Starting phenix.real_space_refine on Wed Jun 18 03:43:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r83_18993/06_2025/8r83_18993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r83_18993/06_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_18993/06_2025/8r83_18993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r83_18993/06_2025/8r83_18993.map" model { file = "/net/cci-nas-00/data/ceres_data/8r83_18993/06_2025/8r83_18993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r83_18993/06_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-5710/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: 18.44, per 1000 atoms: 0.90 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: 4.58 Conformation dependent library (CDL) restraints added in 2.6 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: 3.45 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: 8.50 Time building geometry restraints manager: 5.57 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: 1018.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 53.810 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1077.860 ------------------------------------------------------------------------------- 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 : 2.188 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: 0.5019 time to fit residues: 207.9444 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 : 2.285 ------------------------------------------------------------------------------- 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 = 76)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.185282 restraints weight = 26247.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.184390 restraints weight = 36622.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.180483 restraints weight = 35045.892| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 2.399 Fit side-chains revert: symmetry clash REVERT: B 423 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7229 (mtm110) REVERT: H 415 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: G 418 TRP cc_start: 0.7459 (t-100) cc_final: 0.7056 (t-100) REVERT: E 416 ASP cc_start: 0.7508 (p0) cc_final: 0.6898 (p0) REVERT: F 568 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6699 (tmm) outliers start: 59 outliers final: 23 residues processed: 243 average time/residue: 0.3794 time to fit residues: 136.2430 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 : 2.453 ------------------------------------------------------------------------------- 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: 0.7980 chunk 47 optimal weight: 10.0000 chunk 254 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN H 419 ASN F 450 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.241026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.184948 restraints weight = 26056.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.177752 restraints weight = 34951.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.173782 restraints weight = 38028.963| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20966 Z= 0.144 Angle : 0.570 14.556 28714 Z= 0.291 Chirality : 0.045 0.299 3351 Planarity : 0.004 0.055 3675 Dihedral : 3.764 26.589 2972 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.98 % Allowed : 17.63 % Favored : 80.39 % 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: 0.04 (0.33), residues: 253 sheet: 1.35 (0.16), residues: 949 loop : -0.30 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 418 HIS 0.009 0.001 HIS L 518 PHE 0.017 0.002 PHE F 479 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 0.00527 ( 7) link_NAG-ASN : angle 5.45562 ( 21) link_BETA1-4 : bond 0.01308 ( 1) link_BETA1-4 : angle 1.52499 ( 3) hydrogen bonds : bond 0.04106 ( 648) hydrogen bonds : angle 5.58525 ( 2019) SS BOND : bond 0.00479 ( 38) SS BOND : angle 1.26355 ( 76) covalent geometry : bond 0.00353 (20920) covalent geometry : angle 0.54708 (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 227 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 2.068 Fit side-chains REVERT: L 545 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6793 (t0) REVERT: K 359 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5932 (mm) REVERT: G 418 TRP cc_start: 0.7598 (t-100) cc_final: 0.6714 (t-100) REVERT: F 568 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6614 (tmm) REVERT: A 545 ASN cc_start: 0.7360 (t0) cc_final: 0.6958 (t0) outliers start: 46 outliers final: 25 residues processed: 217 average time/residue: 0.3618 time to fit residues: 116.4318 Evaluate side-chains 180 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 2.317 ------------------------------------------------------------------------------- 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 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 447 VAL Chi-restraints excluded: chain C residue 551 THR 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 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 E residue 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 59 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 179 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 181 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 HIS ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS ** 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 = 0.4241 r_free = 0.4241 target = 0.194858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127154 restraints weight = 23938.