Starting phenix.real_space_refine on Sun Oct 12 03:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r83_18993/10_2025/8r83_18993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r83_18993/10_2025/8r83_18993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r83_18993/10_2025/8r83_18993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r83_18993/10_2025/8r83_18993.map" model { file = "/net/cci-nas-00/data/ceres_data/8r83_18993/10_2025/8r83_18993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r83_18993/10_2025/8r83_18993.cif" } resolution = 3.57 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= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 110 5.16 5 C 12818 2.51 5 N 3487 2.21 5 O 3998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20415 Number of models: 1 Model: "" Number of chains: 20 Chain: "N" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1686 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "L" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 213} Chain: "K" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "H" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "A" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 213} Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain breaks: 1 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.50, per 1000 atoms: 0.22 Number of scatterers: 20415 At special positions: 0 Unit cell: (72.756, 177.66, 202.194, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 110 16.00 O 3998 8.00 N 3487 7.00 C 12818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS N 147 " - pdb=" SG CYS N 181 " distance=2.03 Simple disulfide: pdb=" SG CYS N 163 " - pdb=" SG CYS N 228 " distance=2.03 Simple disulfide: pdb=" SG CYS N 176 " - pdb=" SG CYS N 238 " distance=2.03 Simple disulfide: pdb=" SG CYS N 191 " - pdb=" SG CYS L 414 " distance=2.07 Simple disulfide: pdb=" SG CYS N 208 " - pdb=" SG CYS N 218 " distance=2.04 Simple disulfide: pdb=" SG CYS N 253 " - pdb=" SG CYS N 287 " distance=2.03 Simple disulfide: pdb=" SG CYS N 269 " - pdb=" SG CYS N 335 " distance=2.03 Simple disulfide: pdb=" SG CYS N 282 " - pdb=" SG CYS N 345 " distance=2.03 Simple disulfide: pdb=" SG CYS N 315 " - pdb=" SG CYS N 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.04 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 575 " - pdb=" SG CYS J 14 " distance=2.19 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 414 " - pdb=" SG CYS H 414 " distance=2.04 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 414 " - pdb=" SG CYS F 414 " distance=2.04 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.00 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " 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 I 1 " - " NAG I 2 " NAG-ASN " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 726.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4978 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 66 sheets defined 13.0% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'N' and resid 168 through 180 removed outlier: 3.638A pdb=" N ALA N 172 " --> pdb=" O SER N 168 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU N 179 " --> pdb=" O VAL N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.699A pdb=" N VAL N 280 " --> pdb=" O LYS N 276 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL N 281 " --> pdb=" O GLU N 277 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN N 284 " --> pdb=" O VAL N 280 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU N 285 " --> pdb=" O VAL N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 301 removed outlier: 3.683A pdb=" N CYS N 300 " --> pdb=" O ASP N 297 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR N 301 " --> pdb=" O ARG N 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 297 through 301' Processing helix chain 'N' and resid 321 through 325 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.537A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.630A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.842A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 524 through 531 removed outlier: 3.705A pdb=" N GLY C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 419 removed outlier: 3.644A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 414 through 419' Processing helix chain 'D' and resid 460 through 467 Processing helix chain 'D' and resid 525 through 531 removed outlier: 3.862A pdb=" N GLY D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 361 removed outlier: 3.568A pdb=" N LEU L 359 " --> pdb=" O ALA L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 419 removed outlier: 3.781A pdb=" N TRP L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 467 Processing helix chain 'L' and resid 496 through 498 No H-bonds generated for 'chain 'L' and resid 496 through 498' Processing helix chain 'L' and resid 524 through 531 removed outlier: 3.530A pdb=" N GLY L 531 " --> pdb=" O GLU L 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 420 removed outlier: 4.323A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 466 Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'K' and resid 525 through 530 Processing helix chain 'H' and resid 353 through 357 Processing helix chain 'H' and resid 414 through 420 removed outlier: 3.520A pdb=" N TRP H 418 " --> pdb=" O CYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 467 Processing helix chain 'H' and resid 524 through 530 Processing helix chain 'G' and resid 353 through 360 Processing helix chain 'G' and resid 414 through 421 removed outlier: 3.771A pdb=" N TRP G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 466 removed outlier: 3.981A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 531 removed outlier: 3.965A pdb=" N GLY G 531 " --> pdb=" O GLU G 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.657A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 466 Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.565A pdb=" N ASN F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 415 through 421' Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 525 through 531 removed outlier: 3.979A pdb=" N GLY F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 414 through 420 removed outlier: 3.676A pdb=" N TRP A 418 " --> pdb=" O CYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.696A pdb=" N LEU A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 465' Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.758A pdb=" N GLY A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 148 through 150 removed outlier: 3.563A pdb=" N ASP N 233 " --> pdb=" O ARG N 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN N 188 " --> pdb=" O TRP N 235 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU N 186 " --> pdb=" O GLU N 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 152 through 153 Processing sheet with id=AA3, first strand: chain 'N' and resid 243 through 248 removed outlier: 4.246A pdb=" N ASP N 243 " --> pdb=" O LEU N 260 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU N 257 " --> pdb=" O VAL N 268 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL N 268 " --> pdb=" O LEU N 257 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TRP N 309 " --> pdb=" O TRP N 265 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER N 267 " --> pdb=" O TRP N 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 347 removed outlier: 4.019A pdb=" N ARG B 346 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 370 " --> pdb=" O ARG B 346 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR B 370 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 407 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 411 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR B 363 " --> pdb=" O ILE B 413 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 347 removed outlier: 4.019A pdb=" N ARG B 346 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 370 " --> pdb=" O ARG B 346 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR B 370 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 407 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 410 " --> pdb=" O HIS B 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 380 through 383 removed outlier: 3.761A pdb=" N CYS B 426 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN B 439 " --> pdb=" O CYS B 426 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 428 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 437 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.552A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.552A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.524A pdb=" N VAL B 537 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 565 through 566 removed outlier: 3.545A pdb=" N SER B 569 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 565 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N TYR J 62 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 567 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 346 through 348 removed outlier: 3.629A pdb=" N ASP C 371 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE C 405 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N SER C 406 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 397 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 389 through 390 removed outlier: 4.351A pdb=" N TRP C 382 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 425 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN C 439 " --> pdb=" O CYS C 426 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 453 through 457 removed outlier: 6.125A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 453 through 457 removed outlier: 6.125A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.770A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR D 363 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 413 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N PHE D 405 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER D 406 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 397 " --> pdb=" O SER D 406 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 410 " --> pdb=" O HIS D 393 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.908A pdb=" N TRP D 382 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 441 " --> pdb=" O PHE D 424 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.509A pdb=" N SER D 519 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 520 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 501 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.509A pdb=" N SER D 519 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 493 through 494 removed outlier: 3.525A pdb=" N GLN D 493 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS D 536 " --> pdb=" O ARG D 550 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 550 " --> pdb=" O CYS D 536 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 346 through 350 removed outlier: 4.102A pdb=" N THR L 366 " --> pdb=" O ILE L 350 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY L 409 " --> pdb=" O CYS L 367 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP L 371 " --> pdb=" O PHE L 405 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE L 405 " --> pdb=" O ASP L 371 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 389 through 390 removed outlier: 4.485A pdb=" N TRP L 382 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR L 383 " --> pdb=" O THR L 425 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR L 425 " --> pdb=" O THR L 383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 453 through 457 removed outlier: 6.046A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 453 through 457 removed outlier: 6.046A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AC8, first strand: chain 'H' and resid 561 through 567 removed outlier: 5.933A pdb=" N TYR K 562 " --> pdb=" O ASN H 563 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER H 565 " --> pdb=" O TYR K 562 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL K 564 " --> pdb=" O SER H 565 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL H 567 " --> pdb=" O VAL K 564 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU K 566 " --> pdb=" O VAL H 567 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR L 562 " --> pdb=" O ASN K 563 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER K 565 " --> pdb=" O TYR L 562 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL L 564 " --> pdb=" O SER K 565 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL K 567 " --> pdb=" O VAL L 564 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU L 566 " --> pdb=" O VAL K 567 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER L 569 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE J 22 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA J 15 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP J 9 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 574 through 575 Processing sheet with id=AD1, first strand: chain 'K' and resid 347 through 348 removed outlier: 6.191A pdb=" N LEU K 368 " --> pdb=" O GLY K 409 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY K 409 " --> pdb=" O LEU K 368 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR K 370 " --> pdb=" O ALA K 407 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA K 407 " --> pdb=" O THR K 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU K 372 " --> pdb=" O PHE K 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 411 " --> pdb=" O LEU K 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR K 363 " --> pdb=" O ILE K 413 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 347 through 348 removed outlier: 6.191A pdb=" N LEU K 368 " --> pdb=" O GLY K 409 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY K 409 " --> pdb=" O LEU K 368 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR K 370 " --> pdb=" O ALA K 407 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA K 407 " --> pdb=" O THR K 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU K 372 " --> pdb=" O PHE K 405 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 389 through 390 removed outlier: 3.687A pdb=" N VAL K 390 " --> pdb=" O TRP K 382 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TRP K 382 " --> pdb=" O VAL K 390 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN K 439 " --> pdb=" O CYS K 426 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL K 428 " --> pdb=" O LEU K 437 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU K 437 " --> pdb=" O VAL K 428 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.526A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 472 " --> pdb=" O LEU K 521 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY K 478 " --> pdb=" O TYR K 515 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 485 through 486 removed outlier: 3.507A pdb=" N PHE K 485 " --> pdb=" O ALA K 539 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 