Starting phenix.real_space_refine on Tue Aug 26 06:36:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fct_28992/08_2025/8fct_28992.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fct_28992/08_2025/8fct_28992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fct_28992/08_2025/8fct_28992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fct_28992/08_2025/8fct_28992.map" model { file = "/net/cci-nas-00/data/ceres_data/8fct_28992/08_2025/8fct_28992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fct_28992/08_2025/8fct_28992.cif" } resolution = 3.42 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= -0.002 sd= 0.030 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 180 5.16 5 C 21517 2.51 5 N 6036 2.21 5 O 6572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34329 Number of models: 1 Model: "" Number of chains: 13 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: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "B" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "C" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "E" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "G" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 240 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 38} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 6 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: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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} Time building chain proxies: 8.77, per 1000 atoms: 0.26 Number of scatterers: 34329 At special positions: 0 Unit cell: (180.978, 168.468, 101.748, 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 180 16.00 P 24 15.00 O 6572 8.00 N 6036 7.00 C 21517 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8138 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 35 sheets defined 52.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.728A 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 removed outlier: 3.587A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 334 Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 349 through 353 removed outlier: 4.155A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 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: 3.508A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 555 through 557 No H-bonds generated for 'chain 'F' and resid 555 through 557' Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 609 Processing helix chain 'F' and resid 610 through 611 No H-bonds generated for 'chain 'F' and resid 610 through 611' Processing helix chain 'F' and resid 612 through 615 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 707 Processing helix chain 'F' and resid 732 through 740 removed outlier: 3.581A 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 'A' and resid 43 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: 4.553A 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 231 removed outlier: 3.905A 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 281 through 296 Processing helix chain 'A' and resid 305 through 309 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 431 removed outlier: 4.285A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.637A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.579A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.525A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.073A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 85 through 93 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: 4.665A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.992A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.156A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 431 removed outlier: 4.176A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (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 506 removed outlier: 3.677A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.504A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.973A 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 706 removed outlier: 3.727A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.505A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 removed outlier: 3.556A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 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: 4.610A 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 231 removed outlier: 3.999A 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 281 through 296 Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 334 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 431 removed outlier: 4.526A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.674A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.046A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 706 removed outlier: 3.682A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.520A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 removed outlier: 4.107A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 129 through 134 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: 4.632A 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 231 removed outlier: 4.233A 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 281 through 296 removed outlier: 3.503A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 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: 4.289A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 506 removed outlier: 4.031A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.170A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 612 through 615 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 706 removed outlier: 3.742A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 762 removed outlier: 3.506A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.430A 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 232 removed outlier: 4.228A 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 281 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.637A 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 349 through 353 removed outlier: 4.123A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 384 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 431 removed outlier: 4.088A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (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 