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.123236 restraints weight = 25990.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125448 restraints weight = 21263.649| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20966 Z= 0.150 Angle : 0.562 14.737 28714 Z= 0.285 Chirality : 0.045 0.279 3351 Planarity : 0.004 0.050 3675 Dihedral : 3.861 38.754 2972 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.49 % Allowed : 17.59 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.32), residues: 263 sheet: 1.42 (0.17), residues: 943 loop : -0.33 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 418 HIS 0.007 0.001 HIS L 518 PHE 0.018 0.002 PHE K 516 TYR 0.013 0.001 TYR F 515 ARG 0.003 0.000 ARG K 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 7) link_NAG-ASN : angle 4.99403 ( 21) link_BETA1-4 : bond 0.00618 ( 1) link_BETA1-4 : angle 1.49898 ( 3) hydrogen bonds : bond 0.03657 ( 648) hydrogen bonds : angle 5.36203 ( 2019) SS BOND : bond 0.00576 ( 38) SS BOND : angle 1.17884 ( 76) covalent geometry : bond 0.00375 (20920) covalent geometry : angle 0.54248 (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 218 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 2.136 Fit side-chains revert: symmetry clash REVERT: B 423 ARG cc_start: 0.8363 (mtm110) cc_final: 0.7638 (mtm110) REVERT: C 418 TRP cc_start: 0.6024 (t-100) cc_final: 0.5819 (t-100) REVERT: L 549 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: K 359 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5858 (mm) REVERT: G 418 TRP cc_start: 0.7615 (t-100) cc_final: 0.6465 (t-100) REVERT: E 350 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7619 (pt) REVERT: F 568 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6453 (tmm) REVERT: A 545 ASN cc_start: 0.7093 (t0) cc_final: 0.6545 (t0) outliers start: 58 outliers final: 40 residues processed: 206 average time/residue: 0.3298 time to fit residues: 104.5266 Evaluate side-chains 198 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 2.058 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 551 THR 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 471 THR Chi-restraints excluded: chain L residue 496 SER 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 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 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: 0.5980 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 202 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 220 optimal weight: 0.0040 chunk 216 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.193827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125912 restraints weight = 24010.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122262 restraints weight = 27052.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124363 restraints weight = 22256.658| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20966 Z= 0.149 Angle : 0.556 14.005 28714 Z= 0.283 Chirality : 0.045 0.267 3351 Planarity : 0.004 0.047 3675 Dihedral : 3.995 51.236 2972 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.62 % Allowed : 18.06 % Favored : 79.31 % 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: 0.55 (0.16), residues: 2582 helix: -0.03 (0.32), residues: 264 sheet: 1.45 (0.17), residues: 951 loop : -0.33 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 418 HIS 0.006 0.001 HIS G 518 PHE 0.019 0.002 PHE K 516 TYR 0.018 0.001 TYR N 160 ARG 0.005 0.000 ARG J 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 7) link_NAG-ASN : angle 4.55709 ( 21) link_BETA1-4 : bond 0.00917 ( 1) link_BETA1-4 : angle 1.28620 ( 3) hydrogen bonds : bond 0.03512 ( 648) hydrogen bonds : angle 5.17330 ( 2019) SS BOND : bond 0.00456 ( 38) SS BOND : angle 1.16804 ( 76) covalent geometry : bond 0.00371 (20920) covalent geometry : angle 0.53968 (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 229 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 2.088 Fit side-chains REVERT: B 423 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7635 (mtm110) REVERT: C 525 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6923 (tp30) REVERT: K 359 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5911 (mm) REVERT: H 415 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: H 495 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7571 (mp) REVERT: G 418 TRP cc_start: 0.7734 (t-100) cc_final: 0.6599 (t-100) REVERT: E 350 