Starting phenix.real_space_refine on Wed May 21 00:42:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r83_18993/05_2025/8r83_18993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r83_18993/05_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_18993/05_2025/8r83_18993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r83_18993/05_2025/8r83_18993.map" model { file = "/net/cci-nas-00/data/ceres_data/8r83_18993/05_2025/8r83_18993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r83_18993/05_2025/8r83_18993.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.55, per 1000 atoms: 0.86 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: 5.11 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 3.50 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: 7.69 Time building geometry restraints manager: 5.75 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: 12.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 52.370 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.580 ------------------------------------------------------------------------------- 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 : 4.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (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 TRP 0.012 0.001 TRP K 418 HIS 0.007 0.001 HIS H 518 PHE 0.029 0.001 PHE H 354 TYR 0.014 0.001 TYR L 515 ARG 0.007 0.000 ARG A 546 Details of bonding type rmsd link_NAG-ASN : bond 0.04310 ( 7) link_NAG-ASN : angle 17.46076 ( 21) link_BETA1-4 : bond 0.02198 ( 1) link_BETA1-4 : angle 4.42802 ( 3) hydrogen bonds : bond 0.29130 ( 648) hydrogen bonds : angle 9.24858 ( 2019) SS BOND : bond 0.02691 ( 38) SS BOND : angle 1.13411 ( 76) covalent geometry : bond 0.00678 (20920) covalent geometry : angle 0.81763 (28614) *********************** 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 : 2.271 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: 0.3816 time to fit residues: 157.2895 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 : 2.202 ------------------------------------------------------------------------------- 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 215 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 148 optimal weight: 0.0970 chunk 231 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN D 545 ASN L 545 ASN ** K 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS F 400 HIS F 518 HIS A 465 ASN J 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.244101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.185398 restraints weight = 26247.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.184122 restraints weight = 36761.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.179200 restraints weight = 33684.310| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20966 Z= 0.156 Angle : 0.620 21.441 28714 Z= 0.313 Chirality : 0.045 0.347 3351 Planarity : 0.005 0.069 3675 Dihedral : 4.041 50.009 2975 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.54 % Allowed : 16.73 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2582 helix: -0.08 (0.32), residues: 254 sheet: 1.21 (0.17), residues: 928 loop : -0.24 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 235 HIS 0.008 0.001 HIS F 518 PHE 0.030 0.002 PHE H 424 TYR 0.010 0.001 TYR N 301 ARG 0.005 0.000 ARG G 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 7) link_NAG-ASN : angle 7.77907 ( 21) link_BETA1-4 : bond 0.01438 ( 1) link_BETA1-4 : angle 1.58533 ( 3) hydrogen bonds : bond 0.05082 ( 648) hydrogen bonds : angle 6.21078 ( 2019) SS BOND : bond 0.00462 ( 38) SS BOND : angle 1.28511 ( 76) covalent geometry : bond 0.00371 (20920) covalent geometry : angle 0.58052 (28614) *********************** 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 254 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 2.252 Fit side-chains revert: symmetry clash REVERT: B 423 ARG cc_start: 0.7802 (mtm110) cc_final: 0.7245 (mtm110) REVERT: H 415 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: G 418 TRP cc_start: 0.7471 (t-100) cc_final: 0.7054 (t-100) REVERT: E 416 ASP cc_start: 0.7558 (p0) cc_final: 0.6949 (p0) REVERT: F 568 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6666 (tmm) outliers start: 59 outliers final: 23 residues processed: 243 average time/residue: 0.3629 time to fit residues: 130.4549 Evaluate side-chains 193 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 560 THR 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 226 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 252 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 254 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 400 HIS L 545 ASN H 419 ASN ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.195852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127563 restraints weight = 24662.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121627 restraints weight = 23225.