489 through 490 Processing sheet with id=AD7, first strand: chain 'K' and resid 534 through 535 removed outlier: 4.260A pdb=" N TYR K 534 " --> pdb=" O VAL K 552 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL K 552 " --> pdb=" O TYR K 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 346 through 350 removed outlier: 3.705A pdb=" N ARG H 346 " --> pdb=" O THR H 370 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR H 366 " --> pdb=" O ILE H 350 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS H 364 " --> pdb=" O ILE H 413 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE H 413 " --> pdb=" O LYS H 364 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N THR H 366 " --> pdb=" O ALA H 411 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA H 411 " --> pdb=" O THR H 366 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU H 368 " --> pdb=" O GLY H 409 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLY H 409 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N THR H 370 " --> pdb=" O ALA H 407 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA H 407 " --> pdb=" O THR H 370 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 389 through 390 removed outlier: 4.413A pdb=" N TRP H 382 " --> pdb=" O VAL H 390 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER H 381 " --> pdb=" O THR H 427 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE H 424 " --> pdb=" O ILE H 441 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.614A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.614A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.611A pdb=" N ARG H 550 " --> pdb=" O CYS H 536 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 346 through 347 removed outlier: 3.836A pdb=" N ARG G 346 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR G 370 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA G 407 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA G 411 " --> pdb=" O LEU G 365 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 346 through 347 removed outlier: 3.836A pdb=" N ARG G 346 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR G 370 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA G 407 " --> pdb=" O THR G 370 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 389 through 390 removed outlier: 4.284A pdb=" N TRP G 382 " --> pdb=" O VAL G 390 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR G 379 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE G 424 " --> pdb=" O ILE G 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS G 426 " --> pdb=" O GLN G 439 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN G 439 " --> pdb=" O CYS G 426 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL G 428 " --> pdb=" O LEU G 437 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU G 437 " --> pdb=" O VAL G 428 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.652A pdb=" N SER G 519 " --> pdb=" O CYS G 474 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 501 " --> pdb=" O ILE G 520 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.652A pdb=" N SER G 519 " --> pdb=" O CYS G 474 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AF1, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AF2, first strand: chain 'G' and resid 565 through 567 Processing sheet with id=AF3, first strand: chain 'E' and resid 346 through 348 removed outlier: 6.014A pdb=" N LEU E 368 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY E 409 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 411 " --> pdb=" O LEU E 365 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 346 through 348 removed outlier: 6.014A pdb=" N LEU E 368 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY E 409 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR E 404 " --> pdb=" O HIS E 400 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER E 406 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLU E 398 " --> pdb=" O SER E 406 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL E 408 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE E 396 " --> pdb=" O VAL E 408 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLU E 410 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N THR E 394 " --> pdb=" O GLU E 410 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 379 through 383 removed outlier: 3.641A pdb=" N THR E 379 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR E 429 " --> pdb=" O THR E 379 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 381 " --> pdb=" O THR E 427 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR E 383 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR E 425 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN E 439 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL E 428 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.560A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.560A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AF9, first strand: chain 'F' and resid 347 through 350 removed outlier: 3.973A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS F 364 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE F 413 " --> pdb=" O LYS F 364 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR F 366 " --> pdb=" O ALA F 411 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA F 411 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU F 368 " --> pdb=" O GLY F 409 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY F 409 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR F 370 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA F 407 " --> pdb=" O THR F 370 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 379 through 383 removed outlier: 3.504A pdb=" N THR F 379 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 429 " --> pdb=" O THR F 379 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN F 439 " --> pdb=" O CYS F 426 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 453 through 457 removed outlier: 6.013A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 520 " --> pdb=" O VAL F 501 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 501 " --> pdb=" O ILE F 520 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 453 through 457 removed outlier: 6.013A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AG5, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.690A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 363 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS A 367 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY A 409 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 371 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER A 406 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.524A pdb=" N VAL A 390 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP A 382 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 425 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS A 426 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 439 " --> pdb=" O CYS A 426 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 428 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.630A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 453 through 457 removed outlier: 3.630A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 516 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.631A pdb=" N PHE A 485 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AH2, first strand: chain 'J' and resid 110 through 113 removed outlier: 