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7625 (pt) REVERT: F 527 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: F 568 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6471 (tmm) REVERT: A 545 ASN cc_start: 0.7287 (t0) cc_final: 0.6696 (t0) REVERT: J 70 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.5904 (mtmt) outliers start: 61 outliers final: 39 residues processed: 219 average time/residue: 0.3481 time to fit residues: 115.9395 Evaluate side-chains 206 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 2.365 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain N residue 208 CYS Chi-restraints excluded: chain N residue 280 VAL Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 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 471 THR Chi-restraints excluded: chain L residue 501 VAL 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 560 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 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: 0.4980 chunk 156 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 209 optimal weight: 0.0870 chunk 193 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 249 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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** H 510 GLN ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.4629 r_free = 0.4629 target = 0.241513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.186675 restraints weight = 26099.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.184060 restraints weight = 38429.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.183615 restraints weight = 40051.505| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20966 Z= 0.111 Angle : 0.528 13.776 28714 Z= 0.267 Chirality : 0.044 0.262 3351 Planarity : 0.004 0.044 3675 Dihedral : 3.852 53.908 2972 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.54 % Allowed : 18.45 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.66 (0.16), residues: 2582 helix: -0.02 (0.32), residues: 264 sheet: 1.50 (0.17), residues: 963 loop : -0.23 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP N 159 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 0.004 0.000 ARG N 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 7) link_NAG-ASN : angle 4.29264 ( 21) link_BETA1-4 : bond 0.00849 ( 1) link_BETA1-4 : angle 1.26669 ( 3) hydrogen bonds : bond 0.03062 ( 648) hydrogen bonds : angle 4.93468 ( 2019) SS BOND : bond 0.00455 ( 38) SS BOND : angle 1.20978 ( 76) covalent geometry : bond 0.00271 (20920) covalent geometry : angle 0.51206 (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 224 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 2.227 Fit side-chains revert: symmetry clash REVERT: B 506 MET cc_start: 0.6642 (mtt) cc_final: 0.6318 (mtm) REVERT: C 462 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7468 (pt0) REVERT: C 503 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8571 (t) REVERT: D 506 MET cc_start: 0.7483 (mtt) cc_final: 0.7104 (mtt) REVERT: L 549 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: K 359 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5850 (mm) REVERT: K 364 LYS cc_start: 0.7102 (ptpp) cc_final: 0.6567 (ptpp) REVERT: H 495 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7754 (mp) REVERT: G 418 TRP cc_start: 0.7594 (t-100) cc_final: 0.6829 (t-100) REVERT: E 350 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6829 (pt) REVERT: F 525 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7317 (tm-30) REVERT: F 568 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6670 (tmm) REVERT: A 545 ASN cc_start: 0.7513 (t0) cc_final: 0.6929 (t0) outliers start: 59 outliers final: 40 residues processed: 214 average time/residue: 0.3428 time to fit residues: 111.5246 Evaluate side-chains 203 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 465 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 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 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 518 HIS Chi-restraints excluded: chain L residue 543 LEU Chi-restraints excluded: chain L residue 549 GLU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 456 LEU Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 560 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 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 552 VAL Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain J residue 22 ILE 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: 0.7980 chunk 92 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 227 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4251 r_free = 0.4251 target = 0.193241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125913 restraints weight = 24850.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119593 restraints weight = 26305.