Starting phenix.real_space_refine on Sun Jun 29 09:07:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fct_28992/06_2025/8fct_28992.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fct_28992/06_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_28992/06_2025/8fct_28992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fct_28992/06_2025/8fct_28992.map" model { file = "/net/cci-nas-00/data/ceres_data/8fct_28992/06_2025/8fct_28992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fct_28992/06_2025/8fct_28992.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} 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: 20.14, per 1000 atoms: 0.59 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: 9.06 Conformation dependent library (CDL) restraints added in 4.7 seconds 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: 4.93 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: 15.30 Time building geometry restraints manager: 10.65 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 763 or resid 901 throu \ gh 902)) selection = (chain 'B' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = (chain 'C' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = (chain 'D' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 902)) selection = (chain 'E' and (resid 23 through 499 or resid 509 through 763 or resid 901 throu \ gh 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.510 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 81.130 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.000 TRP F 551 HIS 0.001 0.000 HIS F 735 PHE 0.001 0.000 PHE B 758 TYR 0.001 0.000 TYR D 755 ARG 0.001 0.000 ARG F 89 Details of bonding type rmsd hydrogen bonds : bond 0.21703 ( 1610) hydrogen bonds : angle 6.40237 ( 4500) covalent geometry : bond 0.01068 (34899) covalent geometry : angle 0.81492 (47202) *********************** 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 : 4.539 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: 0.5726 time to fit residues: 679.3068 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 : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 9.9990 chunk 328 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 221 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 394 optimal weight: 0.9980 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 421 GLN A 499 HIS B 340 HIS B 602 ASN C 406 HIS D 296 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.085563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057942 restraints weight = 132482.378| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 5.77 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 34899 Z= 0.149 Angle : 0.708 10.190 47202 Z= 0.344 Chirality : 0.046 0.180 5337 Planarity : 0.005 0.061 6186 Dihedral : 9.225 161.343 4846 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.23 % Favored : 98.75 % Rotamer: Outliers : 1.38 % Allowed : 7.47 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.12), residues: 4326 helix: 1.31 (0.11), residues: 1916 sheet: 0.93 (0.18), residues: 726 loop : 1.19 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 454 HIS 0.004 0.001 HIS A 499 PHE 0.031 0.001 PHE A 674 TYR 0.023 0.002 TYR A 203 ARG 0.008 0.001 ARG C 560 Details of bonding type rmsd hydrogen bonds : bond 0.05381 ( 1610) hydrogen bonds : angle 4.70196 ( 4500) covalent geometry : bond 0.00326 (34899) covalent geometry : angle 0.70775 (47202) *********************** 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 463 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 412 time to evaluate : 4.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 139 PHE cc_start: 0.9071 (m-80) cc_final: 0.8870 (m-10) REVERT: F 320 VAL cc_start: 0.8841 (t) cc_final: 0.8503 (p) REVERT: F 366 GLU cc_start: 0.8352 (pm20) cc_final: 0.7847 (mp0) REVERT: F 442 MET cc_start: 0.9626 (mmp) cc_final: 0.9401 (mmm) REVERT: F 550 MET cc_start: 0.2978 (mmp) cc_final: 0.2754 (mtm) REVERT: A 46 MET cc_start: 0.8491 (tpp) cc_final: 0.8171 (tpp) REVERT: A 427 MET cc_start: 0.8055 (tpt) cc_final: 0.7674 (tpp) REVERT: A 465 ARG cc_start: 0.7086 (tmt170) cc_final: 0.6130 (tpt-90) REVERT: A 508 MET cc_start: 0.8410 (tpp) cc_final: 0.8095 (tpp) REVERT: A 512 LYS cc_start: 0.8948 (mttt) cc_final: 0.8418 (mttm) REVERT: A 550 MET cc_start: 0.1757 (mmp) cc_final: 0.1189 (mmt) REVERT: A 672 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8235 (pp) REVERT: A 736 PHE cc_start: 0.9178 (m-80) cc_final: 0.8859 (m-80) REVERT: B 41 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8651 (mt) REVERT: B 273 GLU cc_start: 0.9260 (tp30) cc_final: 0.8820 (tm-30) REVERT: B 402 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 449 MET cc_start: 0.8850 (tpp) cc_final: 0.8565 (tpp) REVERT: B 450 ASP cc_start: 0.9403 (m-30) cc_final: 0.9057 (t0) REVERT: B 577 ASP cc_start: 0.8923 (t0) cc_final: 0.8076 (t0) REVERT: B 578 GLU cc_start: 0.8296 (mp0) cc_final: 0.7111 (mp0) REVERT: B 675 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9369 (mp) REVERT: B 678 MET cc_start: 0.9139 (mmm) cc_final: 0.8927 (mmm) REVERT: C 46 MET cc_start: 0.8848 (ttt) cc_final: 0.8580 (ttm) REVERT: C 550 MET cc_start: 0.9411 (mpp) cc_final: 0.8836 (mpp) REVERT: C 578 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8719 (mt-10) REVERT: D 196 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8778 (mp0) REVERT: D 321 GLU cc_start: 0.8678 (mp0) cc_final: 0.8334 (mp0) REVERT: D 437 ILE cc_start: 0.7964 (tp) cc_final: 0.7740 (tp) REVERT: D 578 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8650 (mt-10) REVERT: E 275 MET cc_start: 0.9440 (mmp) cc_final: 0.9194 (mmp) REVERT: E 304 ASP cc_start: 0.8314 (t0) cc_final: 0.7550 (t0) REVERT: E 305 GLU cc_start: 0.7855 (mp0) cc_final: 0.6982 (mp0) REVERT: E 508 MET cc_start: -0.3603 (ttt) cc_final: -0.4684 (mmt) outliers start: 51 outliers final: 23 residues processed: 444 average time/residue: 0.5655 time to fit residues: 402.4012 Evaluate side-chains 354 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 328 time to evaluate : 4.927 ------------------------------------------------------------------------------- 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 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 41 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 675 LEU 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 255 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 305 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN C 421 GLN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.081746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.055586 restraints weight = 134561.422| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 5.98 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34899 Z= 0.187 Angle : 0.688 11.554 47202 Z= 0.329 Chirality : 0.046 0.202 5337 Planarity : 0.004 0.045 6186 Dihedral : 8.638 161.837 4846 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.44 % Allowed : 7.79 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.13), residues: 4326 helix: 1.58 (0.12), residues: 1930 sheet: 0.82 (0.18), residues: 732 loop : 1.18 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 454 HIS 0.004 0.001 HIS E 226 PHE 0.034 0.002 PHE A 674 TYR 0.036 0.002 TYR A 203 ARG 0.027 0.001 ARG A 741 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1610) hydrogen bonds : angle 4.53532 ( 4500) covalent geometry : bond 0.00410 (34899) covalent geometry : angle 0.68784 (47202) *********************** 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 397 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 344 time to evaluate : 4.138 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: F 46 MET cc_start: 0.8912 (ttt) cc_final: 0.8657 (ttp) REVERT: F 56 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7741 (t) REVERT: F 427 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8834 (tpt) REVERT: F 442 MET cc_start: 0.9692 (mmp) cc_final: 0.9492 (mmm) REVERT: F 550 MET cc_start: 0.4228 (mmp) cc_final: 0.3652 (mtm) REVERT: A 349 ARG cc_start: 0.8419 (mmm160) cc_final: 0.8179 (mmm160) REVERT: A 368 ASP cc_start: 0.8664 (t0) cc_final: 0.8463 (t0) REVERT: A 404 HIS cc_start: 0.8943 (t-90) cc_final: 0.8740 (t70) REVERT: A 427 MET cc_start: 0.8282 (tpt) cc_final: 0.7987 (tpp) REVERT: A 465 ARG cc_start: 0.7312 (tmt170) cc_final: 0.6300 (tpt-90) REVERT: A 470 GLU cc_start: 0.7895 (mp0) cc_final: 0.7655 (mp0) REVERT: A 512 LYS cc_start: 0.9089 (mttt) cc_final: 0.8480 (mttm) REVERT: A 550 MET cc_start: 0.1678 (mmp) cc_final: 0.1437 (mmp) REVERT: A 678 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8617 (tmm) REVERT: B 138 TYR cc_start: 0.9180 (t80) cc_final: 0.8946 (t80) REVERT: B 275 MET cc_start: 0.9315 (mmm) cc_final: 0.9056 (mmp) REVERT: B 368 ASP cc_start: 0.8831 (t0) cc_final: 0.8588 (t0) REVERT: B 449 MET cc_start: 0.8830 (tpp) cc_final: 0.8625 (tpp) REVERT: B 450 ASP cc_start: 0.9488 (m-30) cc_final: 0.9115 (t0) REVERT: B 550 MET cc_start: 0.9093 (mtm) cc_final: 0.8836 (mtm) REVERT: B 577 ASP cc_start: 0.9050 (t0) cc_final: 0.8683 (t0) REVERT: B 678 MET cc_start: 0.9192 (mmm) cc_final: 0.8927 (mmm) REVERT: C 466 GLU cc_start: 0.9237 (mm-30) cc_final: 0.9032 (mm-30) REVERT: D 162 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8353 (mm-30) REVERT: D 196 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8848 (mp0) REVERT: D 321 GLU cc_start: 0.8939 (mp0) cc_final: 0.8592 (mp0) REVERT: D 509 THR cc_start: 0.9468 (m) cc_final: 0.9266 (p) REVERT: D 546 GLU cc_start: 0.8826 (mp0) cc_final: 0.8420 (mp0) REVERT: D 578 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8806 (mm-30) REVERT: E 275 MET cc_start: 0.9551 (mmp) cc_final: 0.9306 (mmp) REVERT: E 304 ASP cc_start: 0.8478 (t0) cc_final: 0.8137 (t0) REVERT: E 332 MET cc_start: 0.9204 (mmm) cc_final: 0.9002 (mmm) REVERT: E 508 MET cc_start: -0.3323 (ttt) cc_final: -0.4503 (mmt) REVERT: E 567 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7791 (mtm-85) REVERT: E 668 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8335 (mmmt) REVERT: G 50 ASN cc_start: 0.9101 (t0) cc_final: 0.8883 (t0) outliers start: 53 outliers final: 28 residues processed: 380 average time/residue: 0.6061 time to fit residues: 371.4808 Evaluate side-chains 329 