Starting phenix.real_space_refine on Mon Sep 14 05:32:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d05_7785/09_2026/6d05_7785.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d05_7785/09_2026/6d05_7785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d05_7785/09_2026/6d05_7785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d05_7785/09_2026/6d05_7785.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6d05_7785/09_2026/6d05_7785.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d05_7785/09_2026/6d05_7785.cif" model { file = "/net/cci-nas-00/data/ceres_data/6d05_7785/09_2026/6d05_7785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d05_7785/09_2026/6d05_7785.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 S 142 5.16 5 C 18252 2.51 5 N 4850 2.21 5 O 5498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28748 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 458} Chain: "F" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 458} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.89, per 1000 atoms: 0.20 Number of scatterers: 28748 At special positions: 0 Unit cell: (171.45, 148.5, 163.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 142 16.00 O 5498 8.00 N 4850 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.03 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.02 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.04 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.02 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.02 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.02 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.02 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.02 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.04 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.04 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.02 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS F 240 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 316 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG B 802 " - " ASN B 251 " " NAG C 707 " - " ASN C 611 " " NAG D 707 " - " ASN D 611 " " NAG G 1 " - " ASN A 317 " " NAG H 1 " - " ASN A 727 " " NAG I 1 " - " ASN B 317 " " NAG J 1 " - " ASN B 727 " " NAG K 1 " - " ASN C 413 " " NAG L 1 " - " ASN D 413 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6740 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 28 sheets defined 50.9% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.802A pdb=" N SER A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 159 through 176 Processing helix chain 'A' and resid 239 through 245 removed outlier: 3.530A pdb=" N ASP A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.555A pdb=" N LYS A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 415 through 439 removed outlier: 3.606A pdb=" N SER A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.525A pdb=" N THR A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 583 through 603 removed outlier: 3.697A pdb=" N VAL A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 627 removed outlier: 3.547A pdb=" N GLN A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.503A pdb=" N ILE A 632 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.674A pdb=" N TYR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 684 removed outlier: 3.520A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 674 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 683 " --> pdb=" O MET A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 722 removed outlier: 3.846A pdb=" N LYS A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 750 removed outlier: 3.628A pdb=" N SER A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.801A pdb=" N SER B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 159 through 176 Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.529A pdb=" N ASP B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.555A pdb=" N LYS B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 415 through 439 removed outlier: 3.605A pdb=" N SER B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY B 422 " --> pdb=" O LYS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.525A pdb=" N THR B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 583 through 603 removed outlier: 3.697A pdb=" N VAL B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 627 removed outlier: 3.546A pdb=" N GLN B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 removed outlier: 3.502A pdb=" N ILE B 632 " --> pdb=" O TYR B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 662 removed outlier: 3.675A pdb=" N TYR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 684 removed outlier: 3.520A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU B 682 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 removed outlier: 3.846A pdb=" N LYS B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 750 removed outlier: 3.627A pdb=" N SER B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 30 removed outlier: 3.600A pdb=" N ILE C 30 " --> pdb=" O MET C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 63 through 72 removed outlier: 4.123A pdb=" N LEU C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.539A pdb=" N LEU C 214 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 259 through 275 removed outlier: 3.945A pdb=" N ILE C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'C' and resid 350 through 362 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.847A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 472 removed outlier: 3.775A pdb=" N LEU C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 528 Processing helix chain 'C' and resid 536 through 542 removed outlier: 3.732A pdb=" N GLN C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 593 through 609 removed outlier: 3.906A pdb=" N HIS C 606 " --> pdb=" O ARG C 602 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 652 removed outlier: 3.696A pdb=" N TYR C 650 " --> pdb=" O THR C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 663 Processing helix chain 'C' and resid 668 through 677 Processing helix chain 'D' and resid 12 through 30 removed outlier: 3.599A pdb=" N ILE D 30 " --> pdb=" O MET D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 63 through 72 removed outlier: 4.123A pdb=" N LEU D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 135 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 187 through 197 Processing helix chain 'D' and resid 208 through 214 removed outlier: 3.539A pdb=" N LEU D 214 " --> pdb=" O ILE D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 259 through 275 removed outlier: 3.945A pdb=" N ILE D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 317 through 329 Processing helix chain 'D' and resid 350 through 362 Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 392 through 403 