-30) REVERT: E 221 GLU cc_start: 0.8582 (pp20) cc_final: 0.8178 (pp20) REVERT: E 231 LYS cc_start: 0.9272 (pttm) cc_final: 0.8801 (tptt) REVERT: E 332 MET cc_start: 0.8449 (tpt) cc_final: 0.8107 (tpp) REVERT: E 380 ILE cc_start: 0.9523 (mt) cc_final: 0.9218 (tt) REVERT: E 416 SER cc_start: 0.9314 (t) cc_final: 0.9000 (p) REVERT: E 458 GLN cc_start: 0.8949 (mm110) cc_final: 0.8736 (mp10) REVERT: E 543 LYS cc_start: 0.9023 (tppt) cc_final: 0.8219 (tppp) REVERT: E 577 ASP cc_start: 0.8836 (t0) cc_final: 0.7861 (t0) REVERT: E 578 GLU cc_start: 0.9371 (mt-10) cc_final: 0.8683 (mt-10) REVERT: E 671 ASP cc_start: 0.9184 (t0) cc_final: 0.8754 (p0) REVERT: E 736 PHE cc_start: 0.8886 (m-10) cc_final: 0.8649 (m-80) REVERT: F 41 LEU cc_start: 0.9356 (mt) cc_final: 0.9139 (mt) REVERT: F 58 LEU cc_start: 0.9182 (mt) cc_final: 0.8851 (tp) REVERT: F 59 LEU cc_start: 0.9417 (mt) cc_final: 0.9194 (mt) REVERT: F 219 MET cc_start: 0.8935 (mtp) cc_final: 0.8711 (mtt) REVERT: F 326 SER cc_start: 0.9377 (m) cc_final: 0.9109 (p) REVERT: F 332 MET cc_start: 0.8778 (tpt) cc_final: 0.8250 (tpp) REVERT: F 335 LEU cc_start: 0.9300 (mt) cc_final: 0.8545 (mt) REVERT: F 368 ASP cc_start: 0.8949 (t0) cc_final: 0.8438 (t70) REVERT: F 388 MET cc_start: 0.8562 (mmm) cc_final: 0.7720 (mmp) REVERT: F 398 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: F 560 ARG cc_start: 0.8677 (ttp-110) cc_final: 0.8325 (ttm110) REVERT: F 564 ASP cc_start: 0.8554 (m-30) cc_final: 0.8285 (m-30) REVERT: F 577 ASP cc_start: 0.9198 (t0) cc_final: 0.8976 (t0) REVERT: F 614 LYS cc_start: 0.9353 (tppt) cc_final: 0.9097 (ttpp) REVERT: F 630 ASP cc_start: 0.8743 (t0) cc_final: 0.7952 (t0) REVERT: F 633 ILE cc_start: 0.9328 (mt) cc_final: 0.8963 (mm) REVERT: F 660 ASN cc_start: 0.8555 (m110) cc_final: 0.8322 (m-40) REVERT: F 672 LEU cc_start: 0.9360 (mp) cc_final: 0.8956 (tt) REVERT: G 339 LEU cc_start: 0.9549 (mt) cc_final: 0.9264 (mt) outliers start: 1 outliers final: 0 residues processed: 753 average time/residue: 0.2071 time to fit residues: 256.5553 Evaluate side-chains 589 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 588 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 26 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 407 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 203 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 274 optimal weight: 3.9990 chunk 459 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 215 GLN B 340 HIS C 90 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 602 ASN D 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.086258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.062476 restraints weight = 162669.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.064295 restraints weight = 102402.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065523 restraints weight = 73419.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.066406 restraints weight = 58297.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.067034 restraints weight = 49429.701| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 37549 Z= 0.211 Angle : 0.727 12.099 50780 Z= 0.360 Chirality : 0.047 0.228 5734 Planarity : 0.005 0.059 6656 Dihedral : 7.745 137.587 5201 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.03 % Allowed : 0.43 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.12), residues: 4647 helix: 0.88 (0.11), residues: 2123 sheet: 0.35 (0.17), residues: 801 loop : 0.26 (0.16), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 359 TYR 0.034 0.002 TYR F 203 PHE 0.030 0.002 PHE B 552 TRP 0.017 0.002 TRP F 454 HIS 0.009 0.002 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00457 (37549) covalent geometry : angle 0.72693 (50780) hydrogen bonds : bond 0.03809 ( 1713) hydrogen bonds : angle 4.73379 ( 4809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9294 Ramachandran restraints generated. 