Starting phenix.real_space_refine on Thu Apr 11 09:22:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2024/7d0i_30535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2024/7d0i_30535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2024/7d0i_30535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2024/7d0i_30535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2024/7d0i_30535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2024/7d0i_30535_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 72 5.16 5 C 14742 2.51 5 N 3516 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B GLU 559": "OE1" <-> "OE2" Residue "B ASP 585": "OD1" <-> "OD2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "D GLU 559": "OE1" <-> "OE2" Residue "D ASP 585": "OD1" <-> "OD2" Residue "D PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 610": "OE1" <-> "OE2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "D PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 368": "NH1" <-> "NH2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "F ARG 399": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F ARG 406": "NH1" <-> "NH2" Residue "F ARG 414": "NH1" <-> "NH2" Residue "F TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F GLU 559": "OE1" <-> "OE2" Residue "F ASP 585": "OD1" <-> "OD2" Residue "F PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 610": "OE1" <-> "OE2" Residue "F PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 637": "NH1" <-> "NH2" Residue "F PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 278": "NH1" <-> "NH2" Residue "H PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 345": "NH1" <-> "NH2" Residue "H PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 368": "NH1" <-> "NH2" Residue "H ARG 369": "NH1" <-> "NH2" Residue "H ARG 399": "NH1" <-> "NH2" Residue "H ARG 404": "NH1" <-> "NH2" Residue "H ARG 406": "NH1" <-> "NH2" Residue "H ARG 414": "NH1" <-> "NH2" Residue "H TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 470": "OE1" <-> "OE2" Residue "H PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 500": "NH1" <-> "NH2" Residue "H GLU 559": "OE1" <-> "OE2" Residue "H ASP 585": "OD1" <-> "OD2" Residue "H PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 610": "OE1" <-> "OE2" Residue "H PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 637": "NH1" <-> "NH2" Residue "H PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 278": "NH1" <-> "NH2" Residue "J PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 345": "NH1" <-> "NH2" Residue "J PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 368": "NH1" <-> "NH2" Residue "J ARG 369": "NH1" <-> "NH2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J ARG 404": "NH1" <-> "NH2" Residue "J ARG 406": "NH1" <-> "NH2" Residue "J ARG 414": "NH1" <-> "NH2" Residue "J TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 470": "OE1" <-> "OE2" Residue "J PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 500": "NH1" <-> "NH2" Residue "J GLU 559": "OE1" <-> "OE2" Residue "J ASP 585": "OD1" <-> "OD2" Residue "J PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 610": "OE1" <-> "OE2" Residue "J PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 637": "NH1" <-> "NH2" Residue "J PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 278": "NH1" <-> "NH2" Residue "L PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 345": "NH1" <-> "NH2" Residue "L PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 368": "NH1" <-> "NH2" Residue "L ARG 369": "NH1" <-> "NH2" Residue "L ARG 399": "NH1" <-> "NH2" Residue "L ARG 404": "NH1" <-> "NH2" Residue "L ARG 406": "NH1" <-> "NH2" Residue "L ARG 414": "NH1" <-> "NH2" Residue "L TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 470": "OE1" <-> "OE2" Residue "L PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 500": "NH1" <-> "NH2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "L ASP 585": "OD1" <-> "OD2" Residue "L PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 610": "OE1" <-> "OE2" Residue "L PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 637": "NH1" <-> "NH2" Residue "L PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22164 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.41, per 1000 atoms: 0.51 Number of scatterers: 22164 At special positions: 0 Unit cell: (122.01, 125.745, 153.135, 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 72 16.00 O 3834 8.00 N 3516 7.00 C 14742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.10 Conformation dependent library (CDL) restraints added in 3.8 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 12 sheets defined 69.1% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 253 through 287 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 302 through 312 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 345 through 355 removed outlier: 3.908A pdb=" N TYR B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 384 