removed outlier: 3.848A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.775A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 528 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.733A pdb=" N GLN D 540 " --> pdb=" O GLN D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 Processing helix chain 'D' and resid 593 through 609 removed outlier: 3.906A pdb=" N HIS D 606 " --> pdb=" O ARG D 602 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.695A pdb=" N TYR D 650 " --> pdb=" O THR D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 663 Processing helix chain 'D' and resid 668 through 677 Processing helix chain 'E' and resid 196 through 210 removed outlier: 4.383A pdb=" N TYR E 200 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 256 removed outlier: 4.653A pdb=" N THR E 246 " --> pdb=" O ARG E 242 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU E 250 " --> pdb=" O THR E 246 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 263 removed outlier: 4.248A pdb=" N GLN E 263 " --> pdb=" O LYS E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 307 removed outlier: 3.568A pdb=" N LYS E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.710A pdb=" N MET E 335 " --> pdb=" O ASP E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 365 removed outlier: 3.931A pdb=" N LYS E 363 " --> pdb=" O ARG E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 406 removed outlier: 4.479A pdb=" N ILE E 371 " --> pdb=" O ASN E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 477 removed outlier: 4.174A pdb=" N ASP E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLY E 463 " --> pdb=" O GLY E 459 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER E 475 " --> pdb=" O LYS E 471 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR E 477 " --> pdb=" O ILE E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 513 removed outlier: 3.590A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU E 512 " --> pdb=" O GLU E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 567 removed outlier: 3.936A pdb=" N ASN E 566 " --> pdb=" O SER E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 633 removed outlier: 4.036A pdb=" N ASP E 578 " --> pdb=" O GLN E 574 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER E 593 " --> pdb=" O TYR E 589 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 210 removed outlier: 4.383A pdb=" N TYR F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 256 removed outlier: 4.653A pdb=" N THR F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU F 250 " --> pdb=" O THR F 246 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 263 removed outlier: 4.248A pdb=" N GLN F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 307 removed outlier: 3.568A pdb=" N LYS F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.710A pdb=" N MET F 335 " --> pdb=" O ASP F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 365 removed outlier: 3.930A pdb=" N LYS F 363 " --> pdb=" O ARG F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 406 removed outlier: 4.479A pdb=" N ILE F 371 " --> pdb=" O ASN F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 477 removed outlier: 4.174A pdb=" N ASP F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU F 460 " --> pdb=" O ASN F 456 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLY F 463 " --> pdb=" O GLY F 459 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N HIS F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP F 474 " --> pdb=" O SER F 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER F 475 " --> pdb=" O LYS F 471 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR F 477 " --> pdb=" O ILE F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 513 removed outlier: 3.591A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU F 512 " --> pdb=" O GLU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 567 removed outlier: 3.936A pdb=" N ASN F 566 " --> pdb=" O SER F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 633 removed outlier: 4.035A pdb=" N ASP F 578 " --> pdb=" O GLN F 574 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE F 592 " --> pdb=" O SER F 588 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER F 593 " --> pdb=" O TYR F 589 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 193 removed outlier: 3.583A pdb=" N VAL A 403 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR A 402 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR A 480 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A 555 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 214 removed outlier: 7.411A pdb=" N VAL A 200 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.267A pdb=" N VAL A 233 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ARG A 258 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 279 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 193 removed outlier: 3.583A pdb=" N VAL B 403 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR B 402 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 480 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 210 through 214 removed outlier: 7.411A pdb=" N VAL B 200 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.267A pdb=" N VAL B 233 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ARG B 258 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 279 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AB2, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AB3, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.530A pdb=" N ALA C 253 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.427A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 204 " --> pdb=" O CYS C 118 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA C 99 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 225 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 233 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.427A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 204 " --> pdb=" O CYS C 118 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 347 removed outlier: 6.002A pdb=" N VAL C 342 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 369 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TRP C 344 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALA C 371 " --> pdb=" O TRP C 344 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA C 346 " --> pdb=" O ALA C 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 388 through 391 removed outlier: 3.767A pdb=" N LEU C 408 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR C 589 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 530 through 534 Processing sheet with id=AB9, first strand: chain 'C' and resid 530 through 534 removed outlier: 3.912A pdb=" N ALA C 580 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 449 through 450 removed outlier: 6.983A