493 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.524A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.538A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 555 through 557 No H-bonds generated for 'chain 'E' and resid 555 through 557' Processing helix chain 'E' and resid 558 through 569 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 671 through 679 Processing helix chain 'E' and resid 683 through 705 Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.554A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 762 Processing helix chain 'G' and resid 50 through 68 Processing helix chain 'G' and resid 76 through 93 Processing sheet with id=AA1, first strand: chain 'F' and resid 25 through 29 removed outlier: 7.480A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 151 through 156 removed outlier: 6.739A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.121A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.524A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 25 through 29 removed outlier: 7.977A pdb=" N LYS A 81 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER A 42 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP A 74 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 156 removed outlier: 5.399A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AB2, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.202A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.480A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 30 removed outlier: 8.131A pdb=" N LYS B 81 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 42 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP B 74 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 151 through 156 removed outlier: 5.340A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 167 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AB7, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AB8, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.229A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.639A 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: 6.413A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.490A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.227A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 74 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 156 removed outlier: 5.337A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 167 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AC4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AC5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.213A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.476A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 30 removed outlier: 8.049A pdb=" N LYS D 81 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER D 42 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP D 74 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU D 41 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 151 through 156 removed outlier: 5.375A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AD1, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.224A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.467A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 25 through 30 removed outlier: 3.567A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 145 through 147 removed outlier: 10.519A pdb=" N TYR E 110 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N VAL E 181 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS E 112 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS E 183 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AD7, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.202A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.473A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) 1610 hydrogen bonds defined for protein. 4500 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: 8.44 Time building geometry restraints manager: 3.89 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: 7024 1.33 - 1.45: 7281 1.45 - 1.57: 20270 1.57 - 1.69: 36 1.69 - 1.81: 288 Bond restraints: 34899 Sorted by residual: bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 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 ... (remaining 34894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 46407 2.49 - 4.98: 686 4.98 - 7.46: 73 7.46 - 9.95: 30 9.95 - 12.44: 6 Bond angle restraints: 47202 Sorted by residual: angle pdb=" N ILE E 590 " pdb=" CA ILE E 590 " pdb=" C ILE E 590 " ideal model delta sigma weight residual 111.67 106.68 4.99 9.50e-01 1.11e+00 2.76e+01 angle pdb=" N ILE C 590 " pdb=" CA ILE C 590 " pdb=" C ILE C 590 " ideal model delta sigma weight residual 111.67 106.68 4.99 9.50e-01 1.11e+00 2.76e+01 angle pdb=" N ILE D 590 " pdb=" CA ILE D 590 " pdb=" C ILE D 590 " ideal model delta sigma weight residual 111.67 106.70 4.97 9.50e-01 1.11e+00 2.74e+01 angle pdb=" N ILE A 590 " pdb=" CA ILE A 590 " pdb=" C ILE A 590 " ideal model delta sigma weight residual 111.67 106.72 4.95 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N ILE B 590 " pdb=" CA ILE B 590 " pdb=" C ILE B 590 " ideal model delta sigma weight residual 111.67 106.72 4.95 9.50e-01 1.11e+00 2.71e+01 ... (remaining 47197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 21268 32.72 - 65.44: 272 65.44 - 98.16: 42 98.16 - 130.88: 18 130.88 - 163.60: 6 Dihedral angle restraints: 21606 sinusoidal: 9061 harmonic: 12545 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 300.00 136.40 163.60 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O2A ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PA ADP F 901 " pdb=" PB ADP F 901 " ideal model delta sinusoidal sigma weight residual 300.00 153.24 146.76 1 2.00e+01 2.50e-03 4.41e+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 300.00 160.01 139.99 1 2.00e+01 2.50e-03 4.24e+01 ... (remaining 21603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3828 0.048 - 0.095: 890 0.095 - 0.143: 460 0.143 - 0.191: 147 0.191 - 0.239: 12 Chirality restraints: 5337 Sorted by residual: 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 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE E 590 " pdb=" N ILE E 590 " pdb=" C ILE E 590 " pdb=" CB ILE E 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+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 