3.591A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 116 through 117 removed outlier: 3.619A pdb=" N GLU J 120 " --> pdb=" O TYR J 117 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2019 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: 3.99 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6142 1.34 - 1.46: 4123 1.46 - 1.58: 10512 1.58 - 1.70: 1 1.70 - 1.82: 142 Bond restraints: 20920 Sorted by residual: bond pdb=" N VAL E 567 " pdb=" CA VAL E 567 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.33e+01 bond pdb=" N ILE A 413 " pdb=" CA ILE A 413 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N ILE G 413 " pdb=" CA ILE G 413 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" CA PRO K 458 " pdb=" C PRO K 458 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.21e+01 bond pdb=" N VAL C 567 " pdb=" CA VAL C 567 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.19e-02 7.06e+03 1.20e+01 ... (remaining 20915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 24910 1.14 - 2.27: 2663 2.27 - 3.41: 905 3.41 - 4.55: 110 4.55 - 5.68: 26 Bond angle restraints: 28614 Sorted by residual: angle pdb=" C ALA J 132 " pdb=" CA ALA J 132 " pdb=" CB ALA J 132 " ideal model delta sigma weight residual 116.54 111.45 5.09 1.15e+00 7.56e-01 1.96e+01 angle pdb=" N LYS K 361 " pdb=" CA LYS K 361 " pdb=" C LYS K 361 " ideal model delta sigma weight residual 112.86 108.02 4.84 1.22e+00 6.72e-01 1.58e+01 angle pdb=" N VAL E 567 " pdb=" CA VAL E 567 " pdb=" C VAL E 567 " ideal model delta sigma weight residual 112.96 109.00 3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" N THR E 530 " pdb=" CA THR E 530 " pdb=" C THR E 530 " ideal model delta sigma weight residual 113.30 108.15 5.15 1.34e+00 5.57e-01 1.48e+01 angle pdb=" CA ILE K 413 " pdb=" C ILE K 413 " pdb=" O ILE K 413 " ideal model delta sigma weight residual 121.09 117.96 3.13 8.20e-01 1.49e+00 1.46e+01 ... (remaining 28609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 11569 17.45 - 34.91: 966 34.91 - 52.36: 230 52.36 - 69.81: 60 69.81 - 87.26: 13 Dihedral angle restraints: 12838 sinusoidal: 5194 harmonic: 7644 Sorted by residual: dihedral pdb=" CB CYS N 191 " pdb=" SG CYS N 191 " pdb=" SG CYS L 414 " pdb=" CB CYS L 414 " ideal model delta sinusoidal sigma weight residual 93.00 41.37 51.63 1 1.00e+01 1.00e-02 3.64e+01 dihedral pdb=" CB CYS G 367 " pdb=" SG CYS G 367 " pdb=" SG CYS G 426 " pdb=" CB CYS G 426 " ideal model delta sinusoidal sigma weight residual 93.00 49.24 43.76 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS J 108 " pdb=" SG CYS J 108 " pdb=" SG CYS J 133 " pdb=" CB CYS J 133 " ideal model delta sinusoidal sigma weight residual 93.00 130.47 -37.47 1 1.00e+01 1.00e-02 1.98e+01 ... (remaining 12835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 3347 0.280 - 0.559: 2 0.559 - 0.839: 0 0.839 - 1.118: 1 1.118 - 1.398: 1 Chirality restraints: 3351 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 563 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.00 -1.40 2.00e-01 2.50e+01 4.88e+01 chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-01 2.50e+01 3.09e+01 chirality pdb=" C1 NAG H 601 " pdb=" ND2 ASN H 563 " pdb=" C2 NAG H 601 " pdb=" O5 NAG H 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3348 not shown) Planarity restraints: 3682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.078 2.00e-02 2.50e+03 1.61e-01 3.23e+02 pdb=" CG ASN K 563 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " -0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.289 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 563 " -0.110 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" CG ASN C 563 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 563 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 563 " 0.205 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 48 " 0.108 2.00e-02 2.50e+03 1.16e-01 1.69e+02 pdb=" CG ASN J 48 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN J 48 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN J 48 " -0.179 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.145 2.00e-02 2.50e+03 ... (remaining 3679 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2879 2.77 - 3.30: 18072 3.30 - 3.84: 30354 3.84 - 4.37: 34911 4.37 - 4.90: 61188 Nonbonded interactions: 147404 Sorted by model distance: nonbonded pdb=" ND2 ASN C 563 " pdb=" N2 NAG C 601 " model vdw 2.239 2.560 nonbonded pdb=" O SER G 353 " pdb=" OG SER G 356 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASN G 402 " pdb=" OG1 THR G 404 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASN F 402 " pdb=" OG1 THR F 404 " model vdw 2.297 3.040 nonbonded pdb=" OD1 ASN C 402 " pdb=" OG1 THR C 404 " model vdw 2.319 3.040 ... (remaining 147399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 345 through 568) selection = (chain 'B' and resid 345 through 568) selection = (chain 'C' and resid 345 through 568) selection = (chain 'D' and resid 345 through 568) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 345 through 568) selection = (chain 'H' and resid 345 through 568) selection = (chain 'K' and resid 345 through 568) selection = (chain 'L' and resid 345 through 568) } 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: 20.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.730 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 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 : 0.007 0.158 20966 Z= 0.511 Angle : 0.946 36.122 28714 Z= 0.588 Chirality : 0.068 1.398 3351 Planarity : 0.006 0.118 3675 Dihedral : 13.920 87.263 7746 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.13 % Allowed : 17.59 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 2582 helix: -0.76 (0.31), residues: 252 sheet: 0.94 (0.17), residues: 919 loop : -0.37 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.014 0.001 TYR L 515 PHE 0.029 0.001 PHE H 354 TRP 0.012 0.001 TRP K 418 HIS 0.007 0.001 HIS H 518 Details of bonding type rmsd covalent geometry : bond 0.00678 (20920) covalent geometry : angle 0.81763 (28614) SS BOND : bond 0.02691 ( 38) SS BOND : angle 1.13411 ( 76) hydrogen bonds : bond 0.29130 ( 648) hydrogen bonds : angle 9.24858 ( 2019) link_BETA1-4 : bond 0.02198 ( 1) link_BETA1-4 : angle 4.42802 ( 3) link_NAG-ASN : bond 0.04310 ( 7) link_NAG-ASN : angle 17.46076 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 154 LYS cc_start: 0.6512 (tttm) cc_final: 0.6085 (mmtm) REVERT: N 214 THR cc_start: 0.4991 (m) cc_final: 0.4160 (t) REVERT: B 489 MET cc_start: 0.7942 (mtp) cc_final: 0.7604 (mtt) REVERT: B 506 MET cc_start: 0.5631 (mtt) cc_final: 0.5347 (mtm) REVERT: B 532 GLU cc_start: 0.7692 (mp0) cc_final: 0.6914 (mp0) REVERT: C 451 ARG cc_start: 0.7098 (ptp90) cc_final: 0.6523 (ptm-80) REVERT: D 384 ARG cc_start: 0.6469 (mtt180) cc_final: 0.6237 (ttm170) REVERT: D 568 MET cc_start: 0.6412 (ptp) cc_final: 0.6047 (pmm) REVERT: H 415 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6916 (tm-30) REVERT: H 558 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7399 (mtmm) REVERT: E 451 ARG cc_start: 0.7582 (ptp-110) cc_final: 0.7185 (ptm-80) REVERT: F 393 HIS cc_start: 0.7151 (t70) cc_final: 0.6814 (t70) REVERT: F 450 HIS cc_start: 0.7078 (m-70) cc_final: 0.6394 (m-70) REVERT: F 544 PRO cc_start: 0.5474 (Cg_exo) cc_final: 0.5272 (Cg_endo) REVERT: J 70 LYS cc_start: 0.5117 (mttm) cc_final: 0.4915 (mtmt) outliers start: 3 outliers final: 1 residues processed: 286 average time/residue: 0.1728 time to fit residues: 71.3333 Evaluate side-chains 191 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 568 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN L 545 ASN ** K 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS F 518 HIS A 465 ASN J 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.224562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.189787 restraints weight = 24647.