pdb=" N SER C 449 " --> pdb=" O CYS C 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 8 through 10 Processing sheet with id=AC3, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.531A pdb=" N ALA D 253 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.428A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 204 " --> pdb=" O CYS D 118 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA D 99 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 225 " --> pdb=" O LYS D 233 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 233 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.428A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 204 " --> pdb=" O CYS D 118 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 342 through 347 removed outlier: 6.002A pdb=" N VAL D 342 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL D 369 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TRP D 344 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA D 371 " --> pdb=" O TRP D 344 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA D 346 " --> pdb=" O ALA D 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 388 through 391 removed outlier: 3.767A pdb=" N LEU D 408 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 589 " --> pdb=" O PRO D 406 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 530 through 534 Processing sheet with id=AC9, first strand: chain 'D' and resid 530 through 534 removed outlier: 3.914A pdb=" N ALA D 580 " --> pdb=" O ALA D 428 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 449 through 450 removed outlier: 6.983A pdb=" N SER D 449 " --> pdb=" O CYS D 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 1492 hydrogen bonds defined for protein. 4386 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: 5.72 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9261 1.34 - 1.47: 7200 1.47 - 1.59: 12707 1.59 - 1.72: 0 1.72 - 1.84: 192 Bond restraints: 29360 Sorted by residual: bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 NAG C 707 " pdb=" O5 NAG C 707 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.29e+00 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 38136 2.57 - 5.14: 1335 5.14 - 7.70: 137 7.70 - 10.27: 44 10.27 - 12.84: 12 Bond angle restraints: 39664 Sorted by residual: angle pdb=" C ASN C 461 " pdb=" N ILE C 462 " pdb=" CA ILE C 462 " ideal model delta sigma weight residual 120.24 123.62 -3.38 6.30e-01 2.52e+00 2.87e+01 angle pdb=" C LEU D 629 " pdb=" N LEU D 630 " pdb=" CA LEU D 630 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" C LEU C 629 " pdb=" N LEU C 630 " pdb=" CA LEU C 630 " ideal model delta sigma weight residual 121.54 131.73 -10.19 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C ASN D 461 " pdb=" N ILE D 462 " pdb=" CA ILE D 462 " ideal model delta sigma weight residual 120.24 123.60 -3.36 6.30e-01 2.52e+00 2.85e+01 angle pdb=" C ALA C 54 " pdb=" N ASN C 55 " pdb=" CA ASN C 55 " ideal model delta sigma weight residual 122.61 130.74 -8.13 1.56e+00 4.11e-01 2.72e+01 ... (remaining 39659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 16468 17.27 - 34.54: 934 34.54 - 51.81: 233 51.81 - 69.08: 22 69.08 - 86.35: 49 Dihedral angle restraints: 17706 sinusoidal: 7234 harmonic: 10472 Sorted by residual: dihedral pdb=" CA VAL C 1 " pdb=" C VAL C 1 " pdb=" N PRO C 2 " pdb=" CA PRO C 2 " ideal model delta harmonic sigma weight residual -180.00 -93.65 -86.35 0 5.00e+00 4.00e-02 2.98e+02 dihedral pdb=" CA VAL D 1 " pdb=" C VAL D 1 " pdb=" N PRO D 2 " pdb=" CA PRO D 2 " ideal model delta harmonic sigma weight residual -180.00 -93.74 -86.26 0 5.00e+00 4.00e-02 2.98e+02 dihedral pdb=" CA ASP F 407 " pdb=" C ASP F 407 " pdb=" N GLY F 408 " pdb=" CA GLY F 408 " ideal model delta harmonic sigma weight residual -180.00 -105.57 -74.43 0 5.00e+00 4.00e-02 2.22e+02 ... (remaining 17703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4308 0.180 - 0.359: 42 0.359 - 0.539: 2 0.539 - 0.719: 1 0.719 - 0.899: 1 Chirality restraints: 4354 Sorted by residual: chirality pdb=" C1 NAG D 707 " pdb=" ND2 ASN D 611 " pdb=" C2 NAG D 707 " pdb=" O5 NAG D 707 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 251 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C 707 " pdb=" ND2 ASN C 611 " pdb=" C2 NAG C 707 " pdb=" O5 NAG C 707 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 4351 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 728 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C GLU B 728 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU B 728 " -0.020 2.00e-02 2.50e+03 pdb=" N THR B 729 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 728 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C GLU A 728 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU A 728 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 729 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 727 " 0.028 2.00e-02 2.50e+03 2.62e-02 8.59e+00 pdb=" CG ASN B 727 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 727 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 727 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.031 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 268 2.62 - 3.19: 24748 3.19 - 3.76: 44297 3.76 - 4.33: 59133 4.33 - 4.90: 96973 Nonbonded interactions: 225419 Sorted by model distance: nonbonded pdb=" OH TYR D 95 " pdb="FE FE D 703 " model vdw 2.046 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.051 2.260 nonbonded pdb=" OH TYR D 517 " pdb="FE FE D 701 " model vdw 2.055 2.260 nonbonded pdb=" OH TYR C 517 " pdb="FE FE C 701 " model vdw 2.066 2.260 nonbonded pdb="FE FE D 703 " pdb=" O2 CO3 D 704 " model vdw 2.078 2.260 ... (remaining 225414 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 26.000 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.009 0.091 29422 Z= 0.396 Angle : 1.172 20.731 39804 Z= 0.646 Chirality : 0.061 0.899 4354 Planarity : 0.007 0.067 5106 Dihedral : 12.240 86.350 10828 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.28 % Allowed : 7.61 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 1.56 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.11), residues: 3560 helix: -1.98 (0.10), residues: 1720 sheet: -2.10 (0.23), residues: 372 loop : -2.28 (0.13), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 50 TYR 0.031 0.003 TYR F 552 PHE 0.039 0.004 PHE A 346 TRP 0.035 0.004 TRP D 358 HIS 0.019 0.003 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.40 (29360) covalent geometry : angle 1.13652 / 0.64 (39664) SS BOND : bond 0.00680 / 0.42 ( 46) SS BOND : angle 2.16811 / 1.54 ( 92) hydrogen bonds : bond 0.16230 / 10.46 ( 1474) hydrogen bonds : angle 8.59687 / 5.94 ( 4386) link_BETA1-4 : bond 0.01961 / 0.90 ( 6) link_BETA1-4 : angle 7.39746 / 4.26 ( 18) link_NAG-ASN : bond 0.01696 / 0.81 ( 10) link_NAG-ASN : angle 8.20912 / 5.22 