Starting phenix.real_space_refine on Sat Mar 16 19:50:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/03_2024/5wj9_8841_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/03_2024/5wj9_8841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/03_2024/5wj9_8841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/03_2024/5wj9_8841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/03_2024/5wj9_8841_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/03_2024/5wj9_8841_neut_updated.pdb" } resolution = 3.49 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= 0.015 sd= 0.186 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10172 2.51 5 N 2584 2.21 5 O 2684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15540 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "D" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.29, per 1000 atoms: 0.53 Number of scatterers: 15540 At special positions: 0 Unit cell: (109, 109, 120, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2684 8.00 N 2584 7.00 C 10172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.84 Conformation dependent library (CDL) restraints added in 3.0 seconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 4 sheets defined 57.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 4.046A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 64 through 105 removed outlier: 3.520A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'A' and resid 139 through 142 No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 292 through 336 removed outlier: 3.891A pdb=" N SER A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 353 through 377 Processing helix chain 'A' and resid 383 through 404 removed outlier: 3.942A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 417 through 447 Proline residue: A 423 - end of helix removed outlier: 4.081A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.528A pdb=" N PHE A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 removed outlier: 3.921A pdb=" N PHE A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 488 through 506 removed outlier: 3.554A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 524 Processing helix chain 'B' and resid 42 through 49 removed outlier: 4.047A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 105 removed outlier: 3.521A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 Processing helix chain 'B' and resid 139 through 142 No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 292 through 336 removed outlier: 3.891A pdb=" N SER B 296 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 353 through 377 Processing helix chain 'B' and resid 383 through 404 removed outlier: 3.945A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 417 through 447 Proline residue: B 423 - end of helix removed outlier: 4.082A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 removed outlier: 3.528A pdb=" N PHE B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 481 removed outlier: 3.922A pdb=" N PHE B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 488 through 506 removed outlier: 3.554A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 524 Processing helix chain 'C' and resid 42 through 49 removed outlier: 4.045A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 64 through 105 removed outlier: 3.517A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 139 through 142 No H-bonds generated for 'chain 'C' and resid 139 through 142' Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 292 through 336 removed outlier: 3.889A pdb=" N SER C 296 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY C 332 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET C 334 " --> pdb=" O PHE C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 353 through 376 Processing helix chain 'C' and resid 383 through 404 removed outlier: 3.944A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 417 through 447 Proline residue: C 423 - end of helix removed outlier: 4.083A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 469 removed outlier: 3.528A pdb=" N PHE C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 481 removed outlier: 3.921A pdb=" N PHE C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'C' and resid 488 through 506 removed outlier: 3.554A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 524 Processing helix chain 'D' and resid 42 through 49 removed outlier: 4.048A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'D' and resid 64 through 105 removed outlier: 3.518A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 139 through 142 No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 292 through 336 removed outlier: 3.890A pdb=" N SER D 296 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET D 334 " --> pdb=" O PHE D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 353 through 377 Processing helix chain 'D' and resid 383 through 404 removed outlier: 3.943A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 417 through 447 Proline residue: D 423 - end of helix removed outlier: 4.081A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 469 removed outlier: 3.528A pdb=" N PHE D 465 " --> pdb=" O SER D 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 481 removed outlier: 3.921A pdb=" N PHE D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 485 No H-bonds generated for 'chain 'D' and resid 483 through 485' Processing helix chain 'D' and resid 488 through 506 removed outlier: 3.554A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 524 Processing sheet with id= A, first strand: chain 'A' and resid 188 through 195 removed outlier: 3.566A pdb=" N HIS A 234 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR A 170 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 228 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 278 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 188 through 195 removed outlier: 3.566A pdb=" N HIS B 234 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR B 170 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 228 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 278 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 188 through 195 removed outlier: 3.566A pdb=" N HIS C 234 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 228 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 278 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 188 through 195 removed outlier: 3.565A pdb=" N HIS D 234 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR D 170 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU D 228 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 278 " --> pdb=" O SER D 257 " (cutoff:3.500A) 827 hydrogen bonds defined for protein. 