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.190496 restraints weight = 55810.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.190697 restraints weight = 38439.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.189040 restraints weight = 30060.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.189820 restraints weight = 24885.338| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20966 Z= 0.183 Angle : 0.648 20.292 28714 Z= 0.329 Chirality : 0.047 0.278 3351 Planarity : 0.005 0.069 3675 Dihedral : 4.191 47.681 2975 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.75 % Allowed : 16.73 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.16), residues: 2582 helix: -0.10 (0.32), residues: 252 sheet: 1.14 (0.17), residues: 930 loop : -0.31 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 467 TYR 0.012 0.001 TYR L 562 PHE 0.032 0.002 PHE H 424 TRP 0.017 0.001 TRP N 235 HIS 0.011 0.001 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00446 (20920) covalent geometry : angle 0.61671 (28614) SS BOND : bond 0.00524 ( 38) SS BOND : angle 1.30774 ( 76) hydrogen bonds : bond 0.04427 ( 648) hydrogen bonds : angle 6.15202 ( 2019) link_BETA1-4 : bond 0.00456 ( 1) link_BETA1-4 : angle 1.69311 ( 3) link_NAG-ASN : bond 0.00780 ( 7) link_NAG-ASN : angle 7.08000 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 197 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: N 201 ILE cc_start: 0.8137 (mt) cc_final: 0.7875 (mt) REVERT: B 423 ARG cc_start: 0.7513 (mtm110) cc_final: 0.7091 (mtm110) REVERT: B 489 MET cc_start: 0.7749 (mtp) cc_final: 0.7474 (mtt) REVERT: H 415 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: G 418 TRP cc_start: 0.7409 (t-100) cc_final: 0.7064 (t-100) REVERT: E 416 ASP cc_start: 0.7072 (p0) cc_final: 0.6449 (p0) REVERT: F 568 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6637 (tmm) REVERT: J 34 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6956 (tt0) outliers start: 64 outliers final: 26 residues processed: 248 average time/residue: 0.1626 time to fit residues: 59.1140 Evaluate side-chains 193 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain J residue 34 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 170 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN ** K 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 487 GLN H 419 ASN E 450 HIS ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.194955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128400 restraints weight = 24671.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122442 restraints weight = 25027.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125066 restraints weight = 21603.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125461 restraints weight = 15925.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125829 restraints weight = 14956.639| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20966 Z= 0.172 Angle : 0.599 14.603 28714 Z= 0.308 Chirality : 0.046 0.277 3351 Planarity : 0.005 0.054 3675 Dihedral : 3.934 24.091 2972 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.71 % Allowed : 17.25 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.16), residues: 2582 helix: -0.10 (0.32), residues: 270 sheet: 1.27 (0.17), residues: 953 loop : -0.40 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 423 TYR 0.016 0.001 TYR F 515 PHE 0.022 0.002 PHE K 516 TRP 0.028 0.001 TRP E 418 HIS 0.010 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00426 (20920) covalent geometry : angle 0.57800 (28614) SS BOND : bond 0.00508 ( 38) SS BOND : angle 1.23896 ( 76) hydrogen bonds : bond 0.04478 ( 648) hydrogen bonds : angle 5.65690 ( 2019) link_BETA1-4 : bond 0.00980 ( 1) link_BETA1-4 : angle 1.41687 ( 3) link_NAG-ASN : bond 0.00689 ( 7) link_NAG-ASN : angle 5.46442 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 179 time to evaluate : 0.719 Fit side-chains REVERT: N 154 LYS cc_start: 0.6579 (tttm) cc_final: 0.6090 (mmtm) REVERT: B 489 MET cc_start: 0.8087 (mtp) cc_final: 0.7651 (mtt) REVERT: K 359 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5958 (mm) REVERT: K 489 MET cc_start: 0.8797 (mtm) cc_final: 0.8539 (mtp) REVERT: G 418 TRP cc_start: 0.7673 (t-100) cc_final: 0.6522 (t-100) REVERT: A 545 ASN cc_start: 0.7234 (t0) cc_final: 0.6730 (t0) outliers start: 63 outliers final: 38 residues processed: 231 average time/residue: 0.1557 time to fit residues: 53.6854 Evaluate side-chains 194 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 558 LYS Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 450 HIS Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 133 optimal weight: 0.5980 chunk 17 optimal weight: 0.0060 chunk 110 optimal weight: 0.0010 chunk 210 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 36 optimal weight: 0.0000 chunk 34 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 74 optimal weight: 0.0570 chunk 88 optimal weight: 1.9990 overall best weight: 0.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 HIS ** K 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS F 487 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.241182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.181547 restraints weight = 26292.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.179246 restraints weight = 35537.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.172233 restraints weight = 27711.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.172584 restraints weight = 32343.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173304 restraints weight = 28895.998| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20966 Z= 0.088 Angle : 0.511 14.471 28714 Z= 0.258 Chirality : 0.043 0.289 3351 Planarity : 0.004 0.044 3675 Dihedral : 3.685 31.834 2972 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.98 % Allowed : 18.37 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.16), residues: 2582 helix: 0.00 (0.32), residues: 252 sheet: 1.47 (0.16), residues: 953 loop : -0.21 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 451 TYR 0.014 0.001 TYR N 160 PHE 0.018 0.001 PHE H 354 TRP 0.023 0.001 TRP E 418 HIS 0.011 0.001 HIS E 450 Details of bonding type rmsd covalent geometry : bond 0.00199 (20920) covalent geometry : angle 0.49165 (28614) SS BOND : bond 0.00421 ( 38) SS BOND : angle 1.23904 ( 76) hydrogen bonds : bond 0.02949 ( 648) hydrogen bonds : angle 5.10048 ( 2019) link_BETA1-4 : bond 0.00909 ( 1) link_BETA1-4 : angle 1.45855 ( 3) link_NAG-ASN : bond 0.00521 ( 7) link_NAG-ASN : angle 4.60498 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.809 Fit side-chains REVERT: B 423 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7379 (mtm110) REVERT: B 441 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6587 (pp) REVERT: B 489 MET cc_start: 0.7707 (mtp) cc_final: 0.7402 (mtt) REVERT: C 462 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7473 (pt0) REVERT: K 359 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5823 (mm) REVERT: K 364 LYS cc_start: 0.6608 (ptpp) cc_final: 0.6024 (ptpp) REVERT: K 489 MET cc_start: 0.8500 (mtm) cc_final: 0.8259 (mtp) REVERT: H 495 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7794 (mp) REVERT: G 418 TRP cc_start: 0.7676 (t-100) cc_final: 0.6631 (t-100) REVERT: E 350 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7262 (pt) REVERT: F 568 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6466 (tmm) REVERT: A 545 ASN cc_start: 0.7326 (t0) cc_final: 0.6808 (t0) outliers start: 46 outliers final: 20 residues processed: 195 average time/residue: 0.1603 time to fit residues: 46.8470 Evaluate side-chains 185 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 281 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 552 VAL Chi-restraints excluded: chain K residue 560 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 163 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 210 optimal weight: 0.0170 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 ASN B 465 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.240078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.181670 restraints weight = 26278.