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 397 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8642 (tm) REVERT: A 365 MET cc_start: 0.8887 (mmm) cc_final: 0.8679 (mmm) REVERT: A 536 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8248 (p) REVERT: A 671 MET cc_start: 0.8239 (mmm) cc_final: 0.8019 (mmt) REVERT: B 246 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8206 (tm) REVERT: B 349 MET cc_start: 0.8658 (mmt) cc_final: 0.8351 (mmt) REVERT: B 453 TRP cc_start: 0.7613 (m-10) cc_final: 0.7311 (m-10) REVERT: B 655 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7547 (tpp80) REVERT: B 659 ASP cc_start: 0.7798 (m-30) cc_final: 0.7236 (m-30) REVERT: B 671 MET cc_start: 0.8791 (mmm) cc_final: 0.8216 (mmt) REVERT: C 26 MET cc_start: 0.8084 (mmt) cc_final: 0.7744 (tpp) REVERT: C 391 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9026 (pt) REVERT: C 464 MET cc_start: 0.8992 (mmt) cc_final: 0.8683 (mmm) REVERT: C 613 THR cc_start: 0.8145 (p) cc_final: 0.7919 (m) REVERT: D 26 MET cc_start: 0.8083 (mmt) cc_final: 0.7848 (mmt) REVERT: D 464 MET cc_start: 0.8743 (mmt) cc_final: 0.8477 (mmm) REVERT: E 175 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7852 (mp) REVERT: E 306 LEU cc_start: 0.6491 (tt) cc_final: 0.6202 (tp) REVERT: E 324 MET cc_start: 0.6659 (tpp) cc_final: 0.5629 (mmm) REVERT: F 306 LEU cc_start: 0.6458 (tt) cc_final: 0.6154 (tp) REVERT: F 324 MET cc_start: 0.6831 (tpp) cc_final: 0.5682 (mmm) REVERT: F 335 MET cc_start: 0.7409 (tmm) cc_final: 0.7108 (tmm) outliers start: 40 outliers final: 5 residues processed: 432 average time/residue: 0.2081 time to fit residues: 136.6220 Evaluate side-chains 164 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain F residue 175 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 150 ASN A 186 HIS A 275 ASN A 483 ASN A 615 ASN A 626 ASN A 715 ASN A 722 ASN A 743 GLN B 148 ASN B 150 ASN B 186 HIS B 275 ASN B 483 ASN B 626 ASN B 640 GLN B 715 ASN B 722 ASN C 55 ASN C 111 GLN C 207 HIS C 213 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS C 417 ASN C 443 ASN C 451 HIS D 55 ASN D 111 GLN D 207 HIS D 213 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 HIS D 300 HIS D 417 ASN D 451 HIS E 252 ASN E 263 GLN E 273 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 ASN E 428 ASN E 444 ASN E 456 ASN E 503 ASN E 528 ASN E 540 GLN E 591 ASN F 252 ASN F 263 GLN F 273 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN F 428 ASN F 444 ASN F 456 ASN F 464 HIS F 528 ASN F 540 GLN F 591 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082592 restraints weight = 64666.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.080777 restraints weight = 86215.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.081563 restraints weight = 90737.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082782 restraints weight = 56156.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082916 restraints weight = 47411.777| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29422 Z= 0.198 Angle : 0.729 12.652 39804 Z= 0.383 Chirality : 0.045 0.314 4354 Planarity : 0.005 0.053 5106 Dihedral : 6.115 53.997 3890 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.91 % Allowed : 9.46 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 1.56 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 3560 helix: 0.15 (0.12), residues: 1750 sheet: -1.70 (0.24), residues: 368 loop : -1.85 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 264 TYR 0.041 0.002 TYR F 525 PHE 0.020 0.002 PHE E 462 TRP 0.026 0.002 TRP B 740 HIS 0.013 0.001 HIS F 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (29360) covalent geometry : angle 0.71822 / 0.38 (39664) SS BOND : bond 0.00476 / 0.27 ( 46) SS BOND : angle 1.56396 / 1.04 ( 92) hydrogen bonds : bond 0.07248 / 4.62 ( 1474) hydrogen bonds : angle 5.58570 / 3.84 ( 4386) link_BETA1-4 : bond 0.00939 / 0.42 ( 6) link_BETA1-4 : angle 3.91131 / 2.26 ( 18) link_NAG-ASN : bond 0.00755 / 0.35 ( 10) link_NAG-ASN : angle 2.65549 / 1.67 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 182 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8785 (tm) REVERT: A 349 MET cc_start: 0.8209 (mmm) cc_final: 0.7936 (mmm) REVERT: B 246 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8531 (tm) REVERT: B 635 MET cc_start: 0.8285 (mtm) cc_final: 0.8069 (mtm) REVERT: B 671 MET cc_start: 0.8954 (mmm) cc_final: 0.7871 (mmt) REVERT: C 216 ASN cc_start: 0.7518 (t0) cc_final: 0.7125 (m-40) REVERT: C 391 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8456 (pp) REVERT: D 374 THR cc_start: 0.9436 (OUTLIER) cc_final: 0.9202 (m) REVERT: D 382 MET cc_start: 0.8852 (mtp) cc_final: 0.8560 (ttm) REVERT: E 175 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7727 (mp) REVERT: E 335 MET cc_start: 0.6591 (tmm) cc_final: 0.6281 (tpp) REVERT: F 324 MET cc_start: 0.6397 (tpp) cc_final: 0.5366 (mmp) REVERT: F 619 ILE cc_start: 0.7097 (pt) cc_final: 0.6779 (tp) outliers start: 91 outliers final: 41 residues processed: 257 average time/residue: 0.1595 time to fit residues: 69.4671 Evaluate side-chains 170 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 317 GLN Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 510 LEU Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 193 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 299 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS B 186 HIS C 55 ASN C 273 HIS C 411 ASN D 55 ASN D 411 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN ** F 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.106686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.082332 restraints weight = 64402.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.080858 restraints weight = 85875.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081656 restraints weight = 85051.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083100 restraints weight = 53362.