4647 Oldfield, 0 Emsley, 4647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 703 time to evaluate : 1.849 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: A 46 MET cc_start: 0.8820 (mtm) cc_final: 0.8307 (ptp) REVERT: A 217 LYS cc_start: 0.9469 (ptpt) cc_final: 0.9186 (ptpp) REVERT: A 332 MET cc_start: 0.8902 (ttm) cc_final: 0.8463 (ttm) REVERT: A 384 HIS cc_start: 0.8323 (m90) cc_final: 0.7973 (m90) REVERT: A 450 ASP cc_start: 0.8861 (t70) cc_final: 0.8660 (t0) REVERT: A 477 GLU cc_start: 0.9185 (pm20) cc_final: 0.8771 (pm20) REVERT: A 529 LYS cc_start: 0.9241 (mmmt) cc_final: 0.8829 (mmmm) REVERT: A 546 GLU cc_start: 0.9015 (tp30) cc_final: 0.8749 (tp30) REVERT: A 578 GLU cc_start: 0.9124 (mp0) cc_final: 0.8528 (mp0) REVERT: A 608 MET cc_start: 0.8270 (ppp) cc_final: 0.7909 (ppp) REVERT: A 625 ARG cc_start: 0.9076 (tpp-160) cc_final: 0.8648 (tpp80) REVERT: A 638 ARG cc_start: 0.8092 (mmt180) cc_final: 0.7435 (mmt-90) REVERT: A 695 CYS cc_start: 0.9385 (m) cc_final: 0.9119 (t) REVERT: A 751 ASP cc_start: 0.9451 (m-30) cc_final: 0.8929 (t70) REVERT: B 139 PHE cc_start: 0.8670 (m-80) cc_final: 0.8438 (m-80) REVERT: B 150 ASP cc_start: 0.7576 (m-30) cc_final: 0.6971 (t70) REVERT: B 215 GLN cc_start: 0.9434 (OUTLIER) cc_final: 0.9142 (pt0) REVERT: B 236 LYS cc_start: 0.8162 (tppt) cc_final: 0.7891 (tppt) REVERT: B 386 LYS cc_start: 0.9128 (mmpt) cc_final: 0.8714 (mmmt) REVERT: B 440 GLU cc_start: 0.8992 (mp0) cc_final: 0.8721 (mp0) REVERT: B 618 PHE cc_start: 0.8709 (t80) cc_final: 0.7830 (t80) REVERT: B 740 MET cc_start: 0.8451 (mtm) cc_final: 0.8185 (mtt) REVERT: C 46 MET cc_start: 0.8957 (mtp) cc_final: 0.8650 (mtt) REVERT: C 305 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9101 (mm-30) REVERT: C 332 MET cc_start: 0.9165 (tpp) cc_final: 0.8927 (tpp) REVERT: C 373 ASP cc_start: 0.8842 (p0) cc_final: 0.8321 (p0) REVERT: C 491 GLU cc_start: 0.8058 (mp0) cc_final: 0.7835 (pm20) REVERT: C 550 MET cc_start: 0.9119 (mtm) cc_final: 0.8786 (mtp) REVERT: C 608 MET cc_start: 0.9193 (ptp) cc_final: 0.8989 (ptp) REVERT: C 616 ASN cc_start: 0.9175 (t0) cc_final: 0.8743 (t0) REVERT: C 740 MET cc_start: 0.8595 (mmp) cc_final: 0.8347 (mmm) REVERT: D 158 MET cc_start: 0.8569 (mtt) cc_final: 0.8273 (tmm) REVERT: D 204 ASP cc_start: 0.8696 (t70) cc_final: 0.8475 (t0) REVERT: D 261 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8818 (mm-30) REVERT: D 305 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8703 (mm-30) REVERT: D 312 LYS cc_start: 0.8523 (mppt) cc_final: 0.8169 (mppt) REVERT: D 373 ASP cc_start: 0.8419 (p0) cc_final: 0.8133 (p0) REVERT: D 508 MET cc_start: 0.7784 (tmm) cc_final: 0.7410 (tmm) REVERT: D 535 CYS cc_start: 0.8526 (t) cc_final: 0.8297 (t) REVERT: D 548 LEU cc_start: 0.9340 (mt) cc_final: 0.9062 (mt) REVERT: D 678 MET cc_start: 0.9274 (mmp) cc_final: 0.9052 (mmm) REVERT: E 37 SER cc_start: 0.8087 (m) cc_final: 0.7692 (p) REVERT: E 221 GLU cc_start: 0.8663 (pp20) cc_final: 0.8243 (pp20) REVERT: E 231 LYS cc_start: 0.9287 (pttm) cc_final: 0.8855 (tptt) REVERT: E 332 MET cc_start: 0.8539 (tpt) cc_final: 0.8238 (tpp) REVERT: E 380 ILE cc_start: 0.9603 (mt) cc_final: 0.9273 (tt) REVERT: E 543 LYS cc_start: 0.9049 (tppt) cc_final: 0.8224 (tppp) REVERT: E 564 ASP cc_start: 0.9290 (t70) cc_final: 0.9028 (t70) REVERT: E 565 LYS cc_start: 0.9468 (mppt) cc_final: 0.9127 (mmtm) REVERT: E 577 ASP cc_start: 0.8839 (t0) cc_final: 0.7891 (t0) REVERT: E 578 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8640 (mt-10) REVERT: E 671 ASP