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124176 restraints weight = 19632.024| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20966 Z= 0.167 Angle : 0.595 14.549 28714 Z= 0.305 Chirality : 0.046 0.290 3351 Planarity : 0.005 0.055 3675 Dihedral : 3.899 26.157 2972 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.37 % Allowed : 17.33 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2582 helix: -0.03 (0.32), residues: 264 sheet: 1.32 (0.16), residues: 947 loop : -0.37 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 418 HIS 0.011 0.001 HIS L 518 PHE 0.022 0.002 PHE K 516 TYR 0.015 0.001 TYR N 160 ARG 0.005 0.000 ARG C 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 7) link_NAG-ASN : angle 5.27145 ( 21) link_BETA1-4 : bond 0.00870 ( 1) link_BETA1-4 : angle 1.44002 ( 3) hydrogen bonds : bond 0.04296 ( 648) hydrogen bonds : angle 5.61212 ( 2019) SS BOND : bond 0.00590 ( 38) SS BOND : angle 1.24217 ( 76) covalent geometry : bond 0.00414 (20920) covalent geometry : angle 0.57463 (28614) *********************** 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: 55 poor density : 187 time to evaluate : 2.105 Fit side-chains REVERT: N 154 LYS cc_start: 0.6496 (tttm) cc_final: 0.5999 (mmtm) REVERT: L 545 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.6334 (t0) REVERT: K 359 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5978 (mm) REVERT: K 525 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7420 (tm-30) REVERT: G 418 TRP cc_start: 0.7629 (t-100) cc_final: 0.6498 (t-100) REVERT: A 545 ASN cc_start: 0.7260 (t0) cc_final: 0.6871 (t0) REVERT: A 568 MET cc_start: 0.8055 (mtp) cc_final: 0.7815 (mtp) outliers start: 55 outliers final: 33 residues processed: 232 average time/residue: 0.3535 time to fit residues: 122.6436 Evaluate side-chains 200 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 2.065 ------------------------------------------------------------------------------- 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 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL 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 447 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 545 ASN 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 560 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 568 MET 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 538 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 83 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 59 optimal weight: 0.0270 chunk 39 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 222 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN A 540 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.195707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127847 restraints weight = 24751.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123518 restraints weight = 26720.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125675 restraints weight = 22285.638| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20966 Z= 0.137 Angle : 0.550 14.624 28714 Z= 0.279 Chirality : 0.044 0.273 3351 Planarity : 0.004 0.048 3675 Dihedral : 3.873 34.017 2972 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.45 % Allowed : 17.85 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2582 helix: -0.05 (0.32), residues: 264 sheet: 1.37 (0.17), residues: 955 loop : -0.33 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 418 HIS 0.006 0.001 HIS L 518 PHE 0.016 0.001 PHE F 479 TYR 0.015 0.001 TYR N 160 ARG 0.003 0.000 ARG B 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 7) link_NAG-ASN : angle 4.89598 ( 21) link_BETA1-4 : bond 0.00861 ( 1) link_BETA1-4 : angle 1.39518 ( 3) hydrogen bonds : bond 0.03537 ( 648) hydrogen bonds : angle 5.32871 ( 2019) SS BOND : bond 0.00543 ( 38) SS BOND : angle 1.09968 ( 76) covalent geometry : bond 0.00340 (20920) covalent geometry : angle 0.53184 (28614) *********************** 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 222 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 2.078 Fit side-chains REVERT: N 154 LYS cc_start: 0.6550 (tttm) cc_final: 0.6063 (mmtm) REVERT: B 423 ARG cc_start: 0.8325 (mtm110) cc_final: 0.7591 (mtm110) REVERT: C 418 TRP cc_start: 0.6096 (t-100) cc_final: 0.5877 (t-100) REVERT: L 549 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: K 359 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5898 (mm) REVERT: K 364 LYS cc_start: 0.6634 (ptpp) cc_final: 0.6023 (ptpp) REVERT: H 495 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7609 (mp) REVERT: G 418 TRP cc_start: 0.7690 (t-100) cc_final: 0.6486 (t-100) REVERT: E 350 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7571 (pt) REVERT: F 568 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6408 (tmm) REVERT: A 545 ASN cc_start: 0.7247 (t0) cc_final: 0.6696 (t0) outliers start: 57 outliers final: 40 residues processed: 209 average time/residue: 0.3266 time to fit residues: 103.5665 Evaluate side-chains 201 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 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 C residue 414 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR 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 516 PHE 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 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 484 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain E residue 350 ILE 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 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 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 16 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 202 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.194319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125853 restraints weight = 24857.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117848 restraints weight = 21989.