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.083238 restraints weight = 42536.150| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29422 Z= 0.150 Angle : 0.644 14.614 39804 Z= 0.332 Chirality : 0.043 0.336 4354 Planarity : 0.004 0.048 5106 Dihedral : 5.482 50.219 3887 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.07 % Allowed : 10.77 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3560 helix: 1.01 (0.12), residues: 1734 sheet: -1.44 (0.26), residues: 342 loop : -1.63 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 651 TYR 0.023 0.001 TYR F 525 PHE 0.022 0.001 PHE E 462 TRP 0.019 0.001 TRP B 740 HIS 0.014 0.001 HIS F 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (29360) covalent geometry : angle 0.63223 / 0.33 (39664) SS BOND : bond 0.00760 / 0.46 ( 46) SS BOND : angle 1.30802 / 0.94 ( 92) hydrogen bonds : bond 0.06485 / 4.12 ( 1474) hydrogen bonds : angle 5.21588 / 3.58 ( 4386) link_BETA1-4 : bond 0.01125 / 0.52 ( 6) link_BETA1-4 : angle 4.05195 / 2.34 ( 18) link_NAG-ASN : bond 0.00549 / 0.25 ( 10) link_NAG-ASN : angle 2.63644 / 1.69 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 142 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.8335 (mmm) cc_final: 0.8052 (mmt) REVERT: B 125 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: B 135 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9149 (tt) REVERT: B 246 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8554 (tm) REVERT: B 671 MET cc_start: 0.9041 (mmm) cc_final: 0.8008 (mmt) REVERT: C 26 MET cc_start: 0.8047 (mmt) cc_final: 0.7610 (mmp) REVERT: D 276 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7066 (pttm) REVERT: D 382 MET cc_start: 0.8827 (mtp) cc_final: 0.8548 (ttm) REVERT: E 175 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7689 (mp) REVERT: E 218 TYR cc_start: 0.6949 (m-10) cc_final: 0.6455 (m-10) REVERT: E 335 MET cc_start: 0.6585 (tmm) cc_final: 0.6223 (tpp) REVERT: F 324 MET cc_start: 0.6111 (tpp) cc_final: 0.5207 (mmp) outliers start: 96 outliers final: 54 residues processed: 227 average time/residue: 0.1541 time to fit residues: 60.0366 Evaluate side-chains 179 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 121 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 3 optimal weight: 3.9990 chunk 338 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 238 optimal weight: 0.0030 chunk 159 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN A 401 HIS B 603 HIS B 615 ASN C 283 GLN E 413 GLN F 378 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.103744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079796 restraints weight = 64835.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078719 restraints weight = 90099.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.079386 restraints weight = 93731.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080117 restraints weight = 56159.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080808 restraints weight = 47981.449| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 29422 Z= 0.201 Angle : 0.668 12.792 39804 Z= 0.345 Chirality : 0.044 0.326 4354 Planarity : 0.004 0.056 5106 Dihedral : 5.370 54.560 3885 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.96 % Allowed : 11.13 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3560 helix: 1.37 (0.12), residues: 1730 sheet: -1.55 (0.25), residues: 366 loop : -1.53 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 217 TYR 0.031 0.002 TYR F 525 PHE 0.023 0.002 PHE E 462 TRP 0.019 0.002 TRP B 740 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (29360) covalent geometry : angle 0.65698 / 0.34 (39664) SS BOND : bond 0.00381 / 0.23 ( 46) SS BOND : angle 1.44751 / 0.96 ( 92) hydrogen bonds : bond 0.06497 / 4.14 ( 1474) hydrogen bonds : angle 5.06472 / 3.47 ( 4386) link_BETA1-4 : bond 0.00877 / 0.42 ( 6) link_BETA1-4 : angle 3.95766 / 2.28 ( 18) link_NAG-ASN : bond 0.00399 / 0.19 ( 10) link_NAG-ASN : angle 2.37166 / 1.48 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 130 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8833 (tm) REVERT: A 349 MET cc_start: 0.8210 (mmm) cc_final: 0.7544 (mtp) REVERT: A 374 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8500 (ptmm) REVERT: B 120 PHE cc_start: 0.6295 (p90) cc_final: 0.6010 (p90) REVERT: B 125 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: B 135 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9251 (tt) REVERT: B 200 VAL cc_start: 0.9513 (OUTLIER) cc_final: 0.9194 (t) REVERT: B 246 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8804 (tm) REVERT: B 374 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8574 (ptmm) REVERT: B 476 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8957 (tt) REVERT: B 671 MET cc_start: 0.9057 (mmm) cc_final: 0.8098 (mmt) REVERT: C 225 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8308 (pp) REVERT: C 276 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7273 (mmmt) REVERT: D 225 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8419 (pp) REVERT: D 276 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7556 (mmmt) REVERT: E 175 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7678 (mp) REVERT: E 218 TYR cc_start: 0.7446 (m-10) cc_final: 0.7149 (m-10) REVERT: E 335 MET cc_start: 0.6673 (tmm) cc_final: 0.6181 (tpp) REVERT: E 500 TYR cc_start: 0.8127 (t80) cc_final: 0.7907 (t80) REVERT: F 324 MET cc_start: 0.6250 (tpp) cc_final: 0.5261 (mmp) REVERT: F 335 MET cc_start: 0.7028 (tpp) cc_final: 0.6769 (tpp) outliers start: 124 outliers final: 73 residues processed: 244 average time/residue: 0.1507 time to fit residues: 62.9769 Evaluate side-chains 200 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 116 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 312 CYS Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 584 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 228 optimal weight: 40.0000 chunk 51 optimal weight: 0.8980 chunk 263 optimal weight: 8.9990 chunk 329 optimal weight: 9.9990 chunk 336 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 HIS B 379 ASN B 603 HIS B 662 ASN C 108 GLN D 55 ASN F 212 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.102389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.078566 restraints weight = 64920.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076973 restraints weight = 84592.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.077863 restraints weight = 97979.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078193 restraints weight = 57813.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.078797 restraints weight = 49780.792| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 29422 Z= 0.226 Angle : 0.676 14.057 39804 Z= 0.347 Chirality : 0.045 0.323 4354 Planarity : 0.004 0.047 5106 Dihedral : 5.330 58.111 3885 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.87 % Allowed : 11.96 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3560 helix: 1.42 (0.12), residues: 1736 sheet: -1.50 (0.26), residues: 364 loop : -1.47 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 264 TYR 0.028 0.002 TYR E 625 PHE 0.023 0.002 PHE F 462 TRP 0.016 0.002 TRP B 740 HIS 0.007 0.001 HIS B 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (29360) covalent geometry : angle 0.66525 / 0.34 (39664) SS BOND : bond 0.00390 / 0.23 ( 46) SS BOND : angle 1.41121 / 0.93 ( 92) hydrogen bonds : bond 0.06469 / 4.10 ( 1474) hydrogen bonds : angle 5.05801 / 3.47 ( 4386) link_BETA1-4 : bond 0.01030 / 0.47 ( 6) link_BETA1-4 : angle 3.97759 / 2.29 ( 18) link_NAG-ASN : bond 0.00555 / 0.25 ( 10) link_NAG-ASN : angle 2.29366 / 1.47 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 107 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8844 (tm) REVERT: A 374 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8508 (ptmm) REVERT: B 135 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9232 (tt) REVERT: B 246 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8841 (tm) REVERT: B 374 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8580 (ptmm) REVERT: B 476 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9045 (tt) REVERT: B 671 MET cc_start: 0.9058 (mmm) cc_final: 0.8278 (mmt) REVERT: C 225 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8405 (pp) REVERT: D 225 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8426 (pp) REVERT: E 175 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.7946 (mp) REVERT: E 218 TYR cc_start: 0.7673 (m-10) cc_final: 0.7338 (m-10) REVERT: E 335 MET cc_start: 0.6717 (tmm) cc_final: 0.6208 (tpp) REVERT: F 324 MET cc_start: 0.6095 (tpp) cc_final: 0.5077 (mmp) outliers start: 121 outliers final: 81 residues processed: 220 average time/residue: 0.1478 time to fit residues: 55.6682 Evaluate side-chains 191 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 101 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 584 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 188 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 344 optimal weight: 6.9990 chunk 136 optimal weight: 0.0470 chunk 128 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 252 optimal weight: 8.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 603 HIS B 743 GLN D 55 ASN F 241 ASN F 391 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.080434 restraints weight = 64445.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.079662 restraints weight = 90816.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.080590 restraints weight = 93160.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080956 restraints weight = 54522.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081656 restraints weight = 48004.317| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29422 Z= 0.137 Angle : 0.616 12.250 39804 Z= 0.313 Chirality : 0.042 0.325 4354 Planarity : 0.004 0.045 5106 Dihedral : 5.183 58.926 3885 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.55 % Allowed : 12.98 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3560 helix: 1.62 (0.12), residues: 1740 sheet: -1.33 (0.26), residues: 356 loop : -1.38 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 264 TYR 0.022 0.001 TYR F 525 PHE 0.021 0.001 PHE E 462 TRP 0.015 0.001 TRP B 740 HIS 0.007 0.001 HIS B 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (29360) covalent geometry : angle 0.60578 / 0.31 (39664) SS BOND : bond 0.00288 / 0.17 ( 46) SS BOND : angle 1.32404 / 0.86 ( 92) hydrogen bonds : bond 0.05942 / 3.78 ( 1474) hydrogen bonds : angle 4.84044 / 3.33 ( 4386) link_BETA1-4 : bond 0.01110 / 0.51 ( 6) link_BETA1-4 : angle 3.84736 / 2.22 ( 18) link_NAG-ASN : bond 0.00413 / 0.19 ( 10) link_NAG-ASN : angle 2.16254 / 1.36 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 115 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8800 (tm) REVERT: A 266 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: A 374 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8466 (ptmm) REVERT: A 474 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8714 (pp) REVERT: B 246 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8844 (tm) REVERT: B 374 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8499 (ptmm) REVERT: B 476 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8974 (tt) REVERT: B 671 MET cc_start: 0.9042 (mmm) cc_final: 0.8160 (mmt) REVERT: C 26 MET cc_start: 0.7909 (mmt) cc_final: 0.7493 (mmp) REVERT: C 276 LYS cc_start: 0.7460 (mmtt) cc_final: 0.6829 (mmmt) REVERT: D 26 MET cc_start: 0.7788 (mmt) cc_final: 0.7363 (mmp) REVERT: D 225 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8408 (pp) REVERT: D 276 LYS cc_start: 0.7942 (mmtt) cc_final: 0.7192 (mmmt) REVERT: E 175 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7848 (mp) REVERT: E 218 TYR cc_start: 0.7521 (m-10) cc_final: 0.7227 (m-10) REVERT: E 335 MET cc_start: 0.6535 (tmm) cc_final: 0.6075 (tpp) REVERT: F 324 MET cc_start: 0.5926 (tpp) cc_final: 0.4956 (mmp) outliers start: 111 outliers final: 77 residues processed: 220 average time/residue: 0.1478 time to fit residues: 56.1495 Evaluate side-chains 195 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 109 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 584 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 216 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 212 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS B 401 HIS B 603 HIS D 55 ASN E 574 GLN F 574 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.103565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079878 restraints weight = 64333.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078636 restraints weight = 87241.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.079500 restraints weight = 95283.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079728 restraints weight = 59101.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.080637 restraints weight = 50466.699| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29422 Z= 0.164 Angle : 0.627 12.170 39804 Z= 0.320 Chirality : 0.044 0.585 4354 Planarity : 0.004 0.045 5106 Dihedral : 5.085 59.435 3885 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.55 % Allowed : 13.08 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3560 helix: 1.72 (0.12), residues: 1728 sheet: -1.29 (0.27), residues: 346 loop : -1.36 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 264 TYR 0.027 0.001 TYR E 500 PHE 0.021 0.001 PHE F 462 TRP 0.016 0.001 TRP B 740 HIS 0.007 0.001 HIS E 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (29360) covalent geometry : angle 0.61603 / 0.32 (39664) SS BOND : bond 0.00314 / 0.19 ( 46) SS BOND : angle 1.49919 / 0.97 ( 92) hydrogen bonds : bond 0.05923 / 3.76 ( 1474) hydrogen bonds : angle 4.84121 / 3.33 ( 4386) link_BETA1-4 : bond 0.01104 / 0.50 ( 6) link_BETA1-4 : angle 3.70068 / 2.14 ( 18) link_NAG-ASN : bond 0.00294 / 0.14 ( 10) link_NAG-ASN : angle 2.27343 / 1.58 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 109 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8811 (tm) REVERT: A 266 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 365 MET cc_start: 0.8607 (mmm) cc_final: 0.8343 (tpp) REVERT: A 374 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8511 (ptmm) REVERT: A 474 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8710 (pp) REVERT: B 246 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8794 (tm) REVERT: B 374 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8510 (ptmm) REVERT: B 476 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9047 (tt) REVERT: B 671 MET cc_start: 0.9049 (mmm) cc_final: 0.8208 (mmt) REVERT: C 26 MET cc_start: 0.7955 (mmt) cc_final: 0.7525 (mmp) REVERT: C 225 