1.41e+00 ... (remaining 5334 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 82 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C GLN G 82 " -0.043 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 F 534 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C GLU F 534 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU F 534 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS F 535 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 360 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C PHE F 360 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE F 360 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY F 361 " 0.013 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 13964 2.92 - 3.42: 33472 3.42 - 3.91: 58835 3.91 - 4.41: 65421 4.41 - 4.90: 106474 Nonbonded interactions: 278166 Sorted by model distance: nonbonded pdb=" OD2 ASP D 368 " pdb=" NZ LYS D 565 " model vdw 2.429 3.120 nonbonded pdb=" NZ LYS F 512 " pdb=" O GLY F 637 " model vdw 2.453 3.120 nonbonded pdb=" OD2 ASP D 580 " pdb=" NZ LYS D 584 " model vdw 2.454 3.120 nonbonded pdb=" NZ LYS C 112 " pdb=" OD2 ASP C 179 " model vdw 2.459 3.120 nonbonded pdb=" NZ LYS C 63 " pdb=" OE1 GLU C 194 " model vdw 2.464 3.120 ... (remaining 278161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'B' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'C' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'D' and (resid 23 through 499 or resid 509 through 902)) selection = (chain 'E' and (resid 23 through 499 or resid 509 through 902)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.110 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 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 34899 Z= 0.598 Angle : 0.815 12.438 47202 Z= 0.489 Chirality : 0.058 0.239 5337 Planarity : 0.003 0.029 6186 Dihedral : 12.054 163.600 13468 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.34 % Favored : 98.52 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 0.46 (0.12), residues: 4326 helix: -0.14 (0.10), residues: 1911 sheet: 0.74 (0.17), residues: 749 loop : 0.99 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 89 TYR 0.001 0.000 TYR D 755 PHE 0.001 0.000 PHE B 758 TRP 0.002 0.000 TRP F 551 HIS 0.001 0.000 HIS F 735 Details of bonding type rmsd covalent geometry : bond 0.01068 (34899) covalent geometry : angle 0.81492 (47202) hydrogen bonds : bond 0.21703 ( 1610) hydrogen bonds : angle 6.40237 ( 4500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 791 time to evaluate : 1.342 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: E 508 MET cc_start: -0.0799 (ttt) cc_final: -0.3105 (mtt) outliers start: 2 outliers final: 0 residues processed: 793 average time/residue: 0.2196 time to fit residues: 260.7653 Evaluate side-chains 374 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 0.8980 chunk 424 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 260 ASN F 340 HIS A 215 GLN A 327 GLN A 421 GLN B 340 HIS B 602 ASN C 406 HIS D 406 HIS E 43 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.084370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.059489 restraints weight = 134860.492| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 5.64 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34899 Z= 0.176 Angle : 0.718 9.862 47202 Z= 0.351 Chirality : 0.046 0.167 5337 Planarity : 0.005 0.058 6186 Dihedral : 9.288 161.925 4846 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.20 % Favored : 98.77 % Rotamer: Outliers : 1.44 % Allowed : 7.60 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.12), residues: 4326 helix: 1.35 (0.11), residues: 1921 sheet: 0.88 (0.18), residues: 738 loop : 1.20 (0.16), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 599 TYR 0.026 0.002 TYR A 495 PHE 0.032 0.001 PHE A 674 TRP 0.033 0.002 TRP A 454 HIS 0.005 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00385 (34899) covalent geometry : angle 0.71755 (47202) hydrogen bonds : bond 0.05621 ( 1610) hydrogen bonds : angle 4.79270 ( 4500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 397 time to evaluate : 1.441 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: F 56 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7832 (t) REVERT: F 139 PHE cc_start: 0.9127 (m-80) cc_final: 0.8918 (m-10) REVERT: F 320 VAL cc_start: 0.8838 (t) cc_final: 0.8513 (p) REVERT: F 550 MET cc_start: 0.4278 (mmp) cc_final: 0.3513 (mtm) REVERT: A 46 MET cc_start: 0.8567 (tpp) cc_final: 0.8327 (tpp) REVERT: A 213 LEU cc_start: 0.9709 (tt) cc_final: 0.9501 (tp) REVERT: A 427 MET cc_start: 0.8108 (tpt) cc_final: 0.7684 (tpp) REVERT: A 465 ARG cc_start: 0.7317 (tmt170) cc_final: 0.6332 (tpt-90) REVERT: A 508 MET cc_start: 0.8416 (tpp) cc_final: 0.8136 (tpp) REVERT: A 512 LYS cc_start: 0.8980 (mttt) cc_final: 0.8452 (mttm) REVERT: A 550 MET cc_start: 0.1724 (mmp) cc_final: 0.1160 (mmt) REVERT: A 672 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8203 (pp) REVERT: A 736 PHE cc_start: 0.9177 (m-80) cc_final: 0.8860 (m-80) REVERT: B 193 ASP cc_start: 0.9342 (p0) cc_final: 0.9100 (p0) REVERT: B 402 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 449 MET cc_start: 0.8909 (tpp) cc_final: 0.8693 (tpp) REVERT: B 450 ASP cc_start: 0.9450 (m-30) cc_final: 0.9095 (t0) REVERT: B 577 ASP cc_start: 0.8945 (t0) cc_final: 0.8136 (t0) REVERT: B 578 GLU cc_start: 0.8267 (mp0) cc_final: 0.7371 (mp0) REVERT: B 678 MET cc_start: 0.9127 (mmm) cc_final: 0.8921 (mmm) REVERT: C 550 MET cc_start: 0.9419 (mpp) cc_final: 0.8773 (mpp) REVERT: D 196 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8848 (mp0) REVERT: D 321 GLU cc_start: 0.8777 (mp0) cc_final: 0.8431 (mp0) REVERT: D 517 TYR cc_start: 0.8999 (p90) cc_final: 0.8750 (p90) REVERT: D 578 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8657 (mt-10) REVERT: E 275 MET cc_start: 0.9512 (mmp) cc_final: 0.9263 (mmp) REVERT: E 304 ASP cc_start: 0.8285 (t0) cc_final: 0.8055 (t0) REVERT: E 508 MET cc_start: -0.3527 (ttt) cc_final: -0.4697 (mmt) REVERT: E 740 MET cc_start: 0.8485 (tpt) cc_final: 0.8228 (mtp) outliers start: 53 outliers final: 24 residues processed: 431 average time/residue: 0.2085 time to fit residues: 142.1710 Evaluate side-chains 340 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 314 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 296 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 321 optimal weight: 0.0870 chunk 208 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 373 optimal weight: 4.