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121925 restraints weight = 23111.471| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20966 Z= 0.223 Angle : 0.625 13.729 28714 Z= 0.321 Chirality : 0.047 0.257 3351 Planarity : 0.005 0.049 3675 Dihedral : 4.243 52.459 2972 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.75 % Allowed : 18.37 % Favored : 78.88 % 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: 0.38 (0.16), residues: 2582 helix: -0.15 (0.32), residues: 269 sheet: 1.33 (0.17), residues: 968 loop : -0.45 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 418 HIS 0.010 0.001 HIS G 518 PHE 0.031 0.002 PHE K 516 TYR 0.021 0.002 TYR F 515 ARG 0.005 0.000 ARG C 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 7) link_NAG-ASN : angle 4.35154 ( 21) link_BETA1-4 : bond 0.00648 ( 1) link_BETA1-4 : angle 1.19369 ( 3) hydrogen bonds : bond 0.04122 ( 648) hydrogen bonds : angle 5.29227 ( 2019) SS BOND : bond 0.00614 ( 38) SS BOND : angle 1.65646 ( 76) covalent geometry : bond 0.00568 (20920) covalent geometry : angle 0.60931 (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 234 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 2.094 Fit side-chains revert: symmetry clash REVERT: B 506 MET cc_start: 0.6708 (mtt) cc_final: 0.6377 (mtm) REVERT: C 462 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7741 (pt0) REVERT: D 499 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8421 (tptm) REVERT: D 506 MET cc_start: 0.7175 (mtt) cc_final: 0.6841 (mtp) REVERT: L 545 ASN cc_start: 0.7052 (t0) cc_final: 0.6662 (t0) REVERT: L 549 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: K 359 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.6043 (mm) REVERT: K 364 LYS cc_start: 0.7213 (ptpp) cc_final: 0.6624 (ptpp) REVERT: H 495 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7729 (mp) REVERT: G 418 TRP cc_start: 0.7794 (t-100) cc_final: 0.6691 (t-100) REVERT: E 350 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7624 (pt) REVERT: E 467 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7203 (mmp80) REVERT: E 568 MET cc_start: 0.7144 (tpp) cc_final: 0.6038 (mtt) REVERT: F 527 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: J 23 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6609 (tpp-160) outliers start: 64 outliers final: 45 residues processed: 221 average time/residue: 0.3539 time to fit residues: 116.8342 Evaluate side-chains 219 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 2.264 ------------------------------------------------------------------------------- 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 416 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 506 MET 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 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 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 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 E residue 350 ILE 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 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: 0.9980 chunk 201 optimal weight: 0.0050 chunk 210 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.194853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127645 restraints weight = 24860.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122811 restraints weight = 29142.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124999 restraints weight = 24420.957| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20966 Z= 0.140 Angle : 0.568 15.903 28714 Z= 0.288 Chirality : 0.045 0.255 3351 Planarity : 0.004 0.046 3675 Dihedral : 4.134 53.687 2972 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.45 % Allowed : 18.62 % Favored : 78.92 % 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 (0.16), residues: 2582 helix: -0.14 (0.32), residues: 269 sheet: 1.40 (0.17), residues: 963 loop : -0.37 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 418 HIS 0.005 0.001 HIS C 518 PHE 0.017 0.001 PHE L 485 TYR 0.017 0.001 TYR N 160 ARG 0.006 0.000 ARG H 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 7) link_NAG-ASN : angle 4.20178 ( 21) link_BETA1-4 : bond 0.00703 ( 1) link_BETA1-4 : angle 1.14478 ( 3) hydrogen bonds : bond 0.03357 ( 648) hydrogen bonds : angle 5.00993 ( 2019) SS BOND : bond 0.00435 ( 38) SS BOND : angle 1.89169 ( 76) covalent geometry : bond 0.00348 (20920) covalent geometry : angle 0.54867 (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 233 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 2.241 Fit side-chains revert: symmetry clash REVERT: B 506 MET cc_start: 0.6465 (mtt) cc_final: 0.6111 (mtm) REVERT: C 462 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7765 (pt0) REVERT: D 499 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8141 (tptm) REVERT: L 545 ASN cc_start: 0.7017 (t0) cc_final: 0.6590 (t0) REVERT: L 549 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: K 359 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5935 (mm) REVERT: K 364 LYS cc_start: 0.7139 (ptpp) cc_final: 0.6553 (ptpp) REVERT: K 489 MET cc_start: 0.8720 (mtm) cc_final: 0.8414 (mtp) REVERT: H 495 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7642 (mp) REVERT: G 418 TRP cc_start: 0.7777 (t-100) cc_final: 0.6714 (t-100) REVERT: E 350 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7579 (pt) REVERT: E 467 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7228 (mmp80) REVERT: F 525 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7176 (tm-30) REVERT: F 527 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: A 545 ASN cc_start: 0.7483 (t0) cc_final: 0.6972 (t0) outliers start: 57 outliers final: 41 residues processed: 222 average time/residue: 0.3522 time to fit residues: 117.7522 Evaluate side-chains 219 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 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 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 113 optimal weight: 8.9990 chunk 9 optimal weight: 0.0270 chunk 61 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.193904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126971 restraints weight = 24914.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121711 restraints weight = 30480.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124237 restraints weight = 25161.622| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20966 Z= 0.168 Angle : 0.583 13.279 28714 Z= 0.298 Chirality : 0.045 0.261 3351 Planarity : 0.005 0.046 3675 Dihedral : 4.243 48.384 2972 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.62 % Allowed : 18.75 % Favored : 78.62 % 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: 0.44 (0.16), residues: 2582 helix: -0.16 (0.32), residues: 269 sheet: 1.39 (0.17), residues: 959 loop : -0.41 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 159 HIS 0.006 0.001 HIS C 518 PHE 0.021 0.002 PHE F 479 TYR 0.017 0.001 TYR N 160 ARG 0.006 0.000 ARG H 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 7) link_NAG-ASN : angle 4.04739 ( 21) link_BETA1-4 : bond 0.00579 ( 1) link_BETA1-4 : angle 1.04891 ( 3) hydrogen bonds : bond 0.03585 ( 648) hydrogen bonds : angle 5.05377 ( 2019) SS BOND : bond 0.00492 ( 38) SS BOND : angle 1.78408 ( 76) covalent geometry : bond 0.00423 (20920) covalent geometry : angle 0.56618 (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 240 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 2.100 Fit side-chains REVERT: B 465 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7790 (t0) REVERT: B 506 MET cc_start: 0.6455 (mtt) cc_final: 0.6106 (mtm) REVERT: C 462 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7755 (pt0) REVERT: D 499 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8146 (tptm) REVERT: D 506 MET cc_start: 0.7308 (mtt) cc_final: 0.7000 (mtt) REVERT: L 545 ASN cc_start: 0.7177 (t0) cc_final: 0.6775 (t0) REVERT: L 549 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: K 359 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.6027 (mm) REVERT: K 364 LYS cc_start: 0.7314 (ptpp) cc_final: 0.6778 (ptpp) REVERT: H 423 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7394 (ptm-80) REVERT: H 495 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7691 (mp) REVERT: G 418 TRP cc_start: 0.7795 (t-100) cc_final: 0.6753 (t-100) REVERT: E 350 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7579 (pt) REVERT: E 467 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7249 (mmp80) REVERT: F 525 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7103 (tm-30) REVERT: F 527 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: A 545 ASN cc_start: 0.7500 (t0) cc_final: 0.7001 (t0) REVERT: J 23 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6590 (tpp-160) outliers start: 61 outliers final: 43 residues processed: 226 average time/residue: 0.3640 time to fit residues: 123.9571 Evaluate side-chains 224 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 465 ASN 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 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 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 506 MET 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 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 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 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 J residue 22 ILE Chi-restraints excluded: chain J residue 23 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 187 optimal weight: 0.0040 chunk 125 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 overall best weight: 0.5130 ------------------------------------------------------------------------------- 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 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.195879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128941 restraints weight = 25122.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124547 restraints weight = 29365.