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 4.002 ------------------------------------------------------------------------------- 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 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 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 690 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 534 GLU 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 97 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 54 optimal weight: 50.0000 chunk 203 optimal weight: 2.9990 chunk 347 optimal weight: 0.9980 chunk 307 optimal weight: 4.9990 chunk 70 optimal weight: 50.0000 chunk 337 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 327 GLN B 398 GLN E 340 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.080296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054587 restraints weight = 137456.358| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 6.23 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34899 Z= 0.204 Angle : 0.676 10.776 47202 Z= 0.323 Chirality : 0.045 0.155 5337 Planarity : 0.004 0.048 6186 Dihedral : 8.128 154.124 4846 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.52 % Allowed : 8.28 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.13), residues: 4326 helix: 1.67 (0.12), residues: 1936 sheet: 0.82 (0.18), residues: 743 loop : 1.12 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 454 HIS 0.004 0.001 HIS B 183 PHE 0.033 0.001 PHE A 674 TYR 0.036 0.002 TYR E 203 ARG 0.020 0.001 ARG A 700 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 1610) hydrogen bonds : angle 4.47338 ( 4500) covalent geometry : bond 0.00444 (34899) covalent geometry : angle 0.67635 (47202) *********************** 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 354 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 5.297 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: 0.7984 (OUTLIER) cc_final: 0.7761 (t) REVERT: F 550 MET cc_start: 0.4447 (mmp) cc_final: 0.3914 (mtm) REVERT: A 404 HIS cc_start: 0.9011 (t-90) cc_final: 0.8768 (t70) REVERT: A 427 MET cc_start: 0.8197 (tpt) cc_final: 0.7960 (tpp) REVERT: A 465 ARG cc_start: 0.7462 (tmt170) cc_final: 0.6649 (tpt-90) REVERT: A 512 LYS cc_start: 0.9142 (mttt) cc_final: 0.8508 (mttm) REVERT: B 35 ASP cc_start: 0.8873 (t0) cc_final: 0.8552 (t70) REVERT: B 275 MET cc_start: 0.9401 (mmm) cc_final: 0.9168 (mmp) REVERT: B 305 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8987 (mt-10) REVERT: B 450 ASP cc_start: 0.9548 (m-30) cc_final: 0.9138 (t0) REVERT: B 577 ASP cc_start: 0.9079 (t0) cc_final: 0.8704 (t0) REVERT: B 678 MET cc_start: 0.9219 (mmm) cc_final: 0.8930 (mmm) REVERT: B 740 MET cc_start: 0.8936 (tpt) cc_final: 0.8635 (mpp) REVERT: C 150 ASP cc_start: 0.8785 (m-30) cc_final: 0.8502 (t70) REVERT: C 466 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9084 (mm-30) REVERT: C 550 MET cc_start: 0.9484 (OUTLIER) cc_final: 0.8798 (mpp) REVERT: C 608 MET cc_start: 0.9546 (ttp) cc_final: 0.9280 (ttm) REVERT: D 30 GLU cc_start: 0.8608 (pm20) cc_final: 0.8344 (pm20) REVERT: D 162 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8305 (mm-30) REVERT: D 321 GLU cc_start: 0.9110 (mp0) cc_final: 0.8757 (mp0) REVERT: D 449 MET cc_start: 0.8396 (mmm) cc_final: 0.8042 (mmm) REVERT: D 509 THR cc_start: 0.9486 (m) cc_final: 0.9270 (p) REVERT: D 578 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8805 (mm-30) REVERT: E 33 ASN cc_start: 0.8306 (t0) cc_final: 0.7928 (t0) REVERT: E 275 MET cc_start: 0.9558 (mmp) cc_final: 0.9339 (mmp) REVERT: E 304 ASP cc_start: 0.8468 (t0) cc_final: 0.8046 (t0) REVERT: E 466 GLU cc_start: 0.8785 (tp30) cc_final: 0.8556 (tp30) REVERT: E 508 MET cc_start: -0.3197 (ttt) cc_final: -0.4478 (mmt) REVERT: E 757 MET cc_start: 0.9381 (tmm) cc_final: 0.9094 (ptt) outliers start: 56 outliers final: 38 residues processed: 340 average time/residue: 0.6294 time to fit residues: 350.1367 Evaluate side-chains 309 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 3.939 ------------------------------------------------------------------------------- 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 196 GLU 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 666 VAL 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 420 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 534 GLU 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 344 MET 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 175 ILE Chi-restraints excluded: chain E residue 320 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 58 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 324 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 289 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 52 optimal weight: 30.0000 chunk 356 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.079800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054025 restraints weight = 137015.425| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 6.01 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34899 Z= 0.188 Angle : 0.662 9.641 47202 Z= 0.314 Chirality : 0.045 0.154 5337 Planarity : 0.004 0.052 6186 Dihedral : 7.799 