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN C 421 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS E 760 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.080411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054568 restraints weight = 136865.008| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 6.05 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34899 Z= 0.250 Angle : 0.727 10.616 47202 Z= 0.351 Chirality : 0.046 0.172 5337 Planarity : 0.005 0.047 6186 Dihedral : 8.827 163.658 4846 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.44 % Allowed : 8.01 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.69 (0.13), residues: 4326 helix: 1.51 (0.12), residues: 1926 sheet: 0.73 (0.17), residues: 749 loop : 1.08 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 741 TYR 0.032 0.002 TYR A 203 PHE 0.037 0.002 PHE A 674 TRP 0.019 0.002 TRP E 551 HIS 0.004 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00542 (34899) covalent geometry : angle 0.72652 (47202) hydrogen bonds : bond 0.04461 ( 1610) hydrogen bonds : angle 4.71383 ( 4500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 1.206 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: F 46 MET cc_start: 0.8986 (ttt) cc_final: 0.8718 (ttp) REVERT: F 56 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7752 (t) REVERT: F 320 VAL cc_start: 0.8859 (t) cc_final: 0.8656 (p) REVERT: F 427 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8884 (tpt) REVERT: F 442 MET cc_start: 0.9662 (mmp) cc_final: 0.9454 (mmm) REVERT: F 550 MET cc_start: 0.4025 (mmp) cc_final: 0.3487 (mtm) REVERT: A 368 ASP cc_start: 0.8696 (t0) cc_final: 0.8489 (t0) REVERT: A 427 MET cc_start: 0.8321 (tpt) cc_final: 0.8021 (tpp) REVERT: A 449 MET cc_start: 0.9534 (tpp) cc_final: 0.9058 (tpp) REVERT: A 465 ARG cc_start: 0.7272 (tmt170) cc_final: 0.6291 (tpt-90) REVERT: A 512 LYS cc_start: 0.9149 (mttt) cc_final: 0.8548 (mttm) REVERT: A 550 MET cc_start: 0.1828 (mmp) cc_final: 0.1557 (mmp) REVERT: A 678 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8603 (tmm) REVERT: B 134 TYR cc_start: 0.9587 (m-80) cc_final: 0.9376 (m-10) REVERT: B 138 TYR cc_start: 0.9251 (t80) cc_final: 0.9043 (t80) REVERT: B 402 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 450 ASP cc_start: 0.9517 (m-30) cc_final: 0.9144 (t0) REVERT: B 550 MET cc_start: 0.9109 (mtm) cc_final: 0.8836 (mtm) REVERT: B 577 ASP cc_start: 0.9072 (t0) cc_final: 0.8184 (t0) REVERT: B 578 GLU cc_start: 0.8366 (mp0) cc_final: 0.7426 (mp0) REVERT: B 678 MET cc_start: 0.9160 (mmm) cc_final: 0.8877 (mmm) REVERT: C 150 ASP cc_start: 0.8809 (m-30) cc_final: 0.8462 (t70) REVERT: C 388 MET cc_start: 0.9305 (mtm) cc_final: 0.9096 (mtm) REVERT: C 466 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9056 (mm-30) REVERT: C 550 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.8918 (mpp) REVERT: C 598 ASP cc_start: 0.8332 (t0) cc_final: 0.7711 (m-30) REVERT: C 757 MET cc_start: 0.9336 (ptt) cc_final: 0.9104 (ptt) REVERT: D 321 GLU cc_start: 0.9009 (mp0) cc_final: 0.8657 (mp0) REVERT: D 338 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7078 (mpp80) REVERT: D 449 MET cc_start: 0.8456 (mmm) cc_final: 0.8041 (mmm) REVERT: D 578 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8784 (mm-30) REVERT: E 33 ASN cc_start: 0.8217 (t0) cc_final: 0.7836 (t0) REVERT: E 275 MET cc_start: 0.9569 (mmp) cc_final: 0.9347 (mmp) REVERT: E 304 ASP cc_start: 0.8455 (t0) cc_final: 0.8078 (t0) REVERT: E 508 MET cc_start: -0.3252 (ttt) cc_final: -0.4477 (mmt) REVERT: E 567 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7808 (mtm-85) REVERT: E 668 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8360 (mmmt) REVERT: E 740 MET cc_start: 0.8481 (tpt) cc_final: 0.8234 (mtp) REVERT: G 50 ASN cc_start: 0.9115 (t0) cc_final: 0.8899 (t0) outliers start: 53 outliers final: 31 residues processed: 346 average time/residue: 0.2078 time to fit residues: 115.4800 Evaluate side-chains 302 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 42 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 373 optimal weight: 0.8980 chunk 366 optimal weight: 0.5980 chunk 255 optimal weight: 0.0870 chunk 215 optimal weight: 10.0000 chunk 378 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS E 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.082005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.056140 restraints weight = 133521.643| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 6.30 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34899 Z= 0.118 Angle : 0.642 9.307 47202 Z= 0.303 Chirality : 0.045 0.169 5337 Planarity : 0.004 0.045 6186 Dihedral : 8.229 155.153 4846 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.25 % Allowed : 8.58 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.92 (0.13), residues: 4326 helix: 1.77 (0.12), residues: 1908 sheet: 0.86 (0.18), residues: 746 loop : 1.11 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 635 TYR 0.037 0.002 TYR E 203 PHE 0.031 0.001 PHE A 674 TRP 0.026 0.002 TRP D 454 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00261 (34899) covalent geometry : angle 0.64216 (47202) hydrogen bonds : bond 0.03730 ( 1610) hydrogen bonds : angle 4.30927 ( 4500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 333 time to evaluate : 1.006 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: F 56 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7680 (t) REVERT: F 320 VAL cc_start: 0.8836 (t) cc_final: 0.8635 (p) REVERT: F 442 MET cc_start: 0.9635 (mmp) cc_final: 0.9402 (mmm) REVERT: F 550 MET cc_start: 0.4250 (mmp) cc_final: 0.3763 (mtm) REVERT: A 230 PHE cc_start: 0.8929 (m-80) cc_final: 0.8596 (m-80) REVERT: A 368 ASP cc_start: 0.8664 (t0) cc_final: 0.8447 (t0) REVERT: A 427 MET cc_start: 0.8173 (tpt) cc_final: 0.7939 (tpp) REVERT: A 465 ARG cc_start: 0.7322 (tmt170) cc_final: 0.6530 (tpt-90) REVERT: A 512 LYS cc_start: 0.9100 (mttt) cc_final: 0.8460 (mttm) REVERT: B 35 ASP cc_start: 0.8857 (t0) cc_final: 0.8560 (t70) REVERT: B 134 TYR cc_start: 0.9541 (m-80) cc_final: 0.9327 (m-10) REVERT: B 138 TYR cc_start: 0.9231 (t80) cc_final: 0.9019 (t80) REVERT: B 304 ASP cc_start: 0.9079 (t0) cc_final: 0.8840 (t0) REVERT: B 305 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8876 (mt-10) REVERT: B 450 ASP cc_start: 0.9548 (m-30) cc_final: 0.9093 (t0) REVERT: B 550 MET cc_start: 0.9029 (mtm) cc_final: 0.8790 (mtm) REVERT: B 560 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8995 (ptm160) REVERT: B 577 ASP cc_start: 0.9011 (t0) cc_final: 0.8644 (t0) REVERT: B 678 MET cc_start: 0.9213 (mmm) cc_final: 0.8929 (mmm) REVERT: C 150 ASP cc_start: 0.8853 (m-30) cc_final: 0.8576 (m-30) REVERT: C 305 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8318 (mp0) REVERT: C 466 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8926 (mm-30) REVERT: C 608 MET cc_start: 0.9426 (mtp) cc_final: 0.9189 (mtp) REVERT: C 641 GLN cc_start: 0.7924 (mp10) cc_final: 0.7660 (mp10) REVERT: D 231 LYS cc_start: 0.9637 (ptmt) cc_final: 0.9422 (ptpt) REVERT: D 321 GLU cc_start: 0.9068 (mp0) cc_final: 0.8744 (mp0) REVERT: D 509 THR cc_start: 0.9507 (m) cc_final: 0.9293 (p) REVERT: D 517 TYR cc_start: 0.9123 (p90) cc_final: 0.8794 (p90) REVERT: D 578 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8771 (mm-30) REVERT: E 33 ASN cc_start: 0.8206 (t0) cc_final: 0.7807 (t0) REVERT: E 244 TYR cc_start: 0.8328 (p90) cc_final: 0.8070 (p90) REVERT: E 275 MET cc_start: 0.9533 (mmp) cc_final: 0.9323 (mmp) REVERT: E 304 ASP cc_start: 0.8458 (t0) cc_final: 0.8095 (t0) REVERT: E 508 MET cc_start: -0.3268 (ttt) cc_final: -0.4482 (mmt) REVERT: E 740 MET cc_start: 0.8428 (tpt) cc_final: 0.8214 (mtp) REVERT: E 757 MET cc_start: 0.9429 (tmm) cc_final: 0.9147 (ptt) outliers start: 46 outliers final: 23 residues processed: 366 average time/residue: 0.2038 time to fit residues: 119.8293 Evaluate side-chains 314 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 289 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 560 ARG Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 392 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 303 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 296 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 371 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.080064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054239 restraints weight = 136895.558| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 6.18 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34899 Z= 0.194 Angle : 0.673 9.170 47202 Z= 0.319 Chirality : 0.045 0.152 5337 Planarity : 0.004 0.050 6186 Dihedral : 7.894 148.578 4846 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.44 % Allowed : 9.45 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.88 (0.13), residues: 4326 helix: 1.71 (0.12), residues: 1936 sheet: 0.84 (0.18), residues: 742 loop : 1.09 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 567 TYR 0.020 0.002 TYR F 203 PHE 0.021 0.001 PHE D 576 TRP 0.049 0.002 TRP E 551 HIS 0.004 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00425 (34899) covalent geometry : angle 0.67287 (47202) hydrogen bonds : bond 0.03692 ( 1610) hydrogen bonds : angle 4.40034 ( 4500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.889 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: F 56 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7641 (t) REVERT: F 84 MET cc_start: 0.9204 (ttp) cc_final: 0.8775 (tmm) REVERT: F 442 MET cc_start: 0.9677 (mmp) cc_final: 0.9432 (mmm) REVERT: A 84 MET cc_start: 0.8369 (tmm) cc_final: 0.8156 (ppp) REVERT: A 512 LYS cc_start: 0.9143 (mttt) cc_final: 0.8532 (mttm) REVERT: A 757 MET cc_start: 0.9618 (mtm) cc_final: 0.9391 (tmm) REVERT: B 134 TYR cc_start: 0.9555 (m-80) cc_final: 0.9264 (m-10) REVERT: B 304 ASP cc_start: 0.9167 (t0) cc_final: 0.8947 (t0) REVERT: B 305 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8964 (mt-10) REVERT: B 450 ASP cc_start: 0.9503 (m-30) cc_final: 0.9045 (t0) REVERT: B 577 ASP cc_start: 0.9036 (t0) cc_final: 0.8661 (t0) REVERT: B 678 MET cc_start: 0.9221 (mmm) cc_final: 0.8916 (mmm) REVERT: C 150 ASP cc_start: 0.8821 (m-30) cc_final: 0.8604 (t70) REVERT: C 305 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8424 (mp0) REVERT: C 466 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8956 (mm-30) REVERT: C 550 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.8810 (mpp) REVERT: D 321 GLU cc_start: 0.9105 (mp0) cc_final: 0.8753 (mp0) REVERT: D 388 MET cc_start: 0.9036 (mtm) cc_final: 0.8728 (ptp) REVERT: D 449 MET cc_start: 0.8383 (mmm) cc_final: 0.8053 (mmm) REVERT: D 517 TYR cc_start: 0.9218 (p90) cc_final: 0.8776 (p90) REVERT: D 578 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8794 (mm-30) REVERT: E 33 ASN cc_start: 0.8291 (t0) cc_final: 0.7906 (t0) REVERT: E 304 ASP cc_start: 0.8502 (t0) cc_final: 0.8073 (t0) REVERT: E 392 ASP cc_start: 0.9174 (m-30) cc_final: 0.8897 (p0) REVERT: E 508 MET cc_start: -0.3185 (ttt) cc_final: -0.4415 (mmt) REVERT: E 560 ARG cc_start: 0.9480 (mtp-110) cc_final: 0.9215 (mmt180) outliers start: 53 outliers final: 38 residues processed: 320 average time/residue: 0.2072 time to fit residues: 106.7020 Evaluate side-chains 304 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 228 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 374 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 384 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 57 optimal weight: 40.0000 chunk 346 optimal weight: 0.0870 chunk 300 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 ASN E 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.080665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055049 restraints weight = 134706.126| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 6.22 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34899 Z= 0.127 Angle : 0.644 11.862 47202 Z= 0.302 Chirality : 0.044 0.147 5337 Planarity : 0.004 0.048 6186 Dihedral : 7.581 142.697 4846 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.19 % Allowed : 9.91 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.97 (0.13), residues: 4326 helix: 1.82 (0.12), residues: 1937 sheet: 0.86 (0.18), residues: 744 loop : 1.10 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 313 TYR 0.024 0.001 TYR A 143 PHE 0.023 0.001 PHE D 576 TRP 0.030 0.002 TRP E 551 HIS 0.003 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00287 (34899) covalent