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120073 restraints weight = 20114.920| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20966 Z= 0.148 Angle : 0.558 14.004 28714 Z= 0.284 Chirality : 0.045 0.261 3351 Planarity : 0.004 0.046 3675 Dihedral : 3.977 42.121 2972 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.84 % Allowed : 17.89 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2582 helix: -0.09 (0.32), residues: 264 sheet: 1.45 (0.17), residues: 951 loop : -0.34 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 418 HIS 0.007 0.001 HIS G 518 PHE 0.020 0.002 PHE K 516 TYR 0.014 0.001 TYR F 515 ARG 0.003 0.000 ARG G 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 7) link_NAG-ASN : angle 4.48112 ( 21) link_BETA1-4 : bond 0.01259 ( 1) link_BETA1-4 : angle 1.22305 ( 3) hydrogen bonds : bond 0.03509 ( 648) hydrogen bonds : angle 5.17376 ( 2019) SS BOND : bond 0.00567 ( 38) SS BOND : angle 1.19733 ( 76) covalent geometry : bond 0.00370 (20920) covalent geometry : angle 0.54223 (28614) *********************** 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 237 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 171 time to evaluate : 2.212 Fit side-chains REVERT: N 154 LYS cc_start: 0.6684 (tttm) cc_final: 0.6089 (mmtm) REVERT: N 193 LYS cc_start: 0.3860 (mmpt) cc_final: 0.3657 (pttt) REVERT: B 423 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7664 (mtm110) REVERT: L 545 ASN cc_start: 0.7207 (t0) cc_final: 0.6680 (t0) REVERT: K 359 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5933 (mm) REVERT: K 489 MET cc_start: 0.8658 (mtm) cc_final: 0.8361 (mtp) REVERT: H 415 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: H 495 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7690 (mp) REVERT: G 418 TRP cc_start: 0.7694 (t-100) cc_final: 0.6555 (t-100) REVERT: E 350 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7724 (pt) REVERT: E 568 MET cc_start: 0.6949 (tpp) cc_final: 0.5983 (mtt) REVERT: F 525 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7144 (tm-30) REVERT: F 527 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: A 545 ASN cc_start: 0.7444 (t0) cc_final: 0.6853 (t0) REVERT: J 70 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.5970 (mtmt) outliers start: 66 outliers final: 45 residues processed: 227 average time/residue: 0.3379 time to fit residues: 116.8401 Evaluate side-chains 216 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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 185 VAL 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 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR 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 357 ILE Chi-restraints excluded: chain L residue 447 VAL 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 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 415 GLU 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 484 VAL 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 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 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 551 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 70 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 163 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 225 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 209 optimal weight: 0.0670 chunk 193 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 249 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.4728 ------------------------------------------------------------------------------- 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** H 510 GLN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.240489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.184282 restraints weight = 26129.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.182248 restraints weight = 39106.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.178811 restraints weight = 35916.965| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20966 Z= 0.109 Angle : 0.524 13.642 28714 Z= 0.265 Chirality : 0.043 0.259 3351 Planarity : 0.004 0.043 3675 Dihedral : 3.777 40.894 2972 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.28 % Allowed : 18.62 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2582 helix: -0.12 (0.32), residues: 266 sheet: 1.50 (0.17), residues: 963 loop : -0.23 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 418 HIS 0.004 0.001 HIS G 518 PHE 0.023 0.001 PHE H 424 TYR 0.014 0.001 TYR N 160 ARG 0.005 0.000 ARG N 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 7) link_NAG-ASN : angle 4.21838 ( 21) link_BETA1-4 : bond 0.00668 ( 1) link_BETA1-4 : angle 1.30029 ( 3) hydrogen bonds : bond 0.02999 ( 648) hydrogen bonds : angle 4.90730 ( 2019) SS BOND : bond 0.00484 ( 38) SS BOND : angle 1.23845 ( 76) covalent geometry : bond 0.00266 (20920) covalent geometry : angle 0.50863 (28614) *********************** 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 222 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 2.228 Fit side-chains REVERT: N 193 LYS cc_start: 0.4361 (mmpt) cc_final: 0.3811 (pttt) REVERT: B 423 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7313 (mtm110) REVERT: B 506 MET cc_start: 0.6650 (mtt) cc_final: 0.6321 (mtm) REVERT: C 418 TRP cc_start: 0.6089 (t-100) cc_final: 0.5827 (t60) REVERT: C 462 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7486 (pt0) REVERT: C 503 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8536 (t) REVERT: D 506 MET cc_start: 0.7497 (mtt) cc_final: 0.7118 (mtt) REVERT: L 549 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6589 (tt0) REVERT: K 359 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5768 (mm) REVERT: G 418 TRP cc_start: 0.7635 (t-100) cc_final: 0.6802 (t-100) REVERT: E 350 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.6970 (pt) REVERT: E 568 MET cc_start: 0.6922 (tpp) cc_final: 0.6035 (mtt) REVERT: F 525 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7290 (tm-30) REVERT: F 527 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: F 568 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6500 (tmm) REVERT: A 545 ASN cc_start: 0.7570 (t0) cc_final: 0.6971 (t0) outliers start: 53 outliers final: 33 residues processed: 211 average time/residue: 0.3608 time to fit residues: 113.9547 Evaluate side-chains 195 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 TRP Chi-restraints excluded: chain N residue 168 SER 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 465 ASN Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 551 THR 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 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL 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 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 568 MET 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 551 THR 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 82 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 209 optimal weight: 0.3980 chunk 161 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 487 GLN H 419 ASN ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.191798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126168 restraints weight = 25066.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118507 restraints weight = 26314.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120432 restraints weight = 24404.791| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 20966 Z= 0.270 Angle : 0.679 13.780 28714 Z= 0.350 Chirality : 0.049 0.258 3351 Planarity : 0.005 0.050 3675 Dihedral : 4.443 37.335 2972 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.97 % Allowed : 18.28 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2582 helix: -0.30 (0.32), residues: 269 sheet: 1.23 (0.17), residues: 962 loop : -0.59 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 418 HIS 0.011 0.001 HIS C 518 PHE 0.038 0.003 PHE K 516 TYR 0.026 0.002 TYR F 515 ARG 0.005 0.001 ARG E 451 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 7) link_NAG-ASN : angle 4.37847 ( 21) link_BETA1-4 : bond 0.00465 ( 1) link_BETA1-4 : angle 1.05754 ( 3) hydrogen bonds : bond 0.04580 ( 648) hydrogen bonds : angle 5.50950 ( 2019) SS BOND : bond 0.00619 ( 38) SS BOND : angle 1.89493 ( 76) covalent geometry : bond 0.00687 (20920) covalent geometry : angle 0.66232 (28614) *********************** 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 246 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 177 time to evaluate : 2.246 Fit side-chains REVERT: B 506 MET cc_start: 0.6828 (mtt) cc_final: 0.6503 (mtm) REVERT: D 499 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8425 (tptm) REVERT: D 506 MET cc_start: 0.7399 (mtt) cc_final: 0.7040 (mtp) REVERT: L 545 ASN cc_start: 0.7242 (t0) cc_final: 0.6851 (t0) REVERT: L 549 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6998 (tt0) REVERT: K 359 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.6052 (mm) REVERT: K 364 LYS cc_start: 0.7291 (ptpp) cc_final: 0.6575 (ptpp) REVERT: K 516 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8615 (p90) REVERT: H 423 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7524 (ptm-80) REVERT: H 495 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7761 (mp) REVERT: G 418 TRP cc_start: 0.7799 (t-100) cc_final: 0.6743 (t-100) REVERT: E 350 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7750 (pt) REVERT: E 467 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7216 (mmp80) REVERT: E 568 MET cc_start: 0.7002 (tpp) cc_final: 0.6056 (mtt) REVERT: F 527 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: J 23 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6677 (tpp-160) outliers start: 69 outliers final: 47 residues processed: 232 average time/residue: 0.3680 time to fit residues: 128.5557 Evaluate side-chains 225 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR 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 357 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 516 PHE 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 477 THR Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 560 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL 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 467 ARG 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 456 LEU 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 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 551 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 571 THR 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 39 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 185 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 251 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.193648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126262 restraints weight = 25014.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118910 restraints weight = 25369.