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.179038 restraints weight = 37514.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.176154 restraints weight = 36785.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175938 restraints weight = 35849.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.176213 restraints weight = 32197.519| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20966 Z= 0.136 Angle : 0.544 14.132 28714 Z= 0.276 Chirality : 0.044 0.270 3351 Planarity : 0.004 0.044 3675 Dihedral : 3.785 36.306 2972 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.11 % Allowed : 17.98 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.16), residues: 2582 helix: 0.01 (0.32), residues: 265 sheet: 1.52 (0.17), residues: 953 loop : -0.25 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 467 TYR 0.011 0.001 TYR F 515 PHE 0.022 0.002 PHE H 424 TRP 0.015 0.001 TRP N 159 HIS 0.006 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00341 (20920) covalent geometry : angle 0.52650 (28614) SS BOND : bond 0.00454 ( 38) SS BOND : angle 1.32460 ( 76) hydrogen bonds : bond 0.03384 ( 648) hydrogen bonds : angle 5.10918 ( 2019) link_BETA1-4 : bond 0.00816 ( 1) link_BETA1-4 : angle 1.33228 ( 3) link_NAG-ASN : bond 0.00518 ( 7) link_NAG-ASN : angle 4.47293 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.626 Fit side-chains REVERT: B 423 ARG cc_start: 0.7733 (mtm110) cc_final: 0.7329 (mtm110) REVERT: B 441 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6527 (pp) REVERT: B 489 MET cc_start: 0.7765 (mtp) cc_final: 0.7440 (mtt) REVERT: B 506 MET cc_start: 0.6728 (mtt) cc_final: 0.6430 (mtm) REVERT: C 462 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7464 (pt0) REVERT: C 503 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8764 (t) REVERT: L 549 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: K 359 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5965 (mm) REVERT: K 364 LYS cc_start: 0.7041 (ptpp) cc_final: 0.6522 (ptpp) REVERT: K 489 MET cc_start: 0.8490 (mtm) cc_final: 0.8262 (mtp) REVERT: H 495 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7787 (mp) REVERT: G 418 TRP cc_start: 0.7674 (t-100) cc_final: 0.6785 (t-100) REVERT: E 350 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7037 (pt) REVERT: F 525 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7300 (tm-30) outliers start: 49 outliers final: 30 residues processed: 206 average time/residue: 0.1510 time to fit residues: 46.1116 Evaluate side-chains 199 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 357 ILE Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 552 VAL Chi-restraints excluded: chain K residue 560 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 247 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 174 optimal weight: 0.0040 chunk 103 optimal weight: 0.0470 chunk 109 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 59 optimal weight: 0.0670 chunk 157 optimal weight: 9.9990 overall best weight: 0.3830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN H 510 GLN F 487 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.241340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.187013 restraints weight = 26040.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.184230 restraints weight = 37974.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.181094 restraints weight = 37453.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180594 restraints weight = 34035.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179792 restraints weight = 32284.031| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20966 Z= 0.099 Angle : 0.510 13.852 28714 Z= 0.259 Chirality : 0.043 0.265 3351 Planarity : 0.004 0.043 3675 Dihedral : 3.649 36.155 2972 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.98 % Allowed : 18.54 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.16), residues: 2582 helix: 0.01 (0.32), residues: 264 sheet: 1.58 (0.17), residues: 963 loop : -0.15 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 467 TYR 0.015 0.001 TYR N 160 PHE 0.013 0.001 PHE H 354 TRP 0.017 0.001 TRP N 159 HIS 0.004 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00237 (20920) covalent geometry : angle 0.49309 (28614) SS BOND : bond 0.00361 ( 38) SS BOND : angle 1.30994 ( 76) hydrogen bonds : bond 0.02924 ( 648) hydrogen bonds : angle 4.86026 ( 2019) link_BETA1-4 : bond 0.00649 ( 1) link_BETA1-4 : angle 1.34547 ( 3) link_NAG-ASN : bond 0.00551 ( 7) link_NAG-ASN : angle 4.26129 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: B 441 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6589 (pp) REVERT: B 489 MET cc_start: 0.7745 (mtp) cc_final: 0.7419 (mtt) REVERT: B 506 MET cc_start: 0.6585 (mtt) cc_final: 0.6283 (mtm) REVERT: C 462 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7459 (pt0) REVERT: L 549 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6588 (tt0) REVERT: K 359 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5865 (mm) REVERT: K 364 LYS cc_start: 0.7060 (ptpp) cc_final: 0.6538 (ptpp) REVERT: K 489 MET cc_start: 0.8460 (mtm) cc_final: 0.8231 (mtp) REVERT: H 495 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7768 (mp) REVERT: G 418 TRP cc_start: 0.7685 (t-100) cc_final: 0.6833 (t-100) REVERT: E 350 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.6936 (pt) REVERT: E 568 MET cc_start: 0.6988 (tpp) cc_final: 0.6006 (mtt) REVERT: F 525 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7237 (tm-30) REVERT: F 568 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6547 (tmm) REVERT: A 545 ASN cc_start: 0.7450 (t0) cc_final: 0.6938 (t0) outliers start: 46 outliers final: 28 residues processed: 204 average time/residue: 0.1592 time to fit residues: 48.5356 Evaluate side-chains 199 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 552 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 146 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS F 487 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.216067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.184457 restraints weight = 24791.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.170568 restraints weight = 59475.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.159806 restraints weight = 40015.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160098 restraints weight = 43469.