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126666 restraints weight = 24587.882| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20966 Z= 0.114 Angle : 0.543 13.262 28714 Z= 0.276 Chirality : 0.044 0.257 3351 Planarity : 0.004 0.050 3675 Dihedral : 4.109 46.377 2972 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.19 % Allowed : 19.48 % 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: 0.55 (0.17), residues: 2582 helix: -0.15 (0.32), residues: 269 sheet: 1.47 (0.17), residues: 959 loop : -0.32 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 159 HIS 0.013 0.001 HIS K 518 PHE 0.015 0.001 PHE L 485 TYR 0.014 0.001 TYR N 160 ARG 0.005 0.000 ARG G 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 7) link_NAG-ASN : angle 4.02713 ( 21) link_BETA1-4 : bond 0.00588 ( 1) link_BETA1-4 : angle 1.04533 ( 3) hydrogen bonds : bond 0.03101 ( 648) hydrogen bonds : angle 4.84189 ( 2019) SS BOND : bond 0.00403 ( 38) SS BOND : angle 1.46271 ( 76) covalent geometry : bond 0.00280 (20920) covalent geometry : angle 0.52769 (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 230 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 2.469 Fit side-chains revert: symmetry clash REVERT: B 506 MET cc_start: 0.6431 (mtt) cc_final: 0.6103 (mtm) REVERT: C 462 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7778 (pt0) REVERT: D 499 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8139 (tptm) REVERT: L 545 ASN cc_start: 0.7109 (t0) cc_final: 0.6696 (t0) REVERT: L 549 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: K 359 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5928 (mm) REVERT: K 364 LYS cc_start: 0.7220 (ptpp) cc_final: 0.6747 (ptpp) REVERT: K 489 MET cc_start: 0.8662 (mtm) cc_final: 0.8348 (mtp) REVERT: H 384 ARG cc_start: 0.6541 (mpp80) cc_final: 0.5920 (mpp80) REVERT: H 495 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7615 (mp) REVERT: G 418 TRP cc_start: 0.7778 (t-100) cc_final: 0.6697 (t-100) REVERT: E 350 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7556 (pt) REVERT: E 445 LYS cc_start: 0.6257 (mppt) cc_final: 0.5715 (mppt) REVERT: E 467 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7225 (mmp80) REVERT: F 525 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7127 (tm-30) REVERT: F 527 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: A 545 ASN cc_start: 0.7466 (t0) cc_final: 0.6972 (t0) REVERT: J 23 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6530 (tpp-160) outliers start: 51 outliers final: 42 residues processed: 220 average time/residue: 0.3651 time to fit residues: 121.6609 Evaluate side-chains 223 residues out of total 2325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 2.484 ------------------------------------------------------------------------------- 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 518 HIS Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain L residue 447 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 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 506 MET 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 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 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 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 23 ARG 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: 1.9990 chunk 22 optimal weight: 0.0470 chunk 153 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.0020 chunk 143 optimal weight: 0.5980 chunk 230 optimal weight: 0.0170 chunk 122 optimal weight: 0.6980 overall best weight: 0.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** L 518 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 = 0.4282 r_free = 0.4282 target = 0.197240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127760 restraints weight = 24821.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120315 restraints weight = 22626.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122539 restraints weight = 20282.407| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20966 Z= 0.088 Angle : 0.503 12.931 28714 Z= 0.254 Chirality : 0.043 0.249 3351 Planarity : 0.004 0.049 3675 Dihedral : 3.785 40.451 2972 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.51 % Allowed : 20.26 % Favored : 78.24 % 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: 0.76 (0.17), residues: 2582 helix: -0.10 (0.32), residues: 267 sheet: 1.60 (0.17), residues: 959 loop : -0.15 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 202 HIS 0.008 0.001 HIS K 518 PHE 0.017 0.001 PHE H 354 TYR 0.015 0.001 TYR N 160 ARG 0.004 0.000 ARG G 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 7) link_NAG-ASN : angle 3.75841 ( 21) link_BETA1-4 : bond 0.00582 ( 1) link_BETA1-4 : angle 1.08731 ( 3) hydrogen bonds : bond 0.02610 ( 648) hydrogen bonds : angle 4.51898 ( 2019) SS BOND : bond 0.00331 ( 38) SS BOND : angle 1.06721 ( 76) covalent geometry : bond 0.00206 (20920) covalent geometry : angle 0.49079 (28614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8192.76 seconds wall clock time: 144 minutes 50.04 seconds (8690.04 seconds total)