2469 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: 4.25 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.12: 1 1.12 - 1.34: 4699 1.34 - 1.56: 11081 1.56 - 1.78: 26 1.78 - 2.01: 141 Bond restraints: 15948 Sorted by residual: bond pdb=" C PRO B 205 " pdb=" O PRO B 205 " ideal model delta sigma weight residual 1.231 2.007 -0.776 2.00e-02 2.50e+03 1.51e+03 bond pdb=" C HIS D 526 " pdb=" O HIS D 526 " ideal model delta sigma weight residual 1.231 1.761 -0.530 2.00e-02 2.50e+03 7.02e+02 bond pdb=" C HIS A 526 " pdb=" O HIS A 526 " ideal model delta sigma weight residual 1.231 1.678 -0.447 2.00e-02 2.50e+03 5.00e+02 bond pdb=" C HIS C 526 " pdb=" O HIS C 526 " ideal model delta sigma weight residual 1.231 1.668 -0.437 2.00e-02 2.50e+03 4.78e+02 bond pdb=" C PRO D 205 " pdb=" O PRO D 205 " ideal model delta sigma weight residual 1.231 0.893 0.338 2.00e-02 2.50e+03 2.85e+02 ... (remaining 15943 not shown) Histogram of bond angle deviations from ideal: 99.42 - 107.23: 534 107.23 - 115.05: 9100 115.05 - 122.87: 9492 122.87 - 130.69: 2460 130.69 - 138.51: 94 Bond angle restraints: 21680 Sorted by residual: angle pdb=" CA HIS A 526 " pdb=" C HIS A 526 " pdb=" O HIS A 526 " ideal model delta sigma weight residual 120.80 138.51 -17.71 1.70e+00 3.46e-01 1.09e+02 angle pdb=" CA HIS D 526 " pdb=" C HIS D 526 " pdb=" O HIS D 526 " ideal model delta sigma weight residual 120.80 136.18 -15.38 1.70e+00 3.46e-01 8.18e+01 angle pdb=" CA HIS B 526 " pdb=" C HIS B 526 " pdb=" O HIS B 526 " ideal model delta sigma weight residual 120.80 135.60 -14.80 1.70e+00 3.46e-01 7.58e+01 angle pdb=" C VAL A 359 " pdb=" CA VAL A 359 " pdb=" CB VAL A 359 " ideal model delta sigma weight residual 112.22 121.95 -9.73 1.38e+00 5.25e-01 4.97e+01 angle pdb=" O GLY D 448 " pdb=" C GLY D 448 " pdb=" N PRO D 449 " ideal model delta sigma weight residual 121.07 123.02 -1.95 3.60e-01 7.72e+00 2.94e+01 ... (remaining 21675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 8392 16.75 - 33.50: 771 33.50 - 50.25: 166 50.25 - 67.00: 39 67.00 - 83.75: 20 Dihedral angle restraints: 9388 sinusoidal: 3776 harmonic: 5612 Sorted by residual: dihedral pdb=" C VAL A 359 " pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" CB VAL A 359 " ideal model delta harmonic sigma weight residual -122.00 -148.43 26.43 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N VAL A 359 " pdb=" C VAL A 359 " pdb=" CA VAL A 359 " pdb=" CB VAL A 359 " ideal model delta harmonic sigma weight residual 123.40 146.17 -22.77 0 2.50e+00 1.60e-01 8.30e+01 dihedral pdb=" N PHE B 324 " pdb=" C PHE B 324 " pdb=" CA PHE B 324 " pdb=" CB PHE B 324 " ideal model delta harmonic sigma weight residual 122.80 141.88 -19.08 0 2.50e+00 1.60e-01 5.82e+01 ... (remaining 9385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 2388 0.187 - 0.374: 57 0.374 - 0.561: 4 0.561 - 0.748: 1 0.748 - 0.935: 2 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA VAL A 359 " pdb=" N VAL A 359 " pdb=" C VAL A 359 " pdb=" CB VAL A 359 " both_signs ideal model delta sigma weight residual False 2.44 1.51 0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" CA PHE B 324 " pdb=" N PHE B 324 " pdb=" C PHE B 324 " pdb=" CB PHE B 324 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA PHE A 350 " pdb=" N PHE A 350 " pdb=" C PHE A 350 " pdb=" CB PHE A 350 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.37e+00 ... (remaining 2449 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 378 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LYS C 378 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS C 378 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN C 379 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 422 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO D 423 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 422 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 423 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " 0.028 5.00e-02 4.00e+02 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 493 2.76 - 3.29: 17478 3.29 - 3.83: 24871 3.83 - 4.36: 31204 4.36 - 4.90: 51451 Nonbonded interactions: 125497 Sorted by model distance: nonbonded pdb=" OG1 THR B 77 " pdb=" CZ2 TRP B 398 " model vdw 2.225 3.340 nonbonded pdb=" O THR B 394 " pdb=" CD1 TRP B 398 " model vdw 2.323 3.260 nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.495 2.440 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.496 2.440 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.496 2.440 ... (remaining 125492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.010 Extract box with map and model: 6.280 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 41.770 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 0.014 0.776 15948 Z= 1.013 Angle : 1.230 17.712 21680 Z= 0.819 Chirality : 0.075 0.935 2452 Planarity : 0.005 0.051 2692 Dihedral : 14.404 83.745 5748 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.05 % Favored : 90.68 % Rotamer: Outliers : 1.93 % Allowed : 7.55 % Favored : 90.52 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % 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: -3.89 (0.15), residues: 1900 helix: -1.76 (0.12), residues: 1028 sheet: -3.07 (0.32), residues: 196 loop : -3.57 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 345 HIS 0.009 0.002 HIS B 103 PHE 0.027 0.003 PHE C 182 TYR 0.023 0.002 TYR A 355 ARG 0.010 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 643 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7103 (tpt170) REVERT: A 54 ASP cc_start: 0.9116 (m-30) cc_final: 0.8297 (t0) REVERT: A 57 ARG cc_start: 0.8318 (mtt180) cc_final: 0.8106 (ptm-80) REVERT: A 124 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8846 (tm-30) REVERT: A 174 HIS cc_start: 0.8458 (t70) cc_final: 0.7681 (t-90) REVERT: A 185 ASP cc_start: 0.8643 (p0) cc_final: 0.8341 (p0) REVERT: A 196 ASP cc_start: 0.8794 (p0) cc_final: 0.8510 (p0) REVERT: A 252 ASP cc_start: 0.7618 (m-30) cc_final: 0.7417 (m-30) REVERT: A 346 GLU cc_start: 0.8361 (pt0) cc_final: 0.7954 (pm20) REVERT: A 371 MET cc_start: 0.8658 (mmm) cc_final: 0.8382 (ttp) REVERT: A 409 HIS cc_start: 0.8824 (m90) cc_final: 0.8585 (t-170) REVERT: A 436 TYR cc_start: 0.8963 (t80) cc_final: 0.8531 (t80) REVERT: A 451 HIS cc_start: 0.5961 (m-70) cc_final: 0.5740 (m-70) REVERT: A 464 LEU cc_start: 0.8852 (mt) cc_final: 0.8644 (mt) REVERT: A 486 ARG cc_start: 0.8286 (ptp-170) cc_final: 0.8076 (ptm-80) REVERT: A 487 SER cc_start: 0.8719 (m) cc_final: 0.8496 (p) REVERT: A 491 TRP cc_start: 0.8476 (t60) cc_final: 0.8127 (t60) REVERT: A 505 PHE cc_start: 0.8553 (m-10) cc_final: 0.8321 (m-10) REVERT: A 524 ILE cc_start: 0.8809 (tp) cc_final: 0.8459 (tt) REVERT: B 42 ARG cc_start: 0.7609 (ttp-170) cc_final: 0.7190 (tpt170) REVERT: B 54 ASP cc_start: 0.9170 (m-30) cc_final: 