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.160975 restraints weight = 27066.277| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20966 Z= 0.160 Angle : 0.559 13.806 28714 Z= 0.285 Chirality : 0.045 0.260 3351 Planarity : 0.004 0.045 3675 Dihedral : 3.842 30.080 2972 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.54 % Allowed : 18.32 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.16), residues: 2582 helix: -0.09 (0.32), residues: 271 sheet: 1.55 (0.17), residues: 953 loop : -0.27 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 443 TYR 0.017 0.001 TYR N 160 PHE 0.023 0.002 PHE K 516 TRP 0.025 0.001 TRP N 159 HIS 0.007 0.001 HIS G 518 Details of bonding type rmsd covalent geometry : bond 0.00405 (20920) covalent geometry : angle 0.54216 (28614) SS BOND : bond 0.00469 ( 38) SS BOND : angle 1.51932 ( 76) hydrogen bonds : bond 0.03492 ( 648) hydrogen bonds : angle 5.04422 ( 2019) link_BETA1-4 : bond 0.00572 ( 1) link_BETA1-4 : angle 1.21835 ( 3) link_NAG-ASN : bond 0.00550 ( 7) link_NAG-ASN : angle 4.23198 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 0.617 Fit side-chains REVERT: N 308 ILE cc_start: 0.7237 (mt) cc_final: 0.6940 (mt) REVERT: B 441 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6415 (pp) REVERT: B 489 MET cc_start: 0.7808 (mtp) cc_final: 0.7486 (mtt) REVERT: B 506 MET cc_start: 0.6595 (mtt) cc_final: 0.6296 (mtm) REVERT: C 462 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7515 (pt0) REVERT: C 503 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8352 (t) REVERT: L 545 ASN cc_start: 0.6972 (t0) cc_final: 0.6502 (t0) REVERT: L 549 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: K 359 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.6054 (mm) REVERT: K 364 LYS cc_start: 0.7038 (ptpp) cc_final: 0.6439 (ptpp) REVERT: K 489 MET cc_start: 0.8465 (mtm) cc_final: 0.8219 (mtp) REVERT: H 495 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7814 (mp) REVERT: G 418 TRP cc_start: 0.7823 (t-100) cc_final: 0.6789 (t-100) REVERT: E 350 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7410 (pt) REVERT: E 445 LYS cc_start: 0.6241 (mppt) cc_final: 0.5455 (mppt) REVERT: E 568 MET cc_start: 0.7077 (tpp) cc_final: 0.6084 (mtt) REVERT: F 525 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7262 (tm-30) REVERT: F 527 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: F 568 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6431 (tmm) REVERT: J 23 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6666 (tpp-160) outliers start: 59 outliers final: 42 residues processed: 221 average time/residue: 0.1576 time to fit residues: 51.3795 Evaluate side-chains 221 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 552 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 87 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 243 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 chunk 16 optimal weight: 0.0470 chunk 219 optimal weight: 0.5980 chunk 250 optimal weight: 0.0370 chunk 104 optimal weight: 0.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 518 HIS F 487 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.217845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.181876 restraints weight = 24941.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.183247 restraints weight = 56115.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.182690 restraints weight = 38829.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.181733 restraints weight = 27170.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.182233 restraints weight = 23048.505| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20966 Z= 0.104 Angle : 0.511 13.493 28714 Z= 0.259 Chirality : 0.043 0.255 3351 Planarity : 0.004 0.039 3675 Dihedral : 3.703 27.343 2972 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.06 % Allowed : 18.75 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.17), residues: 2582 helix: -0.00 (0.32), residues: 265 sheet: 1.62 (0.17), residues: 963 loop : -0.15 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.017 0.001 TYR N 160 PHE 0.013 0.001 PHE L 485 TRP 0.041 0.001 TRP E 418 HIS 0.004 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00253 (20920) covalent geometry : angle 0.49593 (28614) SS BOND : bond 0.00376 ( 38) SS BOND : angle 1.11492 ( 76) hydrogen bonds : bond 0.02916 ( 648) hydrogen bonds : angle 4.76540 ( 2019) link_BETA1-4 : bond 0.00616 ( 1) link_BETA1-4 : angle 1.18154 ( 3) link_NAG-ASN : bond 0.00568 ( 7) link_NAG-ASN : angle 4.07972 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.718 Fit side-chains REVERT: N 308 ILE cc_start: 0.6968 (mt) cc_final: 0.6659 (mt) REVERT: B 441 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6466 (pp) REVERT: B 489 MET cc_start: 0.7713 (mtp) cc_final: 0.7382 (mtt) REVERT: B 506 MET cc_start: 0.6426 (mtt) cc_final: 0.6117 (mtm) REVERT: C 462 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7433 (pt0) REVERT: C 483 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7800 (p0) REVERT: L 549 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: K 359 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5766 (mm) REVERT: K 364 LYS cc_start: 0.7161 (ptpp) cc_final: 0.6805 (ptpp) REVERT: K 489 MET cc_start: 0.8465 (mtm) cc_final: 0.8209 (mtp) REVERT: H 495 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7697 (mp) REVERT: G 418 TRP cc_start: 0.7605 (t-100) cc_final: 0.6835 (t-100) REVERT: E 350 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6801 (pt) REVERT: F 525 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7212 (tm-30) REVERT: F 527 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: F 568 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6416 (tmm) REVERT: A 545 ASN cc_start: 0.7521 (t0) cc_final: 0.6965 (t0) outliers start: 48 outliers final: 29 residues processed: 205 average time/residue: 0.1485 time to fit residues: 46.5666 Evaluate side-chains 199 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 81 optimal weight: 0.0670 chunk 172 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 144 optimal weight: 0.0870 chunk 37 optimal weight: 0.0370 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.197620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131323 restraints weight = 24949.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131263 restraints weight = 29528.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129001 restraints weight = 18451.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127878 restraints weight = 15276.