geometry : angle 0.64383 (47202) hydrogen bonds : bond 0.03449 ( 1610) hydrogen bonds : angle 4.23701 ( 4500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7625 (t) REVERT: F 84 MET cc_start: 0.9185 (ttp) cc_final: 0.8826 (tmm) REVERT: F 313 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8715 (ttp-170) REVERT: F 442 MET cc_start: 0.9655 (mmp) cc_final: 0.9408 (mmm) REVERT: A 314 GLU cc_start: 0.9584 (pp20) cc_final: 0.9237 (pp20) REVERT: A 315 LYS cc_start: 0.9716 (mmmm) cc_final: 0.9363 (mmmt) REVERT: A 332 MET cc_start: 0.9594 (tpt) cc_final: 0.9330 (tpt) REVERT: A 465 ARG cc_start: 0.7337 (tmt170) cc_final: 0.6569 (tpt-90) REVERT: A 512 LYS cc_start: 0.9158 (mttt) cc_final: 0.8544 (mttm) REVERT: A 550 MET cc_start: 0.2037 (mmp) cc_final: 0.1700 (mmp) REVERT: B 35 ASP cc_start: 0.8845 (t0) cc_final: 0.8554 (t70) REVERT: B 158 MET cc_start: 0.9407 (mmp) cc_final: 0.9196 (mmp) REVERT: B 304 ASP cc_start: 0.9195 (t0) cc_final: 0.8972 (t0) REVERT: B 305 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8977 (mt-10) REVERT: B 450 ASP cc_start: 0.9468 (m-30) cc_final: 0.9013 (t0) REVERT: B 508 MET cc_start: 0.8338 (tpp) cc_final: 0.8023 (tpt) REVERT: B 577 ASP cc_start: 0.8986 (t0) cc_final: 0.8635 (t0) REVERT: B 678 MET cc_start: 0.9264 (mmm) cc_final: 0.8952 (mmm) REVERT: B 740 MET cc_start: 0.8580 (tmm) cc_final: 0.8297 (ppp) REVERT: C 150 ASP cc_start: 0.8818 (m-30) cc_final: 0.8561 (m-30) REVERT: C 305 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8419 (mp0) REVERT: C 332 MET cc_start: 0.9358 (mmm) cc_final: 0.9056 (tpt) REVERT: C 466 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8951 (mm-30) REVERT: C 517 TYR cc_start: 0.9146 (p90) cc_final: 0.8798 (p90) REVERT: C 550 MET cc_start: 0.9485 (OUTLIER) cc_final: 0.8804 (mpp) REVERT: D 321 GLU cc_start: 0.9110 (mp0) cc_final: 0.8794 (mp0) REVERT: D 388 MET cc_start: 0.9055 (mtm) cc_final: 0.8844 (ptp) REVERT: D 449 MET cc_start: 0.8348 (mmm) cc_final: 0.8012 (mmm) REVERT: D 517 TYR cc_start: 0.9207 (p90) cc_final: 0.8874 (p90) REVERT: D 578 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8747 (mm-30) REVERT: E 33 ASN cc_start: 0.8255 (t0) cc_final: 0.7865 (t0) REVERT: E 244 TYR cc_start: 0.8186 (p90) cc_final: 0.7981 (p90) REVERT: E 304 ASP cc_start: 0.8499 (t0) cc_final: 0.8064 (t0) REVERT: E 392 ASP cc_start: 0.9219 (m-30) cc_final: 0.8909 (p0) REVERT: E 466 GLU cc_start: 0.8959 (tp30) cc_final: 0.8665 (tp30) REVERT: E 508 MET cc_start: -0.3149 (ttt) cc_final: -0.4419 (mmt) REVERT: E 560 ARG cc_start: 0.9486 (mtp-110) cc_final: 0.9206 (mmt180) outliers start: 44 outliers final: 32 residues processed: 327 average time/residue: 0.2167 time to fit residues: 115.1115 Evaluate side-chains 303 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 269 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 85 optimal weight: 5.9990 chunk 420 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 378 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 296 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 317 HIS F 327 GLN A 43 GLN B 398 GLN C 317 HIS D 226 HIS D 285 ASN D 317 HIS D 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.077591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.052740 restraints weight = 137662.155| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 5.67 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 34899 Z= 0.260 Angle : 0.738 10.886 47202 Z= 0.350 Chirality : 0.046 0.157 5337 Planarity : 0.004 0.047 6186 Dihedral : 7.423 136.364 4846 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.55 % Allowed : 10.29 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.65 (0.13), residues: 4326 helix: 1.61 (0.12), residues: 1943 sheet: 0.64 (0.18), residues: 785 loop : 0.90 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 313 TYR 0.047 0.002 TYR A 495 PHE 0.020 0.002 PHE D 576 TRP 0.031 0.002 TRP E 551 HIS 0.005 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00564 (34899) covalent geometry : angle 0.73835 (47202) hydrogen bonds : bond 0.03751 ( 1610) hydrogen bonds : angle 4.55377 ( 4500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 257 time to evaluate : 1.497 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: F 56 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7808 (t) REVERT: F 313 ARG cc_start: 0.9017 (ttp80) cc_final: 0.8699 (ttp-170) REVERT: F 320 VAL cc_start: 0.9058 (t) cc_final: 0.8851 (p) REVERT: F 442 MET cc_start: 0.9701 (mmp) cc_final: 0.9275 (mmm) REVERT: A 314 GLU cc_start: 0.9628 (pp20) cc_final: 0.9349 (pp20) REVERT: A 315 LYS cc_start: 0.9763 (mmmm) cc_final: 0.9422 (mmmt) REVERT: A 396 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8921 (mp) REVERT: A 512 LYS cc_start: 0.9200 (mttt) cc_final: 0.8612 (mttm) REVERT: A 736 PHE cc_start: 0.9042 (m-80) cc_final: 0.8619 (m-80) REVERT: B 305 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8939 (mt-10) REVERT: B 450 ASP cc_start: 0.9507 (m-30) cc_final: 0.9043 (t0) REVERT: B 577 ASP cc_start: 0.8999 (t0) cc_final: 0.8680 (t0) REVERT: B 678 MET cc_start: 0.9301 (mmm) cc_final: 0.8979 (mmm) REVERT: B 740 MET cc_start: 0.8601 (tmm) cc_final: 0.8249 (mtp) REVERT: C 305 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8399 (mp0) REVERT: C 550 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.8858 (mpp) REVERT: D 231 LYS cc_start: 0.9668 (ptmt) cc_final: 0.9407 (ptpp) REVERT: D 449 MET cc_start: 0.8329 (mmm) cc_final: 0.8030 (mmm) REVERT: D 550 MET cc_start: 0.9489 (mpp) cc_final: 0.9169 (mpp) REVERT: D 578 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8771 (mm-30) REVERT: D 611 MET cc_start: 0.9040 (mmm) cc_final: 0.8826 (mmm) REVERT: E 33 ASN cc_start: 0.8365 (t0) cc_final: 0.8004 (t0) REVERT: E 305 GLU cc_start: 0.8228 (mp0) cc_final: 0.7794 (mp0) REVERT: E 466 GLU cc_start: 0.8988 (tp30) cc_final: 0.8653 (tp30) REVERT: E 508 MET cc_start: -0.2802 (ttt) cc_final: -0.4324 (mmt) REVERT: E 560 ARG cc_start: 0.9522 (mtp-110) cc_final: 0.9237 (mmt180) outliers start: 57 outliers final: 40 residues processed: 304 average time/residue: 0.2306 time to fit residues: 113.2862 Evaluate side-chains 279 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 145 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 chunk 410 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 