146.018 4846 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.49 % Allowed : 9.58 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.13), residues: 4326 helix: 1.75 (0.12), residues: 1935 sheet: 0.82 (0.18), residues: 736 loop : 1.08 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 551 HIS 0.004 0.001 HIS B 183 PHE 0.017 0.001 PHE D 674 TYR 0.020 0.002 TYR A 203 ARG 0.006 0.000 ARG E 560 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 1610) hydrogen bonds : angle 4.39472 ( 4500) covalent geometry : bond 0.00413 (34899) covalent geometry : angle 0.66198 (47202) *********************** 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 334 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 279 time to evaluate : 5.419 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: F 56 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7677 (t) REVERT: A 396 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8819 (mp) REVERT: A 404 HIS cc_start: 0.9021 (t-90) cc_final: 0.8770 (t70) REVERT: A 512 LYS cc_start: 0.9155 (mttt) cc_final: 0.8549 (mttm) REVERT: B 275 MET cc_start: 0.9415 (mmm) cc_final: 0.9175 (mmp) REVERT: B 305 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8990 (mt-10) REVERT: B 450 ASP cc_start: 0.9566 (m-30) cc_final: 0.9121 (t0) REVERT: B 577 ASP cc_start: 0.9051 (t0) cc_final: 0.8669 (t0) REVERT: B 678 MET cc_start: 0.9261 (mmm) cc_final: 0.8951 (mmm) REVERT: B 740 MET cc_start: 0.8956 (tpt) cc_final: 0.8707 (mpp) REVERT: C 150 ASP cc_start: 0.8770 (m-30) cc_final: 0.8560 (t70) REVERT: C 466 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9043 (mm-30) REVERT: C 550 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.8808 (mpp) REVERT: D 30 GLU cc_start: 0.8635 (pm20) cc_final: 0.8324 (pm20) REVERT: D 578 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8762 (mm-30) REVERT: E 33 ASN cc_start: 0.8282 (t0) cc_final: 0.7911 (t0) REVERT: E 304 ASP cc_start: 0.8528 (t0) cc_final: 0.8056 (t0) REVERT: E 466 GLU cc_start: 0.8881 (tp30) cc_final: 0.8566 (tp30) REVERT: E 508 MET cc_start: -0.3063 (ttt) cc_final: -0.4405 (mmt) REVERT: E 560 ARG cc_start: 0.9479 (mtp-110) cc_final: 0.9195 (mtp180) REVERT: E 567 ARG cc_start: 0.8922 (mtm-85) cc_final: 0.8355 (mtm-85) outliers start: 55 outliers final: 38 residues processed: 322 average time/residue: 0.5241 time to fit residues: 272.4326 Evaluate side-chains 305 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 4.438 ------------------------------------------------------------------------------- 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 196 GLU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 51 LEU 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 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 489 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 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 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 120 ASP Chi-restraints excluded: chain E residue 175 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 416 optimal weight: 30.0000 chunk 419 optimal weight: 2.9990 chunk 402 optimal weight: 1.9990 chunk 356 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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** D 317 HIS D 421 GLN E 43 GLN E 327 GLN E 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.080688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054803 restraints weight = 134166.381| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 6.28 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34899 Z= 0.117 Angle : 0.639 9.422 47202 Z= 0.298 Chirality : 0.044 0.208 5337 Planarity : 0.004 0.049 6186 Dihedral : 7.471 139.969 4846 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.22 % Allowed : 10.10 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.13), residues: 4326 helix: 1.91 (0.12), residues: 1918 sheet: 0.87 (0.18), residues: 740 loop : 1.13 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 551 HIS 0.003 0.001 HIS E 226 PHE 0.022 0.001 PHE D 576 TYR 0.017 0.001 TYR A 203 ARG 0.009 0.000 ARG E 567 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 1610) hydrogen bonds : angle 4.19083 ( 4500) covalent geometry : bond 0.00260 (34899) covalent geometry : angle 0.63923 (47202) *********************** 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 347 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 3.775 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: F 56 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7687 (t) REVERT: F 320 VAL cc_start: 0.8951 (t) cc_final: 0.8741 (p) REVERT: A 46 MET cc_start: 0.9214 (tpp) cc_final: 0.8809 (tmm) REVERT: A 69 CYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8699 (t) REVERT: A 396 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8849 (mp) REVERT: A 404 HIS cc_start: 0.8983 (t-90) cc_final: 0.8707 (t70) REVERT: A 465 ARG cc_start: 0.7349 (tmt170) cc_final: 0.6623 (tpt-90) REVERT: A 512 LYS cc_start: 0.9134 (mttt) cc_final: 0.8560 (mttm) REVERT: A 550 MET cc_start: 0.2145 (mmp) cc_final: 0.1810 (mmp) REVERT: B 35 ASP cc_start: 0.8835 (t0) cc_final: 0.8540 (t70) REVERT: B 275 MET cc_start: 0.9378 (mmm) cc_final: 0.9139 (mmp) REVERT: B 305 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8997 (mt-10) REVERT: B 332 MET cc_start: 0.9334 (mmm) cc_final: 0.8923 (mmm) REVERT: B 450 ASP cc_start: 0.9505 (m-30) cc_final: 0.9046 (t0) REVERT: B 508 MET cc_start: 0.8357 (tpp) cc_final: 0.8038 (tpt) REVERT: B 577 ASP cc_start: 0.8974 (t0) cc_final: 0.8587 (t0) REVERT: B 678 MET cc_start: 0.9275 (mmm) cc_final: 0.8958 (mmm) REVERT: B 740 MET cc_start: 0.8971 (tpt) cc_final: 0.8753 (mpp) REVERT: C 150 ASP cc_start: 0.8811 (m-30) cc_final: 0.8547 (m-30) REVERT: C 517 TYR cc_start: 0.9130 (p90) cc_final: 0.8789 (p90) REVERT: C 550 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.8821 (mpp) REVERT: C 574 LEU cc_start: 0.9609 (tp) cc_final: 0.9325 (tt) REVERT: C 598 ASP cc_start: 0.8476 (t0) cc_final: 0.8170 (p0) REVERT: D 30 GLU cc_start: 0.8621 (pm20) cc_final: 0.8311 (pm20) REVERT: D 321 GLU cc_start: 0.9097 (mp0) cc_final: 0.8768 (mp0) REVERT: D 449 MET cc_start: 0.8309 (mmm) cc_final: 0.8013 (mmm) REVERT: D 550 MET cc_start: 0.9481 (mpp) cc_final: 0.9108 (mpp) REVERT: D 578 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8740 (mm-30) REVERT: D 731 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9137 (tp) REVERT: E 33 ASN cc_start: 0.8248 (t0) cc_final: 0.7855 (t0) REVERT: E 244 TYR cc_start: 0.8232 (p90) cc_final: 0.8017 (p90) REVERT: E 304 ASP cc_start: 0.8493 (t0) cc_final: 0.8052 (t0) REVERT: E 392 ASP cc_start: 0.9233 (m-30) cc_final: 0.8914 (p0) REVERT: E 460 ASN cc_start: 0.9352 (t0) cc_final: 0.9146 (p0) REVERT: E 466 GLU cc_start: 0.8969 (tp30) cc_final: 0.8642 (tp30) REVERT: E 508 MET cc_start: -0.2973 (ttt) cc_final: -0.4291 (mmt) REVERT: E 560 ARG cc_start: 0.9468 (mtp-110) cc_final: 0.9128 (mmt180) REVERT: E 567 ARG cc_start: 0.9002 (mtm-85) cc_final: 0.8761 (mtm-85) REVERT: E 668 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8531 (mmmt) outliers start: 45 outliers final: 27 residues processed: 336 average time/residue: 0.4822 time to fit residues: 258.7947 Evaluate side-chains 306 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 4.189 ------------------------------------------------------------------------------- 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 51 LEU Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 210 ARG 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 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 392 ASP 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 534 GLU 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 235 VAL 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 175 ILE Chi-restraints excluded: chain E residue 468 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 139 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 chunk 45 optimal weight: 40.0000 chunk 49 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 389 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 382 optimal weight: 4.9990 chunk 213 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 C 226 HIS D 43 GLN D 226 HIS D 285 ASN D 296 ASN D 421 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.077126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047890 restraints weight = 138061.817| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 6.19 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 34899 Z= 0.315 Angle : 0.779 11.717 47202 Z= 0.373 Chirality : 0.047 0.171 5337 Planarity : 0.005 0.054 6186 Dihedral : 7.466 134.839 4846 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.41 % Allowed : 10.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.13), residues: 4326 helix: 1.52 (0.12), residues: 1940 sheet: 0.64 (0.18), residues: 750 loop : 0.89 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 454 HIS 0.007 0.002 HIS B 183 PHE 0.021 0.002 PHE D 576 TYR 0.020 0.002 TYR A 203 ARG 0.008 0.001 ARG E 567 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 1610) hydrogen bonds : angle 4.70042 ( 4500) covalent geometry : bond 0.00680 (34899) covalent geometry : angle 0.77942 (47202) *********************** 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 310 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 258 time to evaluate : 8.227 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: 0.8027 (OUTLIER) cc_final: 0.7788 (t) REVERT: F 417 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9132 (mm-30) REVERT: A 396 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8923 (mp) REVERT: A 404 HIS cc_start: 0.8968 (t-90) cc_final: 0.8708 (t70) REVERT: A 512 LYS cc_start: 0.9127 (mttt) cc_final: 0.8570 (mttm) REVERT: A 736 PHE cc_start: 0.9039 (m-80) cc_final: 0.8716 (m-80) REVERT: A 757 MET cc_start: 0.9590 (mtm) cc_final: 0.9340 (tmm) REVERT: B 158 MET cc_start: 0.9448 (mmp) cc_final: 0.9246 (mmp) REVERT: B 275 MET cc_start: 0.9377 (mmm) cc_final: 0.9163 (mmp) REVERT: B 305 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9078 (mt-10) REVERT: B 450 ASP cc_start: 0.9455 (m-30) cc_final: 0.9038 (t0) REVERT: B 678 MET cc_start: 0.9251 (mmm) cc_final: 0.8932 (mmm) REVERT: C 550 