0.8203 (t0) REVERT: B 124 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8836 (tm-30) REVERT: B 174 HIS cc_start: 0.8414 (t70) cc_final: 0.7618 (t-90) REVERT: B 185 ASP cc_start: 0.8626 (p0) cc_final: 0.8308 (p0) REVERT: B 352 ASN cc_start: 0.8614 (m-40) cc_final: 0.8321 (t0) REVERT: B 355 TYR cc_start: 0.8854 (m-80) cc_final: 0.8373 (m-80) REVERT: B 367 SER cc_start: 0.9308 (t) cc_final: 0.9095 (p) REVERT: B 371 MET cc_start: 0.9036 (tpp) cc_final: 0.8810 (ttp) REVERT: B 393 SER cc_start: 0.9536 (t) cc_final: 0.9319 (p) REVERT: B 409 HIS cc_start: 0.8823 (m90) cc_final: 0.8585 (t-170) REVERT: B 436 TYR cc_start: 0.9050 (t80) cc_final: 0.8661 (t80) REVERT: B 451 HIS cc_start: 0.5969 (m-70) cc_final: 0.5732 (m-70) REVERT: B 464 LEU cc_start: 0.8865 (mt) cc_final: 0.8637 (mt) REVERT: B 486 ARG cc_start: 0.8300 (ptp-170) cc_final: 0.8071 (ptm-80) REVERT: B 487 SER cc_start: 0.8715 (m) cc_final: 0.8498 (p) REVERT: B 491 TRP cc_start: 0.8469 (t60) cc_final: 0.8093 (t60) REVERT: B 505 PHE cc_start: 0.8544 (m-10) cc_final: 0.8318 (m-10) REVERT: C 54 ASP cc_start: 0.9103 (m-30) cc_final: 0.8220 (t0) REVERT: C 124 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8830 (tm-30) REVERT: C 185 ASP cc_start: 0.8621 (p0) cc_final: 0.8296 (p0) REVERT: C 252 ASP cc_start: 0.7596 (m-30) cc_final: 0.7382 (m-30) REVERT: C 355 TYR cc_start: 0.8877 (m-80) cc_final: 0.8497 (m-80) REVERT: C 384 ASP cc_start: 0.8591 (p0) cc_final: 0.8374 (p0) REVERT: C 393 SER cc_start: 0.9538 (t) cc_final: 0.9301 (p) REVERT: C 436 TYR cc_start: 0.9071 (t80) cc_final: 0.8712 (t80) REVERT: C 451 HIS cc_start: 0.5988 (m-70) cc_final: 0.5734 (m-70) REVERT: C 464 LEU cc_start: 0.8866 (mt) cc_final: 0.8646 (mt) REVERT: C 486 ARG cc_start: 0.8278 (ptp-170) cc_final: 0.8061 (ptm-80) REVERT: C 487 SER cc_start: 0.8715 (m) cc_final: 0.8494 (p) REVERT: C 491 TRP cc_start: 0.8471 (t60) cc_final: 0.8102 (t60) REVERT: C 505 PHE cc_start: 0.8538 (m-10) cc_final: 0.8338 (m-10) REVERT: D 42 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7320 (tpt170) REVERT: D 54 ASP cc_start: 0.9235 (m-30) cc_final: 0.8148 (t0) REVERT: D 174 HIS cc_start: 0.8419 (t70) cc_final: 0.7633 (t-90) REVERT: D 185 ASP cc_start: 0.8637 (p0) cc_final: 0.8340 (p0) REVERT: D 294 ASP cc_start: 0.6091 (t70) cc_final: 0.4923 (p0) REVERT: D 346 GLU cc_start: 0.8367 (pt0) cc_final: 0.7933 (pm20) REVERT: D 352 ASN cc_start: 0.8534 (t0) cc_final: 0.7571 (t0) REVERT: D 355 TYR cc_start: 0.8947 (m-80) cc_final: 0.8300 (m-80) REVERT: D 384 ASP cc_start: 0.8585 (p0) cc_final: 0.8366 (p0) REVERT: D 393 SER cc_start: 0.9528 (t) cc_final: 0.9295 (p) REVERT: D 436 TYR cc_start: 0.9077 (t80) cc_final: 0.8700 (t80) REVERT: D 451 HIS cc_start: 0.5976 (m-70) cc_final: 0.5751 (m-70) REVERT: D 464 LEU cc_start: 0.8869 (mt) cc_final: 0.8638 (mt) REVERT: D 486 ARG cc_start: 0.8324 (ptp-170) cc_final: 0.8123 (ptm-80) REVERT: D 487 SER cc_start: 0.8746 (m) cc_final: 0.8522 (p) REVERT: D 491 TRP cc_start: 0.8454 (t60) cc_final: 0.8096 (t60) outliers start: 33 outliers final: 10 residues processed: 658 average time/residue: 0.2632 time to fit residues: 256.8589 Evaluate side-chains 435 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 422 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 0.0770 chunk 76 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN B 69 GLN B 79 GLN B 97 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 79 GLN C 97 ASN D 69 GLN D 79 GLN D 97 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15948 Z= 0.237 Angle : 0.781 12.359 21680 Z= 0.394 Chirality : 0.047 0.199 2452 Planarity : 0.005 0.046 2692 Dihedral : 7.574 66.684 2223 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.84 % Rotamer: Outliers : 4.45 % Allowed : 18.03 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.17), residues: 1900 helix: -0.44 (0.13), residues: 1068 sheet: -1.75 (0.35), residues: 176 loop : -2.73 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 335 HIS 0.006 0.001 HIS D 409 PHE 0.023 0.002 PHE A 330 TYR 0.014 0.001 TYR D 499 ARG 0.004 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 426 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7478 (ptp) cc_final: 0.7031 (ptp) REVERT: A 54 ASP cc_start: 0.9185 (m-30) cc_final: 0.8561 (t0) REVERT: A 57 ARG cc_start: 0.8317 (mtt180) cc_final: 0.7988 (mtp85) REVERT: A 89 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 252 ASP cc_start: 0.7621 (m-30) cc_final: 0.7420 (m-30) REVERT: A 364 LEU cc_start: 0.9181 (mp) cc_final: 0.8909 (mp) REVERT: A 371 MET cc_start: 0.8613 (mmm) cc_final: 0.8302 (ttp) REVERT: A 409 HIS cc_start: 0.8926 (m90) cc_final: 0.8638 (t-170) REVERT: A 436 TYR cc_start: 0.8944 (t80) cc_final: 0.8650 (t80) REVERT: A 451 HIS cc_start: 0.6118 (m-70) cc_final: 0.5619 (m-70) REVERT: A 464 LEU cc_start: 0.8833 (mt) cc_final: 0.8618 (mt) REVERT: A 487 SER cc_start: 0.8855 (m) cc_final: 0.8637 (p) REVERT: A 491 TRP cc_start: 0.8563 (t60) cc_final: 0.8163 (t60) REVERT: A 524 ILE cc_start: 0.8765 (tp) cc_final: 0.8443 (tt) REVERT: B 42 ARG cc_start: 0.7525 (ttp-170) cc_final: 0.7034 (tpt170) REVERT: B 50 MET cc_start: 0.7505 (ptp) cc_final: 0.6811 (ptt) REVERT: B 54 ASP cc_start: 0.9022 (m-30) cc_final: 0.8629 (t0) REVERT: B 89 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8118 (mp) REVERT: B 371 MET cc_start: 0.8991 (tpp) cc_final: 0.8768 (ttp) REVERT: B 389 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8538 (mm) REVERT: B 409 HIS cc_start: 0.8914 (m90) cc_final: 0.8634 (t-170) REVERT: B 436 TYR cc_start: 0.9095 (t80) cc_final: 0.8784 (t80) REVERT: B 451 HIS cc_start: 0.6147 (m-70) cc_final: 0.5655 (m-70) REVERT: B 464 LEU cc_start: 0.8839 (mt) cc_final: 0.8617 (mt) REVERT: B 487 SER cc_start: 0.8857 (m) cc_final: 0.8634 (p) REVERT: B 491 TRP cc_start: 0.8577 (t60) cc_final: 0.8161 (t60) REVERT: B 524 ILE cc_start: 0.8757 (tp) cc_final: 0.8431 (tt) REVERT: C 41 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9015 (tp) REVERT: C 54 ASP cc_start: 0.8904 (m-30) cc_final: 0.8353 (t0) REVERT: C 89 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8150 (mp) REVERT: C 315 LEU cc_start: 0.9296 (mt) cc_final: 0.9071 (mt) REVERT: C 334 MET cc_start: 0.5129 (mmm) cc_final: 0.4902 (mmt) REVERT: C 436 TYR cc_start: 0.9081 (t80) cc_final: 0.8742 (t80) REVERT: C 464 LEU cc_start: 0.8838 (mt) cc_final: 0.8611 (mt) REVERT: C 487 SER cc_start: 0.8842 (m) cc_final: 0.8621 (p) REVERT: C 491 TRP cc_start: 0.8573 (t60) cc_final: 0.8159 (t60) REVERT: C 524 ILE cc_start: 0.8770 (tp) cc_final: 0.8442 (tt) REVERT: D 50 MET cc_start: 0.7369 (ptp) cc_final: 0.6681 (ptt) REVERT: D 54 ASP cc_start: 0.9008 (m-30) cc_final: 0.8626 (t0) REVERT: D 89 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8092 (mp) REVERT: D 352 ASN cc_start: 