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8402 (pp) REVERT: C 276 LYS cc_start: 0.7582 (mmtt) cc_final: 0.6969 (mmmt) REVERT: D 26 MET cc_start: 0.7921 (mmt) cc_final: 0.7472 (mmp) REVERT: D 225 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8448 (pp) REVERT: D 276 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7443 (mmmt) REVERT: E 175 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7863 (mp) REVERT: E 218 TYR cc_start: 0.7528 (m-10) cc_final: 0.7133 (m-10) REVERT: E 335 MET cc_start: 0.6645 (tmm) cc_final: 0.6167 (tpp) REVERT: F 324 MET cc_start: 0.5977 (tpp) cc_final: 0.4993 (mmp) outliers start: 111 outliers final: 87 residues processed: 213 average time/residue: 0.1544 time to fit residues: 56.8605 Evaluate side-chains 203 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 106 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 726 PHE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 132 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 229 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 603 HIS D 55 ASN D 541 ASN E 391 HIS ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.105129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081058 restraints weight = 64409.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.079684 restraints weight = 89833.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080874 restraints weight = 91970.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081116 restraints weight = 55635.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.082126 restraints weight = 49145.248| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29422 Z= 0.126 Angle : 0.604 11.979 39804 Z= 0.306 Chirality : 0.042 0.429 4354 Planarity : 0.004 0.044 5106 Dihedral : 4.955 59.451 3885 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.13 % Allowed : 13.71 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3560 helix: 1.85 (0.12), residues: 1730 sheet: -1.20 (0.27), residues: 346 loop : -1.29 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 264 TYR 0.045 0.001 TYR F 625 PHE 0.020 0.001 PHE F 462 TRP 0.015 0.001 TRP B 740 HIS 0.010 0.001 HIS B 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (29360) covalent geometry : angle 0.59420 / 0.30 (39664) SS BOND : bond 0.00270 / 0.16 ( 46) SS BOND : angle 1.21884 / 0.79 ( 92) hydrogen bonds : bond 0.05567 / 3.53 ( 1474) hydrogen bonds : angle 4.72013 / 3.25 ( 4386) link_BETA1-4 : bond 0.01080 / 0.49 ( 6) link_BETA1-4 : angle 3.62425 / 2.10 ( 18) link_NAG-ASN : bond 0.00404 / 0.19 ( 10) link_NAG-ASN : angle 2.00593 / 1.37 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 118 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7558 (mmtt) REVERT: A 246 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8776 (tm) REVERT: A 365 MET cc_start: 0.8618 (mmm) cc_final: 0.8393 (tpp) REVERT: A 374 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8686 (tttp) REVERT: A 474 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8681 (pp) REVERT: B 246 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8774 (tm) REVERT: B 374 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8603 (tttp) REVERT: B 476 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8976 (tt) REVERT: B 671 MET cc_start: 0.8995 (mmm) cc_final: 0.8126 (mmt) REVERT: C 26 MET cc_start: 0.7882 (mmt) cc_final: 0.7475 (mmp) REVERT: C 225 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8356 (pp) REVERT: C 391 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8605 (pp) REVERT: D 26 MET cc_start: 0.7804 (mmt) cc_final: 0.7391 (mmp) REVERT: D 225 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8394 (pp) REVERT: D 276 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7526 (mmmt) REVERT: E 175 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7828 (mp) REVERT: E 218 TYR cc_start: 0.7431 (m-10) cc_final: 0.7030 (m-10) REVERT: E 335 MET cc_start: 0.6551 (tmm) cc_final: 0.6079 (tpp) REVERT: E 592 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8068 (t80) REVERT: F 324 MET cc_start: 0.5891 (tpp) cc_final: 0.4931 (mmp) outliers start: 98 outliers final: 74 residues processed: 208 average time/residue: 0.1524 time to fit residues: 54.5377 Evaluate side-chains 196 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 110 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 235 optimal weight: 8.9990 chunk 43 optimal weight: 0.0770 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 128 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 603 HIS D 108 GLN F 191 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.081756 restraints weight = 64354.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080204 restraints weight = 86921.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081104 restraints weight = 85130.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081896 restraints weight = 53105.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.082224 restraints weight = 45722.602| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29422 Z= 0.122 Angle : 0.595 15.450 39804 Z= 0.299 Chirality : 0.042 0.342 4354 Planarity : 0.004 0.042 5106 Dihedral : 4.842 59.186 3885 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.75 % Allowed : 14.13 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3560 helix: 1.93 (0.12), residues: 1756 sheet: -1.14 (0.27), residues: 346 loop : -1.27 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 264 TYR 0.016 0.001 TYR F 525 PHE 0.019 0.001 PHE F 462 TRP 0.016 0.001 TRP C 441 HIS 0.008 0.001 HIS F 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (29360) covalent geometry : angle 0.58673 / 0.30 (39664) SS BOND : bond 0.00263 / 0.16 ( 46) SS BOND : angle 0.97563 / 0.66 ( 92) hydrogen bonds : bond 0.05341 / 3.38 ( 1474) hydrogen bonds : angle 4.63911 / 3.20 ( 4386) link_BETA1-4 : bond 0.01044 / 0.48 ( 6) link_BETA1-4 : angle 3.61353 / 2.09 ( 18) link_NAG-ASN : bond 0.00388 / 0.18 ( 10) link_NAG-ASN : angle 1.92510 / 1.29 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 124 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7553 (mmtt) REVERT: A 246 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8765 (tm) REVERT: A 374 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8648 (tttp) REVERT: A 474 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8712 (pp) REVERT: B 246 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8770 (tm) REVERT: B 349 MET cc_start: 0.8088 (mmm) cc_final: 0.7662 (mmp) REVERT: B 374 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8611 (tttp) REVERT: B 476 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8927 (tt) REVERT: B 671 MET cc_start: 0.8870 (mmm) cc_final: 0.8081 (mmt) REVERT: C 26 MET cc_start: 0.7792 (mmt) cc_final: 0.7394 (mmp) REVERT: C 225 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 276 