cc_start: 0.9109 (t0) cc_final: 0.8799 (p0) REVERT: E 736 PHE cc_start: 0.8886 (m-10) cc_final: 0.8654 (m-80) REVERT: F 41 LEU cc_start: 0.9372 (mt) cc_final: 0.9142 (mt) REVERT: F 58 LEU cc_start: 0.9235 (mt) cc_final: 0.8984 (mt) REVERT: F 158 MET cc_start: 0.7987 (mmp) cc_final: 0.7784 (mmp) REVERT: F 219 MET cc_start: 0.8971 (mtp) cc_final: 0.8701 (mtt) REVERT: F 326 SER cc_start: 0.9372 (m) cc_final: 0.9131 (p) REVERT: F 332 MET cc_start: 0.8788 (tpt) cc_final: 0.8241 (tpp) REVERT: F 335 LEU cc_start: 0.9283 (mt) cc_final: 0.8507 (mt) REVERT: F 368 ASP cc_start: 0.8978 (t0) cc_final: 0.8728 (t70) REVERT: F 388 MET cc_start: 0.8580 (mmm) cc_final: 0.8187 (mmt) REVERT: F 404 HIS cc_start: 0.8133 (t-90) cc_final: 0.7930 (t-90) REVERT: F 560 ARG cc_start: 0.8747 (ttp-110) cc_final: 0.8364 (ttm110) REVERT: F 561 GLU cc_start: 0.9223 (pm20) cc_final: 0.8910 (pm20) REVERT: F 564 ASP cc_start: 0.8567 (m-30) cc_final: 0.8255 (m-30) REVERT: F 575 PHE cc_start: 0.8861 (t80) cc_final: 0.8518 (t80) REVERT: F 578 GLU cc_start: 0.8670 (mp0) cc_final: 0.8317 (mp0) REVERT: F 614 LYS cc_start: 0.9351 (tppt) cc_final: 0.9145 (ttpp) REVERT: F 625 ARG cc_start: 0.8892 (tpm170) cc_final: 0.8629 (tpm170) REVERT: F 630 ASP cc_start: 0.8815 (t0) cc_final: 0.8056 (t0) REVERT: F 633 ILE cc_start: 0.9451 (mt) cc_final: 0.9237 (mm) REVERT: F 660 ASN cc_start: 0.8686 (m110) cc_final: 0.8469 (m-40) REVERT: F 672 LEU cc_start: 0.9418 (mp) cc_final: 0.9074 (tt) REVERT: F 682 PHE cc_start: 0.5948 (m-80) cc_final: 0.5728 (m-80) REVERT: G 339 LEU cc_start: 0.9529 (mt) cc_final: 0.9241 (mt) outliers start: 1 outliers final: 0 residues processed: 704 average time/residue: 0.2398 time to fit residues: 277.7301 Evaluate side-chains 539 residues out of total 3982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 538 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 321 optimal weight: 0.9990 chunk 327 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 228 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 417 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 167 optimal weight: 0.9980 chunk 368 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 91 ASN B 215 GLN B 327 GLN B 340 HIS C 90 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 602 ASN E 43 GLN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** 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 = 0.3721 r_free = 0.3721 target = 0.088557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.065357 restraints weight = 159679.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.067256 restraints weight = 98890.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.068564 restraints weight = 70422.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.069381 restraints weight = 55372.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.070013 restraints weight = 47003.936| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37549 Z= 0.131 Angle : 0.691 11.148 50780 Z= 0.339 Chirality : 0.047 0.226 5734 Planarity : 0.004 0.057 6656 Dihedral : 7.492 138.349 5201 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.12), residues: 4647 helix: 1.01 (0.12), residues: 2108 sheet: 0.44 (0.18), residues: 778 loop : 0.32 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 323 TYR 0.030 0.002 TYR G 334 PHE 0.035 0.002 PHE B 576 TRP 0.014 0.001 TRP B 551 HIS 0.007 0.001 HIS E 499 Details of bonding type rmsd covalent geometry : bond 0.00296 (37549) covalent geometry : angle 0.69141 (50780) hydrogen bonds : bond 0.03587 ( 1713) hydrogen bonds : angle 4.48532 ( 4809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9234.03 seconds wall clock time: 158 minutes 54.71 seconds (9534.71 seconds total)