316 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 HIS F 317 HIS E 43 GLN E 351 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.079935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.053653 restraints weight = 134490.589| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 6.37 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 34899 Z= 0.111 Angle : 0.664 10.429 47202 Z= 0.310 Chirality : 0.045 0.189 5337 Planarity : 0.004 0.048 6186 Dihedral : 7.230 131.991 4846 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.92 % Allowed : 11.16 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.94 (0.13), residues: 4326 helix: 1.86 (0.12), residues: 1918 sheet: 0.81 (0.18), residues: 749 loop : 1.04 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 210 TYR 0.018 0.001 TYR A 143 PHE 0.017 0.001 PHE D 576 TRP 0.028 0.002 TRP D 454 HIS 0.003 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00247 (34899) covalent geometry : angle 0.66392 (47202) hydrogen bonds : bond 0.03317 ( 1610) hydrogen bonds : angle 4.19847 ( 4500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 1.335 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: F 56 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7658 (t) REVERT: F 84 MET cc_start: 0.9179 (ttp) cc_final: 0.8847 (tmm) REVERT: F 211 LYS cc_start: 0.8804 (tppt) cc_final: 0.8512 (tppt) REVERT: F 313 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8750 (ttp-170) REVERT: F 320 VAL cc_start: 0.8970 (t) cc_final: 0.8763 (p) REVERT: F 442 MET cc_start: 0.9684 (mmp) cc_final: 0.9436 (mmm) REVERT: A 512 LYS cc_start: 0.9182 (mttt) cc_final: 0.8753 (mttm) REVERT: B 305 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9015 (mt-10) REVERT: B 450 ASP cc_start: 0.9528 (m-30) cc_final: 0.9048 (t0) REVERT: B 577 ASP cc_start: 0.8993 (t0) cc_final: 0.8683 (t0) REVERT: B 678 MET cc_start: 0.9278 (mmm) cc_final: 0.8965 (mmm) REVERT: B 740 MET cc_start: 0.8551 (tmm) cc_final: 0.8203 (mtp) REVERT: C 305 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8387 (mp0) REVERT: C 427 MET cc_start: 0.9329 (tmm) cc_final: 0.9117 (tpp) REVERT: C 517 TYR cc_start: 0.9130 (p90) cc_final: 0.8808 (p90) REVERT: C 550 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.8845 (mpp) REVERT: C 574 LEU cc_start: 0.9594 (tp) cc_final: 0.9329 (tt) REVERT: C 577 ASP cc_start: 0.9035 (t0) cc_final: 0.8812 (t0) REVERT: C 598 ASP cc_start: 0.8504 (t0) cc_final: 0.8166 (p0) REVERT: D 321 GLU cc_start: 0.9159 (mp0) cc_final: 0.8859 (mp0) REVERT: D 517 TYR cc_start: 0.9267 (p90) cc_final: 0.8898 (p90) REVERT: D 550 MET cc_start: 0.9501 (mpp) cc_final: 0.9112 (mpp) REVERT: D 578 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8709 (mm-30) REVERT: D 608 MET cc_start: 0.9516 (ptm) cc_final: 0.9042 (ppp) REVERT: D 611 MET cc_start: 0.9031 (mmm) cc_final: 0.8816 (mmm) REVERT: D 731 ILE cc_start: 0.9700 (OUTLIER) cc_final: 0.9234 (tp) REVERT: E 33 ASN cc_start: 0.8305 (t0) cc_final: 0.7908 (t0) REVERT: E 305 GLU cc_start: 0.8347 (mp0) cc_final: 0.7884 (mp0) REVERT: E 392 ASP cc_start: 0.9251 (m-30) cc_final: 0.8933 (p0) REVERT: E 466 GLU cc_start: 0.9018 (tp30) cc_final: 0.8664 (tp30) REVERT: E 508 MET cc_start: -0.3068 (ttt) cc_final: -0.4451 (mmt) REVERT: E 560 ARG cc_start: 0.9493 (mtp-110) cc_final: 0.9211 (mmt180) REVERT: E 668 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8542 (mmmt) outliers start: 34 outliers final: 22 residues processed: 305 average time/residue: 0.2170 time to fit residues: 105.8673 Evaluate side-chains 280 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 303 optimal weight: 10.0000 chunk 54 optimal weight: 50.0000 chunk 361 optimal weight: 6.9990 chunk 432 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 384 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 HIS D 340 HIS E 260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.076639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.050350 restraints weight = 137820.393| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 5.57 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 34899 Z= 0.340 Angle : 0.817 11.582 47202 Z= 0.391 Chirality : 0.047 0.226 5337 Planarity : 0.005 0.066 6186 Dihedral : 7.457 132.389 4846 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.30 % Allowed : 11.00 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.43 (0.13), residues: 4326 helix: 1.45 (0.12), residues: 1923 sheet: 0.57 (0.18), residues: 780 loop : 0.74 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 322 TYR 0.036 0.003 TYR A 644 PHE 0.021 0.002 PHE D 452 TRP 0.033 0.002 TRP E 551 HIS 0.007 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00729 (34899) covalent geometry : angle 0.81705 (47202) hydrogen bonds : bond 0.03914 ( 1610) hydrogen bonds : angle 4.81101 ( 4500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 1.512 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: F 56 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7742 (t) REVERT: F 313 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8773 (ttp-170) REVERT: F 417 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9142 (mm-30) REVERT: F 442 MET cc_start: 0.9702 (mmp) cc_final: 0.9257 (mmm) REVERT: A 315 LYS cc_start: 0.9795 (mmmm) cc_final: 0.9499 (mmmt) REVERT: A 349 ARG cc_start: 0.8905 (mmm160) cc_final: 0.8627 (mmm160) REVERT: A 396 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9027 (mp) REVERT: A 512 LYS cc_start: 0.9219 (mttt) cc_final: 0.8676 (mttm) REVERT: A 736 PHE cc_start: 0.8989 (m-80) cc_final: 0.8646 (m-80) REVERT: B 305 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9120 (mt-10) REVERT: B 332 MET cc_start: 0.9192 (mmm) cc_final: 0.8848 (tpt) REVERT: B 349 ARG cc_start: 0.8919 (mmm-85) cc_final: 0.8328 (mtm110) REVERT: B 450 ASP cc_start: 0.9488 (m-30) cc_final: 0.9068 (t0) REVERT: B 508 MET cc_start: 0.8715 (tpt) cc_final: 0.8277 (tpt) REVERT: B 577 ASP cc_start: 0.9051 (t0) cc_final: 0.8728 (t0) REVERT: B 678 MET cc_start: 0.9221 (mmm) cc_final: 0.8913 (mmm) REVERT: B 740 MET cc_start: 0.8459 (tmm) cc_final: 0.8208 (mtp) REVERT: C 46 MET cc_start: 0.9190 (ttt) cc_final: 0.8846 (ptm) REVERT: C 305 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8498 (mp0) REVERT: C 550 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.8847 (mpp) REVERT: C 577 ASP