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7023 (mmmt) REVERT: C 391 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8587 (pp) REVERT: C 638 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7735 (mt) REVERT: D 26 MET cc_start: 0.7777 (mmt) cc_final: 0.7350 (mmp) REVERT: D 225 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8408 (pp) REVERT: D 276 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7301 (ttpt) REVERT: E 175 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7816 (mp) REVERT: E 218 TYR cc_start: 0.7391 (m-10) cc_final: 0.6996 (m-10) REVERT: E 335 MET cc_start: 0.6659 (tmm) cc_final: 0.6202 (tpp) REVERT: E 592 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7994 (t80) REVERT: F 324 MET cc_start: 0.5955 (tpp) cc_final: 0.5095 (mmm) outliers start: 86 outliers final: 60 residues processed: 204 average time/residue: 0.1457 time to fit residues: 51.6424 Evaluate side-chains 184 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 111 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 206 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 302 optimal weight: 0.7980 chunk 288 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 312 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 328 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 615 ASN B 603 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.105677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081750 restraints weight = 64219.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080584 restraints weight = 88722.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081769 restraints weight = 90459.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081981 restraints weight = 54214.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082864 restraints weight = 48408.382| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29422 Z= 0.127 Angle : 0.603 14.899 39804 Z= 0.303 Chirality : 0.042 0.381 4354 Planarity : 0.004 0.042 5106 Dihedral : 4.789 58.574 3885 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.56 % Allowed : 14.58 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3560 helix: 1.98 (0.12), residues: 1756 sheet: -1.12 (0.27), residues: 346 loop : -1.25 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 264 TYR 0.035 0.001 TYR E 500 PHE 0.020 0.001 PHE F 462 TRP 0.016 0.001 TRP B 740 HIS 0.008 0.001 HIS F 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (29360) covalent geometry : angle 0.59485 / 0.30 (39664) SS BOND : bond 0.00262 / 0.16 ( 46) SS BOND : angle 1.01286 / 0.68 ( 92) hydrogen bonds : bond 0.05297 / 3.35 ( 1474) hydrogen bonds : angle 4.63336 / 3.20 ( 4386) link_BETA1-4 : bond 0.00925 / 0.42 ( 6) link_BETA1-4 : angle 3.59665 / 2.09 ( 18) link_NAG-ASN : bond 0.00353 / 0.17 ( 10) link_NAG-ASN : angle 1.85937 / 1.21 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 116 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7452 (mmtt) REVERT: A 246 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8864 (tm) REVERT: A 349 MET cc_start: 0.8173 (mmm) cc_final: 0.7961 (mmm) REVERT: A 374 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8556 (tttp) REVERT: A 474 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8758 (pp) REVERT: B 246 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8771 (tm) REVERT: B 349 MET cc_start: 0.7909 (mmm) cc_final: 0.7509 (mmp) REVERT: B 374 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8601 (tttp) REVERT: B 476 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8926 (tt) REVERT: B 671 MET cc_start: 0.8929 (mmm) cc_final: 0.8045 (mmt) REVERT: C 26 MET cc_start: 0.7840 (mmt) cc_final: 0.7417 (mmp) REVERT: C 225 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8371 (pp) REVERT: C 276 LYS cc_start: 0.7613 (mmtt) cc_final: 0.6893 (mmmt) REVERT: C 391 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8579 (pp) REVERT: C 638 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7750 (mt) REVERT: D 26 MET cc_start: 0.7808 (mmt) cc_final: 0.7374 (mmp) REVERT: D 225 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8417 (pp) REVERT: D 276 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7325 (ttpt) REVERT: E 175 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7837 (mp) REVERT: E 335 MET cc_start: 0.6606 (tmm) cc_final: 0.6139 (tpp) REVERT: E 592 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7840 (t80) REVERT: F 324 MET cc_start: 0.5994 (tpp) cc_final: 0.5097 (mmm) outliers start: 80 outliers final: 62 residues processed: 191 average time/residue: 0.1546 time to fit residues: 50.6417 Evaluate side-chains 184 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 109 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 726 PHE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 611 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 702 TRP Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 504 THR Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 260 optimal weight: 4.9990 chunk 38 optimal weight: 0.0970 chunk 310 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 353 optimal weight: 0.8980 chunk 314 optimal weight: 3.9990 chunk 347 optimal weight: 1.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 628 HIS ** F 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.105539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.081677 restraints weight = 64698.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080675 restraints weight = 82413.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081466 restraints weight = 89736.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081845 restraints weight = 54729.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082785 restraints weight = 47423.382| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 29422 Z= 0.157 Angle : 0.725 59.175 39804 Z= 0.400 Chirality : 0.043 0.324 4354 Planarity : 0.004 0.083 5106 Dihedral : 4.790 58.580 3885 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.49 % Allowed : 14.61 % Favored : 82.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3560 helix: 1.98 (0.12), residues: 1756 sheet: -1.12 (0.27), residues: 346 loop : -1.25 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 264 TYR 0.028 0.001 TYR F 218 PHE 0.020 0.001 PHE F 462 TRP 0.030 0.001 TRP C 8 HIS 0.123 0.002 HIS B 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (29360) covalent geometry : angle 0.71832 / 0.40 (39664) SS BOND : bond 0.00259 / 0.16 ( 46) SS BOND : angle 1.03097 / 0.69 ( 92) hydrogen bonds : bond 0.05336 / 3.37 ( 1474) hydrogen bonds : angle 4.64050 / 3.21 ( 4386) link_BETA1-4 : bond 0.00807 / 0.38 ( 6) link_BETA1-4 : angle 3.67774 / 2.13 ( 18) link_NAG-ASN : bond 0.00354 / 0.17 ( 10) link_NAG-ASN : angle 1.85736 / 1.21 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3486.19 seconds wall clock time: 61 minutes 53.65 seconds (3713.65 seconds total)