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.8855 (mpp) REVERT: C 611 MET cc_start: 0.8093 (ppp) cc_final: 0.7268 (ppp) REVERT: D 30 GLU cc_start: 0.8797 (pm20) cc_final: 0.8436 (pm20) REVERT: D 231 LYS cc_start: 0.9688 (ptmt) cc_final: 0.9458 (ptpp) REVERT: D 313 ARG cc_start: 0.9041 (mmm-85) cc_final: 0.8818 (tpt170) REVERT: D 449 MET cc_start: 0.8328 (mmm) cc_final: 0.8049 (mmm) REVERT: D 578 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8755 (mm-30) REVERT: D 611 MET cc_start: 0.9087 (mmm) cc_final: 0.8839 (mmm) REVERT: D 731 ILE cc_start: 0.9749 (OUTLIER) cc_final: 0.9283 (tp) REVERT: E 33 ASN cc_start: 0.8520 (t0) cc_final: 0.8196 (t0) REVERT: E 305 GLU cc_start: 0.8279 (mp0) cc_final: 0.7868 (mp0) REVERT: E 508 MET cc_start: -0.2797 (ttt) cc_final: -0.4089 (mmt) REVERT: E 567 ARG cc_start: 0.8990 (mtm-85) cc_final: 0.8602 (mtm110) REVERT: E 668 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8480 (mmmt) outliers start: 52 outliers final: 42 residues processed: 304 average time/residue: 0.7144 time to fit residues: 359.6188 Evaluate side-chains 283 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 7.217 ------------------------------------------------------------------------------- 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 51 LEU Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 210 ARG 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 112 LYS 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 392 ASP 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 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 96 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 198 LEU 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 312 optimal weight: 0.6980 chunk 293 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 412 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 D 348 ASN D 421 GLN E 351 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.077929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.052038 restraints weight = 136948.650| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 6.32 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34899 Z= 0.193 Angle : 0.701 11.818 47202 Z= 0.331 Chirality : 0.045 0.183 5337 Planarity : 0.004 0.049 6186 Dihedral : 7.377 131.663 4846 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.36 % Allowed : 11.13 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.13), residues: 4326 helix: 1.67 (0.12), residues: 1937 sheet: 0.70 (0.18), residues: 748 loop : 0.91 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 454 HIS 0.005 0.001 HIS B 183 PHE 0.021 0.001 PHE D 576 TYR 0.018 0.002 TYR A 203 ARG 0.008 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 1610) hydrogen bonds : angle 4.48264 ( 4500) covalent geometry : bond 0.00425 (34899) covalent geometry : angle 0.70142 (47202) *********************** 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 310 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 time to evaluate : 4.602 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: 0.7871 (OUTLIER) cc_final: 0.7639 (t) REVERT: A 315 LYS cc_start: 0.9724 (mmmt) cc_final: 0.9499 (mmmt) REVERT: A 396 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8913 (mp) REVERT: A 404 HIS cc_start: 0.9052 (t-90) cc_final: 0.8800 (t70) REVERT: A 512 LYS cc_start: 0.9233 (mttt) cc_final: 0.8702 (mttm) REVERT: A 736 PHE cc_start: 0.9117 (m-80) cc_final: 0.8750 (m-80) REVERT: B 35 ASP cc_start: 0.9011 (t0) cc_final: 0.8658 (t70) REVERT: B 150 ASP cc_start: 0.8864 (t0) cc_final: 0.8574 (m-30) REVERT: B 275 MET cc_start: 0.9437 (mmm) cc_final: 0.9213 (mmp) REVERT: B 305 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9030 (mt-10) REVERT: B 332 MET cc_start: 0.9428 (mmm) cc_final: 0.9182 (mmm) REVERT: B 450 ASP cc_start: 0.9506 (m-30) cc_final: 0.9047 (t0) REVERT: B 508 MET cc_start: 0.8470 (tpp) cc_final: 0.8192 (tpt) REVERT: B 678 MET cc_start: 0.9290 (mmm) cc_final: 0.8980 (mmm) REVERT: C 442 MET cc_start: 0.9434 (mtm) cc_final: 0.8669 (mpp) REVERT: C 517 TYR cc_start: 0.9169 (p90) cc_final: 0.8886 (p90) REVERT: C 550 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.8857 (mpp) REVERT: C 611 MET cc_start: 0.8077 (ppp) cc_final: 0.7273 (ppp) REVERT: D 30 GLU cc_start: 0.8776 (pm20) cc_final: 0.8430 (pm20) REVERT: D 313 ARG cc_start: 0.9078 (mmm-85) cc_final: 0.8807 (tpt170) REVERT: D 578 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8755 (mm-30) REVERT: D 611 MET cc_start: 0.9099 (mmm) cc_final: 0.8799 (mmm) REVERT: D 731 ILE cc_start: 0.9754 (OUTLIER) cc_final: 0.9269 (tp) REVERT: E 33 ASN cc_start: 0.8388 (t0) cc_final: 0.8009 (t0) REVERT: E 305 GLU cc_start: 0.8279 (mp0) cc_final: 0.7837 (mp0) REVERT: E 466 GLU cc_start: 0.8941 (tp30) cc_final: 0.8667 (tp30) REVERT: E 508 MET cc_start: -0.2827 (ttt) cc_final: -0.4119 (mmt) REVERT: E 560 ARG cc_start: 0.9485 (mtp-110) cc_final: 0.9233 (mmt180) REVERT: E 668 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8579 (mmmt) outliers start: 50 outliers final: 38 residues processed: 303 average time/residue: 0.5390 time to fit residues: 265.9084 Evaluate side-chains 287 