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128307 restraints weight = 16165.955| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20966 Z= 0.096 Angle : 0.502 13.328 28714 Z= 0.253 Chirality : 0.043 0.259 3351 Planarity : 0.004 0.038 3675 Dihedral : 3.587 22.987 2972 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.94 % Allowed : 19.10 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.17), residues: 2582 helix: 0.00 (0.32), residues: 266 sheet: 1.67 (0.16), residues: 963 loop : -0.09 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.016 0.001 TYR N 160 PHE 0.011 0.001 PHE L 485 TRP 0.026 0.001 TRP E 418 HIS 0.011 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00233 (20920) covalent geometry : angle 0.48834 (28614) SS BOND : bond 0.00359 ( 38) SS BOND : angle 1.04032 ( 76) hydrogen bonds : bond 0.02772 ( 648) hydrogen bonds : angle 4.62483 ( 2019) link_BETA1-4 : bond 0.00574 ( 1) link_BETA1-4 : angle 1.17446 ( 3) link_NAG-ASN : bond 0.00596 ( 7) link_NAG-ASN : angle 3.90119 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.641 Fit side-chains REVERT: N 308 ILE cc_start: 0.7211 (mt) cc_final: 0.6951 (mt) REVERT: B 441 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6206 (pp) REVERT: B 465 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7905 (t0) REVERT: B 489 MET cc_start: 0.7921 (mtp) cc_final: 0.7536 (mtt) REVERT: B 506 MET cc_start: 0.6364 (mtt) cc_final: 0.6056 (mtm) REVERT: C 462 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7691 (pt0) REVERT: C 483 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7770 (p0) REVERT: L 549 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: K 359 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5958 (mm) REVERT: K 364 LYS cc_start: 0.6981 (ptpp) cc_final: 0.6476 (ptpp) REVERT: K 415 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7078 (tm-30) REVERT: K 489 MET cc_start: 0.8587 (mtm) cc_final: 0.8281 (mtp) REVERT: H 384 ARG cc_start: 0.6435 (mpp80) cc_final: 0.5921 (mpp80) REVERT: H 495 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7504 (mp) REVERT: G 418 TRP cc_start: 0.7763 (t-100) cc_final: 0.6732 (t-100) REVERT: E 350 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7354 (pt) REVERT: E 467 ARG cc_start: 0.7566 (mmp80) cc_final: 0.7326 (mmp80) REVERT: F 525 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7026 (tm-30) REVERT: F 527 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: F 568 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6418 (tmm) REVERT: A 545 ASN cc_start: 0.7328 (t0) cc_final: 0.6787 (t0) outliers start: 45 outliers final: 33 residues processed: 201 average time/residue: 0.1548 time to fit residues: 46.9151 Evaluate side-chains 209 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 54 optimal weight: 0.3980 chunk 132 optimal weight: 0.0270 chunk 176 optimal weight: 0.0060 chunk 238 optimal weight: 2.9990 chunk 235 optimal weight: 0.0030 chunk 203 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 197 optimal weight: 0.0170 chunk 227 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 163 optimal weight: 8.9990 overall best weight: 0.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 419 ASN ** K 518 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 = 0.4304 r_free = 0.4304 target = 0.199095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.130473 restraints weight = 24828.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123867 restraints weight = 22902.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125569 restraints weight = 20125.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126129 restraints weight = 16088.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126211 restraints weight = 15070.452| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20966 Z= 0.083 Angle : 0.493 13.323 28714 Z= 0.248 Chirality : 0.042 0.260 3351 Planarity : 0.004 0.036 3675 Dihedral : 3.495 22.556 2972 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.42 % Allowed : 19.57 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.17), residues: 2582 helix: 0.03 (0.32), residues: 265 sheet: 1.73 (0.17), residues: 957 loop : 0.02 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 467 TYR 0.015 0.001 TYR N 160 PHE 0.010 0.001 PHE K 479 TRP 0.027 0.001 TRP E 418 HIS 0.019 0.001 HIS K 518 Details of bonding type rmsd covalent geometry : bond 0.00189 (20920) covalent geometry : angle 0.48053 (28614) SS BOND : bond 0.00296 ( 38) SS BOND : angle 0.88489 ( 76) hydrogen bonds : bond 0.02510 ( 648) hydrogen bonds : angle 4.46633 ( 2019) link_BETA1-4 : bond 0.00586 ( 1) link_BETA1-4 : angle 1.16012 ( 3) link_NAG-ASN : bond 0.00650 ( 7) link_NAG-ASN : angle 3.85053 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5164 Ramachandran restraints generated. 2582 Oldfield, 0 Emsley, 2582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.715 Fit side-chains REVERT: N 308 ILE cc_start: 0.7199 (mt) cc_final: 0.6957 (mt) REVERT: B 441 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5932 (pp) REVERT: B 489 MET cc_start: 0.7893 (mtp) cc_final: 0.7531 (mtt) REVERT: B 506 MET cc_start: 0.6158 (mtt) cc_final: 0.5860 (mtm) REVERT: C 462 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7717 (pt0) REVERT: C 483 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7672 (p0) REVERT: K 359 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5910 (mm) REVERT: K 364 LYS cc_start: 0.6642 (ptpp) cc_final: 0.6146 (ptpp) REVERT: K 489 MET cc_start: 0.8561 (mtm) cc_final: 0.8252 (mtp) REVERT: H 384 ARG cc_start: 0.6096 (mpp80) cc_final: 0.5545 (mpp80) REVERT: H 495 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7533 (mp) REVERT: G 418 TRP cc_start: 0.7657 (t-100) cc_final: 0.6614 (t-100) REVERT: E 350 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.6940 (tp) REVERT: E 568 MET cc_start: 0.6844 (tpp) cc_final: 0.5877 (mtt) REVERT: F 525 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7046 (tm-30) REVERT: F 527 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: F 568 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6392 (tmm) REVERT: A 545 ASN cc_start: 0.7301 (t0) cc_final: 0.6763 (t0) outliers start: 33 outliers final: 24 residues processed: 189 average time/residue: 0.1628 time to fit residues: 45.6672 Evaluate side-chains 191 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 518 HIS Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain G residue 568 MET Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 158 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 125 optimal weight: 0.2980 chunk 237 optimal weight: 0.9990 chunk 243 optimal weight: 0.0870 chunk 79 optimal weight: 0.3980 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 225 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 0.0270 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN ** K 518 HIS ** 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 = 0.4291 r_free = 0.4291 target = 0.198215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.129450 restraints weight = 24795.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126709 restraints weight = 27906.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128559 restraints weight = 21652.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129116 restraints weight = 16701.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129318 restraints weight = 16013.630| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20966 Z= 0.090 Angle : 0.493 13.254 28714 Z= 0.248 Chirality : 0.043 0.256 3351 Planarity : 0.004 0.038 3675 Dihedral : 3.445 22.151 2972 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.63 % Allowed : 19.35 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.17), residues: 2582 helix: 0.07 (0.32), residues: 266 sheet: 1.79 (0.17), residues: 953 loop : 0.03 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 467 TYR 0.014 0.001 TYR N 160 PHE 0.015 0.001 PHE H 354 TRP 0.024 0.001 TRP E 418 HIS 0.012 0.001 HIS K 518 Details of bonding type rmsd covalent geometry : bond 0.00216 (20920) covalent geometry : angle 0.47992 (28614) SS BOND : bond 0.00319 ( 38) SS BOND : angle 0.94211 ( 76) hydrogen bonds : bond 0.02571 ( 648) hydrogen bonds : angle 4.43760 ( 2019) link_BETA1-4 : bond 0.00631 ( 1) link_BETA1-4 : angle 1.15309 ( 3) link_NAG-ASN : bond 0.00620 ( 7) link_NAG-ASN : angle 3.79849 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.43 seconds wall clock time: 62 minutes 35.81 seconds (3755.81 seconds total)