0.8716 (t0) cc_final: 0.8000 (t0) REVERT: D 355 TYR cc_start: 0.8772 (m-80) cc_final: 0.8555 (m-80) REVERT: D 371 MET cc_start: 0.8618 (ttm) cc_final: 0.8395 (ttp) REVERT: D 436 TYR cc_start: 0.9127 (t80) cc_final: 0.8803 (t80) REVERT: D 451 HIS cc_start: 0.6104 (m-70) cc_final: 0.5625 (m-70) REVERT: D 464 LEU cc_start: 0.8845 (mt) cc_final: 0.8621 (mt) REVERT: D 487 SER cc_start: 0.8871 (m) cc_final: 0.8649 (p) REVERT: D 491 TRP cc_start: 0.8540 (t60) cc_final: 0.8138 (t60) REVERT: D 524 ILE cc_start: 0.8797 (tp) cc_final: 0.8484 (tt) outliers start: 76 outliers final: 41 residues processed: 462 average time/residue: 0.2405 time to fit residues: 170.0667 Evaluate side-chains 427 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 380 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 509 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 58 optimal weight: 0.0050 chunk 137 optimal weight: 5.9990 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 15948 Z= 0.614 Angle : 0.919 9.559 21680 Z= 0.467 Chirality : 0.051 0.203 2452 Planarity : 0.006 0.044 2692 Dihedral : 6.735 51.404 2210 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.37 % Rotamer: Outliers : 7.55 % Allowed : 18.21 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.18), residues: 1900 helix: -0.15 (0.14), residues: 1088 sheet: -1.72 (0.36), residues: 204 loop : -2.71 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 335 HIS 0.017 0.002 HIS D 451 PHE 0.023 0.003 PHE C 83 TYR 0.019 0.003 TYR C 218 ARG 0.007 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 367 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7383 (ptp) cc_final: 0.7143 (ptp) REVERT: A 54 ASP cc_start: 0.9194 (m-30) cc_final: 0.8571 (t0) REVERT: A 57 ARG cc_start: 0.8455 (mtt180) cc_final: 0.8072 (mtp-110) REVERT: A 115 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9212 (p0) REVERT: A 249 GLU cc_start: 0.7979 (tp30) cc_final: 0.7693 (mm-30) REVERT: A 252 ASP cc_start: 0.7675 (m-30) cc_final: 0.7475 (m-30) REVERT: A 371 MET cc_start: 0.8743 (mmm) cc_final: 0.8477 (ttm) REVERT: A 376 GLU cc_start: 0.9097 (tt0) cc_final: 0.8780 (tt0) REVERT: A 409 HIS cc_start: 0.8899 (m90) cc_final: 0.8597 (t-170) REVERT: A 491 TRP cc_start: 0.8297 (t60) cc_final: 0.8074 (t60) REVERT: A 524 ILE cc_start: 0.8706 (tp) cc_final: 0.8368 (tt) REVERT: B 50 MET cc_start: 0.7544 (ptp) cc_final: 0.7042 (ptp) REVERT: B 54 ASP cc_start: 0.9026 (m-30) cc_final: 0.8502 (t0) REVERT: B 115 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.9017 (p0) REVERT: B 249 GLU cc_start: 0.7977 (tp30) cc_final: 0.7716 (mm-30) REVERT: B 276 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 409 HIS cc_start: 0.8883 (m90) cc_final: 0.8614 (t-170) REVERT: B 491 TRP cc_start: 0.8318 (t60) cc_final: 0.8090 (t60) REVERT: B 524 ILE cc_start: 0.8704 (tp) cc_final: 0.8364 (tt) REVERT: C 41 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8990 (tp) REVERT: C 50 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6976 (ptp) REVERT: C 54 ASP cc_start: 0.8968 (m-30) cc_final: 0.8717 (t0) REVERT: C 115 ASP cc_start: 0.9315 (OUTLIER) cc_final: 0.9001 (p0) REVERT: C 334 MET cc_start: 0.5193 (mmm) cc_final: 0.4750 (mmt) REVERT: C 335 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.8133 (m100) REVERT: C 355 TYR cc_start: 0.8936 (m-80) cc_final: 0.8686 (m-80) REVERT: C 371 MET cc_start: 0.8720 (ttp) cc_final: 0.8402 (ttm) REVERT: C 491 TRP cc_start: 0.8373 (t60) cc_final: 0.8162 (t60) REVERT: C 524 ILE cc_start: 0.8706 (tp) cc_final: 0.8365 (tt) REVERT: D 50 MET cc_start: 0.7284 (ptp) cc_final: 0.6739 (ptp) REVERT: D 54 ASP cc_start: 0.9023 (m-30) cc_final: 0.8526 (t0) REVERT: D 115 ASP cc_start: 0.9449 (OUTLIER) cc_final: 0.9206 (p0) REVERT: D 249 GLU cc_start: 0.7910 (tp30) cc_final: 0.7576 (mm-30) REVERT: D 335 TRP cc_start: 0.7878 (m100) cc_final: 0.7260 (m100) REVERT: D 352 ASN cc_start: 0.8371 (t0) cc_final: 0.8069 (t0) REVERT: D 444 TRP cc_start: 0.8363 (t60) cc_final: 0.7993 (t60) REVERT: D 491 TRP cc_start: 0.8272 (t60) cc_final: 0.8042 (t60) REVERT: D 524 ILE cc_start: 0.8720 (tp) cc_final: 0.8385 (tt) outliers start: 129 outliers final: 74 residues processed: 426 average time/residue: 0.2259 time to fit residues: 147.6669 Evaluate side-chains 403 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 322 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 496 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 181 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15948 Z= 0.207 Angle : 0.715 10.252 21680 Z= 0.352 Chirality : 0.045 0.270 2452 Planarity : 0.004 0.043 2692 Dihedral : 6.078 55.617 2202 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 6.03 % Allowed : 19.85 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 1900 helix: 0.10 (0.14), residues: 1088 sheet: -1.15 (0.38), residues: 204 loop : -2.75 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 444 HIS 0.017 0.001 HIS D 451 PHE 0.020 0.002 PHE D 49 TYR 0.011 0.001 TYR D 497 ARG 0.006 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 381 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9178 (m-30) cc_final: 0.8582 (t0) REVERT: A 57 ARG cc_start: 0.8441 (mtt180) cc_final: 0.8072 (mtp85) REVERT: A 115 ASP cc_start: 0.9473 (OUTLIER) cc_final: 0.9262 (p0) REVERT: A 249 GLU cc_start: 0.7961 (tp30) cc_final: 0.7645 (mm-30) REVERT: A 276 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8218 (mm-30) REVERT: A 371 MET cc_start: 0.8756 (mmm) cc_final: 0.8483 (ttm) REVERT: A 409 HIS cc_start: 0.8880 (m90) cc_final: 0.8578 (t-170) REVERT: A 487 SER cc_start: 0.8753 (m) cc_final: 0.8520 (p) REVERT: A 491 TRP cc_start: 0.8375 (t60) cc_final: 0.8128 (t60) REVERT: A 524 ILE cc_start: 0.8796 (tp) cc_final: 0.8478 (tt) REVERT: B 50 MET cc_start: 0.7442 (ptp) cc_final: 0.6727 (ptp) REVERT: B 54 ASP cc_start: 0.9013 (m-30) cc_final: 0.8440 (t0) REVERT: B 115 ASP cc_start: 0.9359 (OUTLIER) cc_final: 0.9071 (p0) REVERT: B 249 GLU cc_start: 0.8024 (tp30) cc_final: 0.7817 (mm-30) REVERT: B 276 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8230 (mm-30) REVERT: B 371 MET cc_start: 0.8540 (ttm) cc_final: 0.8312 (ttp) REVERT: B 409 HIS cc_start: 0.8877 (m90) cc_final: 0.8577 (t-170) REVERT: B 487 SER cc_start: 0.8780 (m) cc_final: 0.8548 (p) REVERT: B 491 TRP cc_start: 0.8389 (t60) cc_final: 0.8149 (t60) REVERT: B 524 ILE cc_start: 0.8787 (tp) cc_final: 0.8481 (tt) REVERT: C 50 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7200 (ptp) REVERT: C 54 ASP cc_start: 0.8941 (m-30) cc_final: 0.8623 (t0) REVERT: C 115 ASP cc_start: 0.9345 (OUTLIER) cc_final: 0.9046 (p0) REVERT: C 249 GLU cc_start: 0.7828 (tp30) cc_final: 0.7551 (mm-30) REVERT: C 276 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8231 (mm-30) REVERT: C 334 MET cc_start: 