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 4.878 ------------------------------------------------------------------------------- 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 459 SER Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain A residue 51 LEU 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 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 359 ARG 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 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 295 LYS Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 492 LEU 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 175 ILE Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain G residue 62 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 95 optimal weight: 4.9990 chunk 404 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 351 optimal weight: 0.0170 chunk 401 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 292 optimal weight: 0.1980 chunk 149 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 84 optimal weight: 0.0970 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 GLN D 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.080203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.054273 restraints weight = 135587.566| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 6.41 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34899 Z= 0.114 Angle : 0.688 13.728 47202 Z= 0.323 Chirality : 0.045 0.214 5337 Planarity : 0.004 0.051 6186 Dihedral : 7.080 132.429 4846 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.00 % Allowed : 11.38 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.13), residues: 4326 helix: 1.86 (0.12), residues: 1914 sheet: 0.84 (0.18), residues: 743 loop : 1.07 (0.16), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 454 HIS 0.004 0.001 HIS E 406 PHE 0.025 0.001 PHE E 674 TYR 0.027 0.001 TYR E 244 ARG 0.008 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 1610) hydrogen bonds : angle 4.18492 ( 4500) covalent geometry : bond 0.00251 (34899) covalent geometry : angle 0.68836 (47202) *********************** 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 323 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 3.981 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: F 56 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7673 (t) REVERT: F 211 LYS cc_start: 0.8847 (tppt) cc_final: 0.8565 (tppt) REVERT: A 315 LYS cc_start: 0.9751 (mmmt) cc_final: 0.9541 (mmmm) REVERT: A 332 MET cc_start: 0.9619 (tpt) cc_final: 0.9319 (tpt) REVERT: A 512 LYS cc_start: 0.9225 (mttt) cc_final: 0.8736 (mttm) REVERT: A 550 MET cc_start: 0.2521 (mmp) cc_final: 0.2298 (mmp) REVERT: A 736 PHE cc_start: 0.9123 (m-80) cc_final: 0.8914 (m-80) REVERT: A 740 MET cc_start: 0.8651 (tmm) cc_final: 0.7582 (mtp) REVERT: B 35 ASP cc_start: 0.8996 (t0) cc_final: 0.8646 (t70) REVERT: B 150 ASP cc_start: 0.8828 (t0) cc_final: 0.8593 (m-30) REVERT: B 305 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9059 (mt-10) REVERT: B 349 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8390 (mtp-110) REVERT: B 450 ASP cc_start: 0.9469 (m-30) cc_final: 0.8947 (t0) REVERT: B 508 MET cc_start: 0.8415 (tpp) cc_final: 0.8075 (tpt) REVERT: B 678 MET cc_start: 0.9320 (mmm) cc_final: 0.8984 (mmm) REVERT: C 46 MET cc_start: 0.9180 (ttt) cc_final: 0.8846 (ptm) REVERT: C 442 MET cc_start: 0.9284 (mtm) cc_final: 0.9042 (mpp) REVERT: C 449 MET cc_start: 0.8563 (tpp) cc_final: 0.8299 (mmm) REVERT: C 517 TYR cc_start: 0.9076 (p90) cc_final: 0.8783 (p90) REVERT: C 550 MET cc_start: 0.9454 (OUTLIER) cc_final: 0.8841 (mpp) REVERT: C 574 LEU cc_start: 0.9590 (tp) cc_final: 0.9300 (tt) REVERT: C 611 MET cc_start: 0.8030 (ppp) cc_final: 0.7124 (ppp) REVERT: D 313 ARG cc_start: 0.9082 (mmm-85) cc_final: 0.8815 (tpt170) REVERT: D 564 ASP cc_start: 0.9641 (t0) cc_final: 0.9417 (m-30) REVERT: D 578 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8763 (mm-30) REVERT: D 608 MET cc_start: 0.9623 (ptm) cc_final: 0.9200 (ppp) REVERT: D 611 MET cc_start: 0.9029 (mmm) cc_final: 0.8731 (mmm) REVERT: D 731 ILE cc_start: 0.9734 (OUTLIER) cc_final: 0.9277 (tp) REVERT: E 33 ASN cc_start: 0.8309 (t0) cc_final: 0.7916 (t0) REVERT: E 305 GLU cc_start: 0.8319 (mp0) cc_final: 0.7848 (mp0) REVERT: E 508 MET cc_start: -0.2899 (ttt) cc_final: -0.4169 (mmt) REVERT: E 560 ARG cc_start: 0.9456 (mtp-110) cc_final: 0.9204 (mmt180) REVERT: E 668 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8589 (mmmt) outliers start: 37 outliers final: 24 residues processed: 317 average time/residue: 0.4687 time to fit residues: 243.1339 Evaluate side-chains 287 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 5.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain A residue 51 LEU 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 82 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain C residue 534 GLU 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 492 LEU Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 351 ASN 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 256 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 376 optimal weight: 0.0570 chunk 383 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 380 optimal weight: 5.9990 chunk 237 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 overall best weight: 2.