through 387 No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 401 through 404 removed outlier: 3.737A pdb=" N ARG B 404 " --> pdb=" O PRO B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 404' Processing helix chain 'B' and resid 407 through 410 No H-bonds generated for 'chain 'B' and resid 407 through 410' Processing helix chain 'B' and resid 412 through 425 removed outlier: 4.134A pdb=" N VAL B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 447 removed outlier: 4.100A pdb=" N TYR B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 452 Processing helix chain 'B' and resid 461 through 464 No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 472 through 491 removed outlier: 3.928A pdb=" N SER B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA B 484 " --> pdb=" O ASN B 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA B 485 " --> pdb=" O ASP B 481 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 520 removed outlier: 3.740A pdb=" N LEU B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 555 removed outlier: 3.702A pdb=" N SER B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 576 removed outlier: 4.085A pdb=" N PHE B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 591 through 599 Processing helix chain 'B' and resid 603 through 623 removed outlier: 3.959A pdb=" N ILE B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Proline residue: B 618 - end of helix Processing helix chain 'B' and resid 626 through 638 removed outlier: 4.980A pdb=" N GLN B 630 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B 631 " --> pdb=" O CYS B 628 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 638 " --> pdb=" O PHE B 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 198 through 223 Processing helix chain 'D' and resid 253 through 287 Proline residue: D 277 - end of helix Processing helix chain 'D' and resid 302 through 312 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 345 through 355 removed outlier: 3.908A pdb=" N TYR D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 382 Processing helix chain 'D' and resid 384 through 387 No H-bonds generated for 'chain 'D' and resid 384 through 387' Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 401 through 404 removed outlier: 3.738A pdb=" N ARG D 404 " --> pdb=" O PRO D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 407 through 410 No H-bonds generated for 'chain 'D' and resid 407 through 410' Processing helix chain 'D' and resid 412 through 425 removed outlier: 4.134A pdb=" N VAL D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 447 removed outlier: 4.099A pdb=" N TYR D 432 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASN D 443 " --> pdb=" O PHE D 439 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 452 Processing helix chain 'D' and resid 461 through 464 No H-bonds generated for 'chain 'D' and resid 461 through 464' Processing helix chain 'D' and resid 472 through 491 removed outlier: 3.929A pdb=" N SER D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA D 484 " --> pdb=" O ASN D 480 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA D 485 " --> pdb=" O ASP D 481 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 520 removed outlier: 3.739A pdb=" N LEU D 501 " --> pdb=" O ASN D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 555 removed outlier: 3.702A pdb=" N SER D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 576 removed outlier: 4.085A pdb=" N PHE D 575 " --> pdb=" O ARG D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 591 through 599 Processing helix chain 'D' and resid 603 through 623 removed outlier: 3.960A pdb=" N ILE D 614 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) Proline residue: D 618 - end of helix Processing helix chain 'D' and resid 626 through 638 removed outlier: 4.979A pdb=" N GLN D 630 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP D 631 " --> pdb=" O CYS D 628 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 638 " --> pdb=" O PHE D 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 198 through 223 Processing helix chain 'F' and resid 253 through 287 Proline residue: F 277 - end of helix Processing helix chain 'F' and resid 302 through 312 Processing helix chain 'F' and resid 336 through 343 Processing helix chain 'F' and resid 345 through 355 removed outlier: 3.909A pdb=" N TYR F 349 " --> pdb=" O ARG F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 382 Processing helix chain 'F' and resid 384 through 387 No H-bonds generated for 'chain 'F' and resid 384 through 387' Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 401 through 404 removed outlier: 3.738A pdb=" N ARG F 404 " --> pdb=" O PRO F 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 401 through 404' Processing helix chain 'F' and resid 407 through 410 No H-bonds generated for 'chain 'F' and resid 407 through 410' Processing helix chain 'F' and resid 412 through 425 removed outlier: 4.134A pdb=" N