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121248 restraints weight = 22366.364| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3464 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= 0.160 Angle : 0.582 14.455 28714 Z= 0.298 Chirality : 0.045 0.250 3351 Planarity : 0.004 0.047 3675 Dihedral : 4.237 35.441 2972 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.75 % Allowed : 18.92 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2582 helix: -0.26 (0.32), residues: 269 sheet: 1.30 (0.17), residues: 963 loop : -0.49 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 418 HIS 0.006 0.001 HIS C 518 PHE 0.018 0.002 PHE L 485 TYR 0.018 0.001 TYR N 160 ARG 0.006 0.000 ARG H 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 7) link_NAG-ASN : angle 4.21106 ( 21) link_BETA1-4 : bond 0.00623 ( 1) link_BETA1-4 : angle 1.08377 ( 3) hydrogen bonds : bond 0.03533 ( 648) hydrogen bonds : angle 5.13481 ( 2019) SS BOND : bond 0.00482 ( 38) SS BOND : angle 1.91224 ( 76) covalent geometry : bond 0.00404 (20920) covalent geometry : angle 0.56282 (28614) *********************** 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 240 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 2.173 Fit side-chains REVERT: B 506 MET cc_start: 0.6531 (mtt) cc_final: 0.6189 (mtm) REVERT: C 418 TRP cc_start: 0.6079 (t-100) cc_final: 0.5606 (t60) REVERT: C 462 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7773 (pt0) REVERT: D 499 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8112 (tptm) REVERT: L 549 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: K 359 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5930 (mm) REVERT: K 364 LYS cc_start: 0.7072 (ptpp) cc_final: 0.6258 (ptpp) REVERT: H 423 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7399 (ptm-80) REVERT: H 495 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7679 (mp) REVERT: G 418 TRP cc_start: 0.7775 (t-100) cc_final: 0.6686 (t-100) REVERT: E 350 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7766 (pt) REVERT: E 467 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7247 (mmp80) REVERT: E 568 MET cc_start: 0.6994 (tpp) cc_final: 0.6034 (mtt) REVERT: F 525 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7171 (tm-30) REVERT: F 527 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: F 568 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6370 (tmm) REVERT: A 545 ASN cc_start: 0.7567 (t0) cc_final: 0.7047 (t0) REVERT: J 23 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6617 (tpp-160) outliers start: 64 outliers final: 41 residues processed: 225 average time/residue: 0.3552 time to fit residues: 120.0187 Evaluate side-chains 220 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 308 ILE 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 551 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 466 LEU 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 501 VAL Chi-restraints excluded: chain L residue 516 PHE 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 522 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 560 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL 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 467 ARG 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 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 113 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** ** G 540 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 = 0.4230 r_free = 0.4230 target = 0.191057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125171 restraints weight = 24951.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115606 restraints weight = 23772.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118810 restraints weight = 23734.759| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 20966 Z= 0.259 Angle : 0.673 13.416 28714 Z= 0.348 Chirality : 0.049 0.258 3351 Planarity : 0.005 0.051 3675 Dihedral : 4.609 29.642 2972 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.71 % Allowed : 19.10 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2582 helix: -0.39 (0.32), residues: 269 sheet: 1.09 (0.17), residues: 965 loop : -0.65 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 159 HIS 0.009 0.001 HIS C 518 PHE 0.032 0.003 PHE K 516 TYR 0.021 0.002 TYR F 515 ARG 0.005 0.000 ARG E 451 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 7) link_NAG-ASN : angle 4.21262 ( 21) link_BETA1-4 : bond 0.00495 ( 1) link_BETA1-4 : angle 0.94882 ( 3) hydrogen bonds : bond 0.04410 ( 648) hydrogen bonds : angle 5.47180 ( 2019) SS BOND : bond 0.00655 ( 38) SS BOND : angle 2.05054 ( 76) covalent geometry : bond 0.00662 (20920) covalent geometry : angle 0.65565 (28614) *********************** 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 242 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 179 time to evaluate : 2.272 Fit side-chains REVERT: B 506 MET cc_start: 0.6704 (mtt) cc_final: 0.6350 (mtm) REVERT: C 462 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7797 (pt0) REVERT: D 499 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8481 (tptm) REVERT: D 506 MET cc_start: 0.7404 (mtt) cc_final: 0.7085 (mtp) REVERT: L 549 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: K 359 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6097 (mm) REVERT: K 364 LYS cc_start: 0.7149 (ptpp) cc_final: 0.6364 (ptpp) REVERT: H 423 ARG cc_start: 0.8312 (mtt180) cc_final: 0.7301 (ptm-80) REVERT: H 495 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7753 (mp) REVERT: G 418 TRP cc_start: 0.7789 (t-100) cc_final: 0.6705 (t-100) REVERT: E 350 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7884 (pt) REVERT: E 467 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7234 (mmp80) REVERT: F 527 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: A 545 ASN cc_start: 0.7570 (t0) cc_final: 0.7120 (t0) REVERT: J 23 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6574 (tpp-160) outliers start: 63 outliers final: 48 residues processed: 231 average time/residue: 0.3713 time to fit residues: 128.0437 Evaluate side-chains 225 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 2.230 ------------------------------------------------------------------------------- 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 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 466 LEU 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 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 