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.078941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.053377 restraints weight = 137620.288| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 6.36 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34899 Z= 0.153 Angle : 0.697 11.061 47202 Z= 0.326 Chirality : 0.045 0.216 5337 Planarity : 0.004 0.049 6186 Dihedral : 6.999 131.940 4846 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.84 % Allowed : 12.00 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.13), residues: 4326 helix: 1.83 (0.12), residues: 1941 sheet: 0.81 (0.18), residues: 743 loop : 1.03 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 454 HIS 0.004 0.001 HIS E 226 PHE 0.026 0.001 PHE E 674 TYR 0.042 0.002 TYR A 644 ARG 0.006 0.000 ARG E 567 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 1610) hydrogen bonds : angle 4.27335 ( 4500) covalent geometry : bond 0.00344 (34899) covalent geometry : angle 0.69660 (47202) ********************** 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 298 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 267 time to evaluate : 4.190 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: 0.7829 (OUTLIER) cc_final: 0.7604 (t) REVERT: F 211 LYS cc_start: 0.8882 (tppt) cc_final: 0.8627 (tppt) REVERT: A 349 ARG cc_start: 0.8901 (mmm160) cc_final: 0.8593 (mmm160) REVERT: A 512 LYS cc_start: 0.9267 (mttt) cc_final: 0.8761 (mttm) REVERT: A 736 PHE cc_start: 0.9164 (m-80) cc_final: 0.8941 (m-80) REVERT: A 740 MET cc_start: 0.8630 (tmm) cc_final: 0.7564 (mtp) REVERT: A 757 MET cc_start: 0.9620 (mtm) cc_final: 0.9352 (tmm) REVERT: B 35 ASP cc_start: 0.9038 (t0) cc_final: 0.8685 (t70) REVERT: B 150 ASP cc_start: 0.8812 (t0) cc_final: 0.8553 (m-30) REVERT: B 305 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9060 (mt-10) REVERT: B 450 ASP cc_start: 0.9529 (m-30) cc_final: 0.9056 (t0) REVERT: B 508 MET cc_start: 0.8438 (tpp) cc_final: 0.8097 (tpt) REVERT: B 678 MET cc_start: 0.9337 (mmm) cc_final: 0.9003 (mmm) REVERT: C 46 MET cc_start: 0.9233 (ttt) cc_final: 0.8894 (ptm) REVERT: C 442 MET cc_start: 0.9377 (mtm) cc_final: 0.9101 (mpp) REVERT: C 517 TYR cc_start: 0.9150 (p90) cc_final: 0.8796 (p90) REVERT: C 550 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.8794 (mpp) REVERT: C 574 LEU cc_start: 0.9603 (tp) cc_final: 0.9311 (tt) REVERT: C 611 MET cc_start: 0.8100 (ppp) cc_final: 0.7198 (ppp) REVERT: D 313 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8813 (tpt170) REVERT: D 449 MET cc_start: 0.8173 (mmm) cc_final: 0.7854 (mmm) REVERT: D 564 ASP cc_start: 0.9634 (t0) cc_final: 0.9420 (m-30) REVERT: D 578 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8739 (mm-30) REVERT: D 608 MET cc_start: 0.9669 (ptm) cc_final: 0.9155 (ppp) REVERT: D 611 MET cc_start: 0.9044 (mmm) cc_final: 0.8707 (mmm) REVERT: D 731 ILE cc_start: 0.9758 (OUTLIER) cc_final: 0.9297 (tp) REVERT: E 33 ASN cc_start: 0.8399 (t0) cc_final: 0.8012 (t0) REVERT: E 305 GLU cc_start: 0.8319 (mp0) cc_final: 0.7837 (mp0) REVERT: E 508 MET cc_start: -0.2783 (ttt) cc_final: -0.4031 (mmm) REVERT: E 560 ARG cc_start: 0.9465 (mtp-110) cc_final: 0.9213 (mmt180) REVERT: E 668 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8586 (mmmt) outliers start: 31 outliers final: 25 residues processed: 294 average time/residue: 0.4845 time to fit residues: 232.9046 Evaluate side-chains 283 residues out of total 3700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain A residue 51 LEU 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 678 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 278 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 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 295 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 175 ILE 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 203 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.079470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053765 restraints weight = 137242.904| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 6.21 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34899 Z= 0.140 Angle : 0.692 14.668 47202 Z= 0.325 Chirality : 0.045 0.186 5337 Planarity : 0.004 0.050 6186 Dihedral : 6.941 131.997 4846 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.79 % Allowed : 11.97 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.13), residues: 4326 helix: 1.86 (0.12), residues: 1933 sheet: 0.86 (0.18), residues: 740 loop : 1.05 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 454 HIS 0.010 0.001 HIS D 340 PHE 0.027 0.001 PHE E 674 TYR 0.029 0.002 TYR A 495 ARG 0.006 0.000 ARG B 741 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 1610) hydrogen bonds : angle 4.28397 ( 4500) covalent geometry : bond 0.00316 (34899) covalent geometry : angle 0.69237 (47202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17848.09 seconds wall clock time: 317 minutes 47.38 seconds (19067.38 seconds total)