cc_start: 0.9057 (t0) cc_final: 0.8848 (t0) REVERT: D 295 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.8967 (ptmm) REVERT: D 550 MET cc_start: 0.9548 (mpp) cc_final: 0.9032 (mpp) REVERT: D 578 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8723 (mm-30) REVERT: D 608 MET cc_start: 0.9555 (ptm) cc_final: 0.9249 (ppp) REVERT: D 611 MET cc_start: 0.9088 (mmm) cc_final: 0.8724 (mmm) REVERT: D 731 ILE cc_start: 0.9755 (OUTLIER) cc_final: 0.9365 (tp) REVERT: E 33 ASN cc_start: 0.8538 (t0) cc_final: 0.8178 (t0) REVERT: E 305 GLU cc_start: 0.8293 (mp0) cc_final: 0.7813 (mp0) REVERT: E 466 GLU cc_start: 0.9071 (tp30) cc_final: 0.8870 (tp30) REVERT: E 508 MET cc_start: -0.2863 (ttt) cc_final: -0.4334 (mmt) REVERT: E 560 ARG cc_start: 0.9516 (mtp-110) cc_final: 0.9245 (mmt180) REVERT: E 668 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8590 (mmmt) outliers start: 48 outliers final: 36 residues processed: 277 average time/residue: 0.2161 time to fit residues: 96.8763 Evaluate side-chains 270 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 600 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 374 optimal weight: 8.9990 chunk 239 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 337 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 316 optimal weight: 8.9990 chunk 320 optimal weight: 0.0970 chunk 93 optimal weight: 0.6980 chunk 311 optimal weight: 4.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 GLN D 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.079165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.053661 restraints weight = 137228.860| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 6.26 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34899 Z= 0.121 Angle : 0.692 13.075 47202 Z= 0.324 Chirality : 0.045 0.198 5337 Planarity : 0.004 0.050 6186 Dihedral : 7.206 132.119 4846 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.87 % Allowed : 11.76 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.82 (0.13), residues: 4326 helix: 1.79 (0.12), residues: 1914 sheet: 0.73 (0.18), residues: 747 loop : 0.95 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 210 TYR 0.035 0.002 TYR A 644 PHE 0.017 0.001 PHE E 503 TRP 0.041 0.002 TRP D 454 HIS 0.010 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00274 (34899) covalent geometry : angle 0.69250 (47202) hydrogen bonds : bond 0.03348 ( 1610) hydrogen bonds : angle 4.31428 ( 4500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 1.449 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: F 56 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7678 (t) REVERT: F 211 LYS cc_start: 0.8862 (tppt) cc_final: 0.8599 (tppt) REVERT: F 313 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8752 (ttm170) REVERT: F 427 MET cc_start: 0.9133 (ppp) cc_final: 0.8887 (tpt) REVERT: F 442 MET cc_start: 0.9704 (mmp) cc_final: 0.9452 (mmm) REVERT: A 315 LYS cc_start: 0.9790 (mmmm) cc_final: 0.9477 (mmmt) REVERT: A 512 LYS cc_start: 0.9233 (mttt) cc_final: 0.8770 (mttm) REVERT: A 736 PHE cc_start: 0.9009 (m-80) cc_final: 0.8632 (m-80) REVERT: B 305 GLU cc_start: 0.9306 (mt-10) cc_final: 0.9022 (mt-10) REVERT: B 450 ASP cc_start: 0.9538 (m-30) cc_final: 0.9070 (t0) REVERT: B 508 MET cc_start: 0.8623 (tpt) cc_final: 0.7911 (tpt) REVERT: B 577 ASP cc_start: 0.9010 (t0) cc_final: 0.8712 (t0) REVERT: B 678 MET cc_start: 0.9306 (mmm) cc_final: 0.8973 (mmm) REVERT: B 740 MET cc_start: 0.8479 (tmm) cc_final: 0.8246 (ppp) REVERT: C 46 MET cc_start: 0.9200 (ttt) cc_final: 0.8860 (ptm) REVERT: C 305 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8407 (mp0) REVERT: C 517 TYR cc_start: 0.9111 (p90) cc_final: 0.8820 (p90) REVERT: C 550 MET cc_start: 0.9457 (OUTLIER) cc_final: 0.8833 (mpp) REVERT: C 574 LEU cc_start: 0.9625 (tp) cc_final: 0.9338 (tt) REVERT: C 598 ASP cc_start: 0.8486 (t0) cc_final: 0.8184 (p0) REVERT: D 321 GLU cc_start: 0.9149 (mp0) cc_final: 0.8832 (mp0) REVERT: D 517 TYR cc_start: 0.9319 (p90) cc_final: 0.8903 (p90) REVERT: D 550 MET cc_start: 0.9569 (mpp) cc_final: 0.9103 (mpp) REVERT: D 578 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8765 (mm-30) REVERT: D 611 MET cc_start: 0.9063 (mmm) cc_final: 0.8693 (mmm) REVERT: D 731 ILE cc_start: 0.9742 (OUTLIER) cc_final: 0.9316 (tp) REVERT: E 33 ASN cc_start: 0.8386 (t0) cc_final: 0.7994 (t0) REVERT: E 305 GLU cc_start: 0.8310 (mp0) cc_final: 0.7829 (mp0) REVERT: E 466 GLU cc_start: 0.9106 (tp30) cc_final: 0.8719 (tp30) REVERT: E 508 MET cc_start: -0.2732 (ttt) cc_final: -0.4063 (mmt) REVERT: E 560 ARG cc_start: 0.9490 (mtp-110) cc_final: 0.9219 (mmt180) REVERT: E 668 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8610 (mmmt) outliers start: 32 outliers final: 25 residues processed: 286 average time/residue: 0.2154 time to fit residues: 99.6619 Evaluate side-chains 278 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 468 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 150 optimal weight: 0.9980 chunk 419 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 303 optimal weight: 8.9990 chunk 326 optimal weight: 2.9990 chunk 163 optimal weight: 0.0670 chunk 55 optimal weight: 50.0000 chunk 352 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.079924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054387 restraints weight = 137092.639| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 6.33 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34899 Z= 0.120 Angle : 0.671 11.805 47202 Z= 0.313 Chirality : 0.045 0.181 5337 Planarity : 0.004 0.050 6186 Dihedral : 6.911 132.427 4846 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.87 % Allowed : 11.70 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % 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: 1.92 (0.13), residues: 4326 helix: 1.90 (0.12), residues: 1902 sheet: 0.77 (0.18), residues: 749 loop : 0.98 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 313 TYR 0.036 0.001 TYR A 644 PHE 0.014 0.001 PHE D 576 TRP 0.044 0.002 TRP D 454 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00271 (34899) covalent geometry : angle 0.67064 (47202) hydrogen bonds : bond 0.03181 ( 1610) hydrogen bonds : angle 4.22230 ( 4500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7502.72 seconds wall clock time: 129 minutes 26.55 seconds (7766.55 seconds total)