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 522 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 560 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 484 VAL 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 467 ARG Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 456 LEU 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 A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 68 CYS Chi-restraints excluded: chain J residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 42 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 chunk 187 optimal weight: 0.0000 chunk 125 optimal weight: 2.9990 chunk 221 optimal weight: 0.2980 chunk 163 optimal weight: 0.0050 chunk 126 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 171 optimal weight: 0.5980 chunk 103 optimal weight: 0.0010 overall best weight: 0.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 ASN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS 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 = 0.4284 r_free = 0.4284 target = 0.197019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130288 restraints weight = 25092.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126885 restraints weight = 30295.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129120 restraints weight = 23833.448| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3631 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= 0.094 Angle : 0.529 13.062 28714 Z= 0.270 Chirality : 0.043 0.249 3351 Planarity : 0.004 0.054 3675 Dihedral : 3.992 29.194 2972 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.38 % Allowed : 20.69 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2582 helix: -0.26 (0.31), residues: 265 sheet: 1.41 (0.17), residues: 949 loop : -0.33 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 418 HIS 0.005 0.001 HIS L 393 PHE 0.016 0.001 PHE H 354 TYR 0.014 0.001 TYR N 160 ARG 0.004 0.000 ARG G 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 7) link_NAG-ASN : angle 3.91469 ( 21) link_BETA1-4 : bond 0.00593 ( 1) link_BETA1-4 : angle 1.04707 ( 3) hydrogen bonds : bond 0.02746 ( 648) hydrogen bonds : angle 4.76839 ( 2019) SS BOND : bond 0.00308 ( 38) SS BOND : angle 1.28339 ( 76) covalent geometry : bond 0.00214 (20920) covalent geometry : angle 0.51438 (28614) ********************** 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 210 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 2.211 Fit side-chains REVERT: B 506 MET cc_start: 0.6180 (mtt) cc_final: 0.5889 (mtm) REVERT: L 549 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6789 (tt0) REVERT: K 359 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5846 (mm) REVERT: K 415 GLU cc_start: 0.7743 (tm-30) cc_final: 0.6891 (tm-30) REVERT: K 489 MET cc_start: 0.8583 (mtm) cc_final: 0.8250 (mtp) REVERT: H 384 ARG cc_start: 0.6440 (mpp80) cc_final: 0.5941 (mpp80) REVERT: G 418 TRP cc_start: 0.7708 (t-100) cc_final: 0.6714 (t-100) REVERT: E 350 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7106 (tp) REVERT: E 445 LYS cc_start: 0.6170 (mppt) cc_final: 0.5662 (mppt) REVERT: E 467 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7340 (mmp80) REVERT: F 525 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7186 (tm-30) REVERT: F 527 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: F 568 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6393 (tmm) REVERT: A 545 ASN cc_start: 0.7411 (t0) cc_final: 0.6868 (t0) outliers start: 32 outliers final: 22 residues processed: 199 average time/residue: 0.3508 time to fit residues: 104.9130 Evaluate side-chains 199 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 272 ASN Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain C residue 491 ARG Chi-restraints excluded: chain C residue 551 THR 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 471 THR Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain F residue 527 GLU 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 538 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 193 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 153 optimal weight: 0.0050 chunk 79 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 230 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.196024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128039 restraints weight = 25236.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123790 restraints weight = 27473.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.125931 restraints weight = 22217.363| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20966 Z= 0.113 Angle : 0.529 13.073 28714 Z= 0.270 Chirality : 0.044 0.250 3351 Planarity : 0.004 0.050 3675 Dihedral : 3.946 28.805 2972 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.46 % Allowed : 20.69 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2582 helix: -0.25 (0.32), residues: 265 sheet: 1.45 (0.17), residues: 959 loop : -0.34 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP N 202 HIS 0.021 0.001 HIS K 518 PHE 0.018 0.001 PHE H 354 TYR 0.014 0.001 TYR N 160 ARG 0.004 0.000 ARG B 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 7) link_NAG-ASN : angle 3.91311 ( 21) link_BETA1-4 : bond 0.00605 ( 1) link_BETA1-4 : angle 1.09054 ( 3) hydrogen bonds : bond 0.02899 ( 648) hydrogen bonds : angle 4.75986 ( 2019) SS BOND : bond 0.00408 ( 38) SS BOND : angle 1.33414 ( 76) covalent geometry : bond 0.00278 (20920) covalent geometry : angle 0.51429 (28614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6837.20 seconds wall clock time: 120 minutes 59.82 seconds (7259.82 seconds total)