0.5168 (mmm) cc_final: 0.4591 (mmt) REVERT: C 335 TRP cc_start: 0.8303 (m-10) cc_final: 0.8016 (m100) REVERT: C 371 MET cc_start: 0.8763 (ttp) cc_final: 0.8420 (ttm) REVERT: C 487 SER cc_start: 0.8834 (m) cc_final: 0.8597 (p) REVERT: C 524 ILE cc_start: 0.8788 (tp) cc_final: 0.8476 (tt) REVERT: D 50 MET cc_start: 0.7450 (ptp) cc_final: 0.6884 (ptp) REVERT: D 54 ASP cc_start: 0.9004 (m-30) cc_final: 0.8487 (t0) REVERT: D 115 ASP cc_start: 0.9466 (OUTLIER) cc_final: 0.9247 (p0) REVERT: D 276 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8228 (mm-30) REVERT: D 335 TRP cc_start: 0.7760 (m100) cc_final: 0.7221 (m100) REVERT: D 352 ASN cc_start: 0.8421 (t0) cc_final: 0.8025 (t0) REVERT: D 371 MET cc_start: 0.8634 (ttm) cc_final: 0.8407 (ttp) REVERT: D 436 TYR cc_start: 0.9172 (t80) cc_final: 0.8761 (t80) REVERT: D 444 TRP cc_start: 0.8340 (t60) cc_final: 0.8030 (t60) REVERT: D 487 SER cc_start: 0.8792 (m) cc_final: 0.8564 (p) REVERT: D 491 TRP cc_start: 0.8354 (t60) cc_final: 0.8102 (t60) REVERT: D 524 ILE cc_start: 0.8807 (tp) cc_final: 0.8491 (tt) outliers start: 103 outliers final: 55 residues processed: 432 average time/residue: 0.2245 time to fit residues: 151.7029 Evaluate side-chains 413 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 353 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15948 Z= 0.210 Angle : 0.715 11.249 21680 Z= 0.349 Chirality : 0.046 0.372 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.958 56.366 2202 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.53 % Favored : 94.42 % Rotamer: Outliers : 4.51 % Allowed : 23.54 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1900 helix: 0.16 (0.15), residues: 1080 sheet: -0.88 (0.39), residues: 204 loop : -2.70 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 444 HIS 0.007 0.001 HIS B 451 PHE 0.027 0.002 PHE D 501 TYR 0.010 0.001 TYR D 497 ARG 0.005 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 379 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9145 (m-30) cc_final: 0.8710 (t0) REVERT: A 57 ARG cc_start: 0.8411 (mtt180) cc_final: 0.8077 (mtp85) REVERT: A 115 ASP cc_start: 0.9475 (OUTLIER) cc_final: 0.9266 (p0) REVERT: A 249 GLU cc_start: 0.7925 (tp30) cc_final: 0.7702 (mm-30) REVERT: A 276 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8213 (mm-30) REVERT: A 371 MET cc_start: 0.8700 (mmm) cc_final: 0.8254 (ttp) REVERT: A 409 HIS cc_start: 0.8888 (m90) cc_final: 0.8574 (t-170) REVERT: A 436 TYR cc_start: 0.8889 (t80) cc_final: 0.8510 (t80) REVERT: A 464 LEU cc_start: 0.9091 (mt) cc_final: 0.8869 (mt) REVERT: A 480 MET cc_start: 0.8091 (mmp) cc_final: 0.7767 (mmm) REVERT: A 487 SER cc_start: 0.8806 (m) cc_final: 0.8573 (p) REVERT: A 491 TRP cc_start: 0.8343 (t60) cc_final: 0.7968 (t60) REVERT: A 524 ILE cc_start: 0.8791 (tp) cc_final: 0.8481 (tt) REVERT: B 50 MET cc_start: 0.7426 (ptp) cc_final: 0.6938 (ptp) REVERT: B 54 ASP cc_start: 0.9018 (m-30) cc_final: 0.8487 (t0) REVERT: B 115 ASP cc_start: 0.9363 (OUTLIER) cc_final: 0.9077 (p0) REVERT: B 249 GLU cc_start: 0.8084 (tp30) cc_final: 0.7859 (mm-30) REVERT: B 276 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 329 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8433 (tp30) REVERT: B 338 ARG cc_start: 0.6185 (mmt180) cc_final: 0.5432 (mmp-170) REVERT: B 354 TRP cc_start: 0.7763 (m100) cc_final: 0.7535 (m100) REVERT: B 371 MET cc_start: 0.8547 (ttm) cc_final: 0.8314 (ttp) REVERT: B 409 HIS cc_start: 0.8838 (m90) cc_final: 0.8557 (t-170) REVERT: B 436 TYR cc_start: 0.9009 (t80) cc_final: 0.8520 (t80) REVERT: B 480 MET cc_start: 0.8184 (mmp) cc_final: 0.7883 (mmm) REVERT: B 487 SER cc_start: 0.8806 (m) cc_final: 0.8574 (p) REVERT: B 491 TRP cc_start: 0.8395 (t60) cc_final: 0.7996 (t60) REVERT: B 524 ILE cc_start: 0.8801 (tp) cc_final: 0.8495 (tt) REVERT: C 50 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7319 (ptp) REVERT: C 54 ASP cc_start: 0.8923 (m-30) cc_final: 0.8651 (t0) REVERT: C 115 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.9049 (p0) REVERT: C 276 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8213 (mm-30) REVERT: C 334 MET cc_start: 0.5155 (mmm) cc_final: 0.4449 (mmt) REVERT: C 335 TRP cc_start: 0.8333 (m-10) cc_final: 0.8015 (m100) REVERT: C 354 TRP cc_start: 0.7777 (m100) cc_final: 0.7472 (m100) REVERT: C 371 MET cc_start: 0.8788 (ttp) cc_final: 0.8447 (ttm) REVERT: C 436 TYR cc_start: 0.9050 (t80) cc_final: 0.8790 (t80) REVERT: C 487 SER cc_start: 0.8864 (m) cc_final: 0.8622 (p) REVERT: C 524 ILE cc_start: 0.8793 (tp) cc_final: 0.8485 (tt) REVERT: D 50 MET cc_start: 0.7387 (ptp) cc_final: 0.6811 (ptp) REVERT: D 54 ASP cc_start: 0.9000 (m-30) cc_final: 0.8479 (t0) REVERT: D 115 ASP cc_start: 0.9468 (OUTLIER) cc_final: 0.9259 (p0) REVERT: D 249 GLU cc_start: 0.8188 (tp30) cc_final: 0.7888 (mp0) REVERT: D 276 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8219 (mm-30) REVERT: D 336 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7744 (mmm160) REVERT: D 352 ASN cc_start: 0.8432 (t0) cc_final: 0.8194 (t0) REVERT: D 371 MET cc_start: 0.8628 (ttm) cc_final: 0.8408 (ttp) REVERT: D 487 SER cc_start: 0.8802 (m) cc_final: 0.8573 (p) REVERT: D 491 TRP cc_start: 0.8299 (t60) cc_final: 0.7915 (t60) REVERT: D 524 ILE cc_start: 0.8796 (tp) cc_final: 0.8484 (tt) outliers start: 77 outliers final: 50 residues processed: 422 average time/residue: 0.2128 time to fit residues: 142.0715 Evaluate side-chains 417 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 360 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 84 optimal weight: 0.0570 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15948 Z= 0.198 Angle : 0.700 8.994 21680 Z= 0.340 Chirality : 0.044 0.260 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.399 21.353 2196 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.84 % Rotamer: Outliers : 4.04 % Allowed : 23.71 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.19), residues: 1900 helix: 0.23 (0.15), residues: 1088 sheet: -0.74 (0.38), residues: 204 loop : -2.71 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 444 HIS 0.012 0.001 HIS D 451 PHE 0.031 0.002 PHE A 235 TYR 0.015 0.001 TYR A 411 ARG 0.003 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 381 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9135 (m-30) cc_final: 0.8686 (t0) REVERT: A 57 ARG cc_start: 0.8388 (mtt180) cc_final: 0.8015 (mtp-110) REVERT: A 276 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8196 (mm-30) REVERT: A 371 MET cc_start: 0.8740 (mmm) cc_final: 0.8277 (ttp) REVERT: A 409 HIS cc_start: 0.8896 (m90) cc_final: 0.8536 (t-170) REVERT: A 436 TYR cc_start: 0.8808 (t80) cc_final: 0.8499 (t80) REVERT: A 464 LEU cc_start: 0.9127 (mt) cc_final: 0.8870 (mt) REVERT: A 487 SER cc_start: 0.8861 (m) cc_final: 0.8630 (p) REVERT: A 491 TRP cc_start: 0.8323 (t60) cc_final: 0.7972 (t60) REVERT: A 524 ILE cc_start: 0.8798 (tp) cc_final: 0.8498 (tt) REVERT: B 50 MET cc_start: 0.7411 (ptp) cc_final: 0.6904 (ptp) REVERT: B 54 ASP cc_start: 0.8989 (m-30) cc_final: 0.8440 (t0) REVERT: B 115 ASP cc_start: 0.9364 (OUTLIER) cc_final: 0.9080 (p0) REVERT: B 249 GLU cc_start: 0.8040 (tp30) cc_final: 0.7818 (mm-30) REVERT: B 276 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8195 (mm-30) REVERT: B 335 TRP cc_start: 0.6908 (t-100) cc_final: 0.5835 (t-100) REVERT: B 338 ARG cc_start: 0.6302 (mmt180) cc_final: 0.5563 (mmp-170) REVERT: B 354 TRP cc_start: 0.7737 (m100) cc_final: 0.7504 (m100) REVERT: B 371 MET cc_start: 0.8552 (ttm) cc_final: 0.8322 (ttp) REVERT: B 409 HIS cc_start: 0.8842 (m90) cc_final: 0.8569 (t-170) REVERT: B 436 TYR cc_start: 0.8952 (t80) cc_final: 0.8621 (t80) REVERT: B 487 SER cc_start: 0.8862 (m) cc_final: 0.8632 (p) REVERT: B 491 TRP cc_start: 0.8396 (t60) cc_final: 0.8020 (t60) REVERT: B 524 ILE cc_start: 0.8798 (tp) cc_final: 0.8497 (tt) REVERT: C 50 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.6941 (ptt) REVERT: C 54 ASP cc_start: 0.8914 (m-30) cc_final: 0.8505 (t0) REVERT: C 115 ASP cc_start: 0.9348 (OUTLIER) cc_final: 0.9053 (p0) REVERT: C 249 GLU cc_start: 0.7912 (tp30) cc_final: 0.7487 (mp0) REVERT: C 276 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8194 (mm-30) REVERT: C 334 MET cc_start: 0.5075 (mmm) cc_final: 0.4324 (mmt) REVERT: C 335 TRP cc_start: 0.8268 (OUTLIER) cc_final: 0.7949 (m100) REVERT: C 354 TRP cc_start: 0.7707 (m100) cc_final: 0.7398 (m100) REVERT: C 371 MET cc_start: 0.8816 (ttp) cc_final: 0.8473 (ttm) REVERT: C 487 SER cc_start: 0.8921 (m) cc_final: 0.8677 (p) REVERT: C 524 ILE cc_start: 0.8800 (tp) cc_final: 0.8498 (tt) REVERT: D 50 MET cc_start: 0.7389 (ptp) cc_final: 0.6822 (ptp) REVERT: D 54 ASP cc_start: 0.8994 (m-30) cc_final: 0.8461 (t0) REVERT: D 88 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: D 115 ASP cc_start: 0.9453 (OUTLIER) cc_final: 0.9249 (p0) REVERT: D 249 GLU cc_start: 0.8197 (tp30) cc_final: 0.7838 (mp0) REVERT: D 276 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8205 (mm-30) REVERT: D 352 ASN cc_start: 0.8370 (t0) cc_final: 0.8148 (t0) REVERT: D 371 MET cc_start: 0.8585 (ttm) cc_final: 0.8360 (ttp) REVERT: D 436 TYR cc_start: 0.8963 (t80) cc_final: 0.8510 (t80) REVERT: D 487 SER cc_start: 0.8850 (m) cc_final: 0.8620 (p) REVERT: D 491 TRP cc_start: 0.8304 (t60) cc_final: 0.7910 (t60) REVERT: D 524 ILE cc_start: 0.8805 (tp) cc_final: 0.8495 (tt) outliers start: 69 outliers final: 51 residues processed: 418 average time/residue: 0.2194 time to fit residues: 145.2120 Evaluate side-chains 411 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 354 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 181 optimal weight: 0.0030 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15948 Z= 0.200 Angle : 0.705 11.330 21680 Z= 0.343 Chirality : 0.044 0.239 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.358 21.538 2196 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 4.45 % Allowed : 24.12 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.19), residues: 1900 helix: 0.36 (0.15), residues: 1080 sheet: -0.54 (0.39), residues: 204 loop : -2.71 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 444 HIS 0.017 0.001 HIS B 451 PHE 0.026 0.002 PHE D 235 TYR 0.021 0.001 TYR C 436 ARG 0.003 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 372 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9123 (m-30) cc_final: 0.8664 (t0) REVERT: A 57 ARG cc_start: 0.8398 (mtt180) cc_final: 0.8019 (mtp-110) REVERT: A 88 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: A 115 ASP cc_start: 0.9467 (OUTLIER) cc_final: 0.9257 (p0) REVERT: A 276 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8188 (mm-30) REVERT: A 334 MET cc_start: 0.3721 (mmm) cc_final: 0.3497 (mmt) REVERT: A 371 MET cc_start: 0.8748 (mmm) cc_final: 0.8279 (ttp) REVERT: A 409 HIS cc_start: 0.8848 (m90) cc_final: 0.8550 (t-170) REVERT: A 436 TYR cc_start: 0.8778 (t80) cc_final: 0.8475 (t80) REVERT: A 444 TRP cc_start: 0.8252 (t60) cc_final: 0.7968 (t-100) REVERT: A 464 LEU cc_start: 0.9157 (mt) cc_final: 0.8902 (mt) REVERT: A 487 SER cc_start: 0.8839 (m) cc_final: 0.8634 (p) REVERT: A 491 TRP cc_start: 0.8393 (t60) cc_final: 0.8050 (t60) REVERT: A 493 PHE cc_start: 0.8960 (t80) cc_final: 0.8694 (t80) REVERT: A 524 ILE cc_start: 0.8788 (tp) cc_final: 0.8473 (tt) REVERT: B 50 MET cc_start: 0.7331 (ptp) cc_final: 0.6833 (ptp) REVERT: B 54 ASP cc_start: 0.8981 (m-30) cc_final: 0.8426 (t0) REVERT: B 88 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: B 115 ASP cc_start: 0.9358 (OUTLIER) cc_final: 0.9071 (p0) REVERT: B 276 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8187 (mm-30) REVERT: B 329 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: B 335 TRP cc_start: 0.6961 (t-100) cc_final: 0.5929 (t-100) REVERT: B 338 ARG cc_start: 0.6125 (mmt180) cc_final: 0.5541 (mmp-170) REVERT: B 371 MET cc_start: 0.8552 (ttm) cc_final: 0.8306 (ttp) REVERT: B 409 HIS cc_start: 0.8824 (m90) cc_final: 0.8566 (t-170) REVERT: B 436 TYR cc_start: 0.8932 (t80) cc_final: 0.8680 (t80) REVERT: B 444 TRP cc_start: 0.8274 (t60) cc_final: 0.8009 (t-100) REVERT: B 487 SER cc_start: 0.8819 (m) cc_final: 0.8604 (p) REVERT: B 491 TRP cc_start: 0.8449 (t60) cc_final: 0.8083 (t60) REVERT: B 493 PHE cc_start: 0.8962 (t80) cc_final: 0.8704 (t80) REVERT: B 524 ILE cc_start: 0.8787 (tp) cc_final: 0.8469 (tt) REVERT: C 50 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6973 (ptt) REVERT: C 54 ASP cc_start: 0.8889 (m-30) cc_final: 0.8444 (t0) REVERT: C 88 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: C 115 ASP cc_start: 0.9343 (OUTLIER) cc_final: 0.9053 (p0) REVERT: C 276 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8192 (mm-30) REVERT: C 334 MET cc_start: 0.5193 (mmm) cc_final: 0.4427 (mmt) REVERT: C 335 TRP cc_start: 0.8274 (OUTLIER) cc_final: 0.7957 (m100) REVERT: C 371 MET cc_start: 0.8824 (ttp) cc_final: 0.8460 (ttp) REVERT: C 487 SER cc_start: 0.8955 (m) cc_final: 0.8741 (p) REVERT: C 524 ILE cc_start: 0.8787 (tp) cc_final: 0.8468 (tt) REVERT: D 50 MET cc_start: 0.7404 (ptp) cc_final: 0.6934 (ptp) REVERT: D 54 ASP cc_start: 0.8981 (m-30) cc_final: 0.8470 (t0) REVERT: D 88 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: D 249 GLU cc_start: 0.8234 (tp30) cc_final: 0.7858 (mp0) REVERT: D 276 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8199 (mm-30) REVERT: D 371 MET cc_start: 0.8577 (ttm) cc_final: 0.8362 (ttp) REVERT: D 444 TRP cc_start: 0.8273 (t60) cc_final: 0.8038 (t-100) REVERT: D 487 SER cc_start: 0.8845 (m) cc_final: 0.8632 (p) REVERT: D 491 TRP cc_start: 0.8421 (t60) cc_final: 0.8124 (t60) REVERT: D 524 ILE cc_start: 0.8731 (tp) cc_final: 0.8411 (tt) outliers start: 76 outliers final: 49 residues processed: 419 average time/residue: 0.2381 time to fit residues: 159.6653 Evaluate side-chains 417 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 358 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 123 optimal weight: 0.0770 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15948 Z= 0.279 Angle : 0.736 10.997 21680 Z= 0.358 Chirality : 0.045 0.289 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.376 22.670 2196 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.37 % Favored : 93.58 % Rotamer: Outliers : 4.51 % Allowed : 24.59 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1900 helix: 0.32 (0.15), residues: 1088 sheet: -0.57 (0.39), residues: 204 loop : -2.67 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 444 HIS 0.011 0.001 HIS A 451 PHE 0.020 0.002 PHE B 235 TYR 0.015 0.001 TYR D 355 ARG 0.003 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 371 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9115 (m-30) cc_final: 0.8656 (t0) REVERT: A 57 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8020 (mtp-110) REVERT: A 88 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: A 249 GLU cc_start: 0.7789 (tp30) cc_final: 0.7367 (mm-30) REVERT: A 276 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8211 (mm-30) REVERT: A 371 MET cc_start: 0.8760 (mmm) cc_final: 0.8274 (ttp) REVERT: A 409 HIS cc_start: 0.8830 (m90) cc_final: 0.8529 (t-170) REVERT: A 487 SER cc_start: 0.8904 (m) cc_final: 0.8691 (p) REVERT: A 491 TRP cc_start: 0.8414 (t60) cc_final: 0.8033 (t60) REVERT: A 493 PHE cc_start: 0.9018 (t80) cc_final: 0.8699 (t80) REVERT: A 524 ILE cc_start: 0.8784 (tp) cc_final: 0.8478 (tt) REVERT: B 50 MET cc_start: 0.7378 (ptp) cc_final: 0.6899 (ptp) REVERT: B 54 ASP cc_start: 0.8980 (m-30) cc_final: 0.8422 (t0) REVERT: B 88 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: B 115 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.9094 (p0) REVERT: B 249 GLU cc_start: 0.8183 (tp30) cc_final: 0.7648 (mp0) REVERT: B 276 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8197 (mm-30) REVERT: B 329 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: B 335 TRP cc_start: 0.7012 (t-100) cc_final: 0.5942 (t-100) REVERT: B 338 ARG cc_start: 0.6320 (mmt180) cc_final: 0.5489 (mmp-170) REVERT: B 354 TRP cc_start: 0.7738 (m100) cc_final: 0.7501 (m100) REVERT: B 371 MET cc_start: 0.8554 (ttm) cc_final: 0.8312 (ttp) REVERT: B 409 HIS cc_start: 0.8811 (m90) cc_final: 0.8539 (t-170) REVERT: B 487 SER cc_start: 0.8893 (m) cc_final: 0.8682 (p) REVERT: B 491 TRP cc_start: 0.8473 (t60) cc_final: 0.8132 (t60) REVERT: B 493 PHE cc_start: 0.9012 (t80) cc_final: 0.8728 (t80) REVERT: B 524 ILE cc_start: 0.8781 (tp) cc_final: 0.8473 (tt) REVERT: C 50 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7019 (ptt) REVERT: C 54 ASP cc_start: 0.8933 (m-30) cc_final: 0.8519 (t0) REVERT: C 88 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: C 115 ASP cc_start: 0.9356 (OUTLIER) cc_final: 0.9067 (p0) REVERT: C 276 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8201 (mm-30) REVERT: C 334 MET cc_start: 0.5270 (mmm) cc_final: 0.4777 (mmt) REVERT: C 335 TRP cc_start: 0.8251 (OUTLIER) cc_final: 0.7860 (m100) REVERT: C 371 MET cc_start: 0.8843 (ttp) cc_final: 0.8464 (ttm) REVERT: C 444 TRP cc_start: 0.8285 (t60) cc_final: 0.8031 (t-100) REVERT: C 480 MET cc_start: 0.8068 (mmp) cc_final: 0.7851 (mmp) REVERT: C 487 SER cc_start: 0.8939 (m) cc_final: 0.8717 (p) REVERT: C 524 ILE cc_start: 0.8781 (tp) cc_final: 0.8473 (tt) REVERT: D 50 MET cc_start: 0.7379 (ptp) cc_final: 0.6906 (ptp) REVERT: D 54 ASP cc_start: 0.8993 (m-30) cc_final: 0.8484 (t0) REVERT: D 88 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: D 276 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8212 (mm-30) REVERT: D 371 MET cc_start: 0.8594 (ttm) cc_final: 0.8377 (ttp) REVERT: D 487 SER cc_start: 0.8919 (m) cc_final: 0.8705 (p) REVERT: D 491 TRP cc_start: 0.8379 (t60) cc_final: 0.8046 (t60) REVERT: D 512 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8262 (mm) REVERT: D 524 ILE cc_start: 0.8726 (tp) cc_final: 0.8411 (tt) outliers start: 77 outliers final: 59 residues processed: 418 average time/residue: 0.2152 time to fit residues: 142.0559 Evaluate side-chains 416 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 347 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 0.2980 chunk 159 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15948 Z= 0.207 Angle : 0.754 11.906 21680 Z= 0.358 Chirality : 0.045 0.370 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.318 22.432 2196 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 3.92 % Allowed : 25.76 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1900 helix: 0.29 (0.15), residues: 1112 sheet: -0.47 (0.39), residues: 204 loop : -2.65 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 444 HIS 0.004 0.001 HIS D 451 PHE 0.018 0.002 PHE D 493 TYR 0.022 0.001 TYR C 436 ARG 0.005 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 366 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9113 (m-30) cc_final: 0.8722 (t0) REVERT: A 57 ARG cc_start: 0.8422 (mtt180) cc_final: 0.8123 (mtp85) REVERT: A 88 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: A 249 GLU cc_start: 0.7878 (tp30) cc_final: 0.7465 (mp0) REVERT: A 276 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8124 (mm-30) REVERT: A 371 MET cc_start: 0.8761 (mmm) cc_final: 0.8273 (ttp) REVERT: A 409 HIS cc_start: 0.8813 (m90) cc_final: 0.8529 (t-170) REVERT: A 444 TRP cc_start: 0.8096 (t60) cc_final: 0.7668 (t-100) REVERT: A 491 TRP cc_start: 0.8383 (t60) cc_final: 0.8049 (t60) REVERT: A 524 ILE cc_start: 0.8707 (tp) cc_final: 0.8384 (tt) REVERT: B 50 MET cc_start: 0.7354 (ptp) cc_final: 0.6869 (ptp) REVERT: B 54 ASP cc_start: 0.8973 (m-30) cc_final: 0.8404 (t0) REVERT: B 88 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: B 115 ASP cc_start: 0.9352 (OUTLIER) cc_final: 0.9065 (p0) REVERT: B 249 GLU cc_start: 0.8078 (tp30) cc_final: 0.7589 (mp0) REVERT: B 276 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8112 (mm-30) REVERT: B 329 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8455 (tp30) REVERT: B 335 TRP cc_start: 0.6911 (t-100) cc_final: 0.5920 (t-100) REVERT: B 371 MET cc_start: 0.8546 (ttm) cc_final: 0.8304 (ttp) REVERT: B 409 HIS cc_start: 0.8794 (m90) cc_final: 0.8538 (t-170) REVERT: B 444 TRP cc_start: 0.8103 (t60) cc_final: 0.7696 (t-100) REVERT: B 491 TRP cc_start: 0.8450 (t60) cc_final: 0.8108 (t60) REVERT: B 524 ILE cc_start: 0.8706 (tp) cc_final: 0.8379 (tt) REVERT: C 50 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6946 (ptp) REVERT: C 54 ASP cc_start: 0.8916 (m-30) cc_final: 0.8285 (t0) REVERT: C 88 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: C 115 ASP cc_start: 0.9338 (OUTLIER) cc_final: 0.9038 (p0) REVERT: C 276 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8130 (mm-30) REVERT: C 334 MET cc_start: 0.5846 (mmm) cc_final: 0.5164 (mmt) REVERT: C 335 TRP cc_start: 0.8208 (m-10) cc_final: 0.7914 (m100) REVERT: C 371 MET cc_start: 0.8828 (ttp) cc_final: 0.8455 (ttp) REVERT: C 444 TRP cc_start: 0.8255 (t60) cc_final: 0.8015 (t-100) REVERT: C 487 SER cc_start: 0.8866 (m) cc_final: 0.8659 (p) REVERT: C 524 ILE cc_start: 0.8703 (tp) cc_final: 0.8367 (tt) REVERT: D 50 MET cc_start: 0.7399 (ptp) cc_final: 0.6942 (ptp) REVERT: D 54 ASP cc_start: 0.8988 (m-30) cc_final: 0.8470 (t0) REVERT: D 88 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: D 249 GLU cc_start: 0.8071 (tp30) cc_final: 0.7697 (mp0) REVERT: D 276 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8194 (mm-30) REVERT: D 371 MET cc_start: 0.8465 (ttm) cc_final: 0.8242 (ttp) REVERT: D 436 TYR cc_start: 0.8880 (t80) cc_final: 0.8634 (t80) REVERT: D 444 TRP cc_start: 0.8062 (t60) cc_final: 0.7640 (t-100) REVERT: D 491 TRP cc_start: 0.8392 (t60) cc_final: 0.8059 (t60) REVERT: D 524 ILE cc_start: 0.8706 (tp) cc_final: 0.8368 (tt) outliers start: 67 outliers final: 56 residues processed: 409 average time/residue: 0.2105 time to fit residues: 138.3439 Evaluate side-chains 409 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 345 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 489 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 124 optimal weight: 0.5980 chunk 187 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 0.0020 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15948 Z= 0.192 Angle : 0.750 12.231 21680 Z= 0.355 Chirality : 0.045 0.309 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.285 21.330 2196 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.58 % Favored : 94.37 % Rotamer: Outliers : 3.28 % Allowed : 26.41 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.19), residues: 1900 helix: 0.34 (0.15), residues: 1112 sheet: -0.40 (0.39), residues: 204 loop : -2.63 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 444 HIS 0.005 0.001 HIS C 451 PHE 0.018 0.002 PHE C 235 TYR 0.013 0.001 TYR A 147 ARG 0.003 0.000 ARG C 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 364 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.9111 (m-30) cc_final: 0.8716 (t0) REVERT: A 57 ARG cc_start: 0.8431 (mtt180) cc_final: 0.8129 (mtp85) REVERT: A 88 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: A 276 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 371 MET cc_start: 0.8768 (mmm) cc_final: 0.8278 (ttp) REVERT: A 403 ARG cc_start: 0.7874 (tmt170) cc_final: 0.7522 (tmm160) REVERT: A 409 HIS cc_start: 0.8844 (m90) cc_final: 0.8526 (t-170) REVERT: A 444 TRP cc_start: 0.8204 (t60) cc_final: 0.7853 (t-100) REVERT: A 491 TRP cc_start: 0.8401 (t60) cc_final: 0.8039 (t60) REVERT: A 524 ILE cc_start: 0.8739 (tp) cc_final: 0.8419 (tt) REVERT: B 50 MET cc_start: 0.7346 (ptp) cc_final: 0.6849 (ptp) REVERT: B 54 ASP cc_start: 0.8973 (m-30) cc_final: 0.8394 (t0) REVERT: B 88 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: B 115 ASP cc_start: 0.9343 (OUTLIER) cc_final: 0.9064 (p0) REVERT: B 249 GLU cc_start: 0.8120 (tp30) cc_final: 0.7655 (mp0) REVERT: B 276 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8121 (mm-30) REVERT: B 329 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8419 (tp30) REVERT: B 335 TRP cc_start: 0.6909 (t-100) cc_final: 0.5908 (t-100) REVERT: B 371 MET cc_start: 0.8520 (ttm) cc_final: 0.8312 (ttp) REVERT: B 409 HIS cc_start: 0.8767 (m90) cc_final: 0.8506 (t-170) REVERT: B 436 TYR cc_start: 0.8969 (t80) cc_final: 0.8754 (t80) REVERT: B 444 TRP cc_start: 0.8244 (t60) cc_final: 0.7891 (t-100) REVERT: B 491 TRP cc_start: 0.8468 (t60) cc_final: 0.8106 (t60) REVERT: B 512 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8247 (mm) REVERT: B 524 ILE cc_start: 0.8722 (tp) cc_final: 0.8390 (tt) REVERT: C 50 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6711 (ptp) REVERT: C 54 ASP cc_start: 0.8901 (m-30) cc_final: 0.8225 (t0) REVERT: C 88 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: C 115 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.9034 (p0) REVERT: C 276 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8120 (mm-30) REVERT: C 309 CYS cc_start: 0.9261 (m) cc_final: 0.9007 (m) REVERT: C 334 MET cc_start: 0.5845 (mmm) cc_final: 0.5332 (mmt) REVERT: C 335 TRP cc_start: 0.8151 (m-10) cc_final: 0.7847 (m100) REVERT: C 371 MET cc_start: 0.8819 (ttp) cc_final: 0.8442 (ttp) REVERT: C 487 SER cc_start: 0.8816 (m) cc_final: 0.8611 (p) REVERT: C 524 ILE cc_start: 0.8714 (tp) cc_final: 0.8376 (tt) REVERT: D 50 MET cc_start: 0.7413 (ptp) cc_final: 0.6812 (ptp) REVERT: D 54 ASP cc_start: 0.8989 (m-30) cc_final: 0.8436 (t0) REVERT: D 88 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: D 249 GLU cc_start: 0.8006 (tp30) cc_final: 0.7528 (mp0) REVERT: D 276 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8128 (mm-30) REVERT: D 309 CYS cc_start: 0.9257 (m) cc_final: 0.9028 (m) REVERT: D 371 MET cc_start: 0.8445 (ttm) cc_final: 0.8228 (ttp) REVERT: D 444 TRP cc_start: 0.8186 (t60) cc_final: 0.7923 (t-100) REVERT: D 491 TRP cc_start: 0.8389 (t60) cc_final: 0.8076 (t60) REVERT: D 524 ILE cc_start: 0.8742 (tp) cc_final: 0.8406 (tt) outliers start: 56 outliers final: 43 residues processed: 396 average time/residue: 0.2106 time to fit residues: 133.1892 Evaluate side-chains 400 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 348 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 489 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 0.0040 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.118228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095179 restraints weight = 40997.140| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 4.80 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15948 Z= 0.201 Angle : 0.750 11.810 21680 Z= 0.357 Chirality : 0.045 0.318 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.252 21.775 2196 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.53 % Favored : 94.42 % Rotamer: Outliers : 3.57 % Allowed : 26.93 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.19), residues: 1900 helix: 0.46 (0.15), residues: 1096 sheet: -0.26 (0.40), residues: 204 loop : -2.60 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 444 HIS 0.004 0.001 HIS A 280 PHE 0.018 0.002 PHE C 235 TYR 0.018 0.001 TYR D 436 ARG 0.007 0.000 ARG C 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3600.62 seconds wall clock time: 65 minutes 36.67 seconds (3936.67 seconds total)