VAL F 417 " --> pdb=" O ARG F 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 424 " --> pdb=" O PHE F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 447 removed outlier: 4.101A pdb=" N TYR F 432 " --> pdb=" O ILE F 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN F 443 " --> pdb=" O PHE F 439 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU F 444 " --> pdb=" O ARG F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 452 Processing helix chain 'F' and resid 461 through 464 No H-bonds generated for 'chain 'F' and resid 461 through 464' Processing helix chain 'F' and resid 472 through 491 removed outlier: 3.928A pdb=" N SER F 482 " --> pdb=" O ARG F 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA F 484 " --> pdb=" O ASN F 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA F 485 " --> pdb=" O ASP F 481 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 491 " --> pdb=" O SER F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 520 removed outlier: 3.739A pdb=" N LEU F 501 " --> pdb=" O ASN F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 555 removed outlier: 3.702A pdb=" N SER F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE F 555 " --> pdb=" O VAL F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 576 removed outlier: 4.084A pdb=" N PHE F 575 " --> pdb=" O ARG F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 583 No H-bonds generated for 'chain 'F' and resid 581 through 583' Processing helix chain 'F' and resid 591 through 599 Processing helix chain 'F' and resid 603 through 623 removed outlier: 3.958A pdb=" N ILE F 614 " --> pdb=" O GLU F 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 615 " --> pdb=" O ILE F 611 " (cutoff:3.500A) Proline residue: F 618 - end of helix Processing helix chain 'F' and resid 626 through 638 removed outlier: 4.980A pdb=" N GLN F 630 " --> pdb=" O SER F 627 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP F 631 " --> pdb=" O CYS F 628 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 638 " --> pdb=" O PHE F 635 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 195 Processing helix chain 'H' and resid 198 through 223 Processing helix chain 'H' and resid 253 through 287 Proline residue: H 277 - end of helix Processing helix chain 'H' and resid 302 through 312 Processing helix chain 'H' and resid 336 through 343 Processing helix chain 'H' and resid 345 through 355 removed outlier: 3.909A pdb=" N TYR H 349 " --> pdb=" O ARG H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 382 Processing helix chain 'H' and resid 384 through 387 No H-bonds generated for 'chain 'H' and resid 384 through 387' Processing helix chain 'H' and resid 396 through 398 No H-bonds generated for 'chain 'H' and resid 396 through 398' Processing helix chain 'H' and resid 401 through 404 removed outlier: 3.737A pdb=" N ARG H 404 " --> pdb=" O PRO H 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 401 through 404' Processing helix chain 'H' and resid 407 through 410 No H-bonds generated for 'chain 'H' and resid 407 through 410' Processing helix chain 'H' and resid 412 through 425 removed outlier: 4.133A pdb=" N VAL H 417 " --> pdb=" O ARG H 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 424 " --> pdb=" O PHE H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 447 removed outlier: 4.102A pdb=" N TYR H 432 " --> pdb=" O ILE H 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN H 443 " --> pdb=" O PHE H 439 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU H 444 " --> pdb=" O ARG H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 452 Processing helix chain 'H' and resid 461 through 464 No H-bonds generated for 'chain 'H' and resid 461 through 464' Processing helix chain 'H' and resid 472 through 491 removed outlier: 3.927A pdb=" N SER H 482 " --> pdb=" O ARG H 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR H 483 " --> pdb=" O ILE H 479 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA H 484 " --> pdb=" O ASN H 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA H 485 " --> pdb=" O ASP H 481 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER H 491 " --> pdb=" O SER H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 520 removed outlier: 3.741A pdb=" N LEU H 501 " --> pdb=" O ASN H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 555 removed outlier: 3.702A pdb=" N SER H 554 " --> pdb=" O ALA H 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE H 555 " --> pdb=" O VAL H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 576 removed outlier: 4.084A pdb=" N PHE H 575 " --> pdb=" O ARG H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 583 No H-bonds generated for 'chain 'H' and resid 581 through 583' Processing helix chain 'H' and resid 591 through 599 Processing helix chain 'H' and resid 603 through 623 removed outlier: 3.961A pdb=" N ILE H 614 " --> pdb=" O GLU H 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU H 615 " --> pdb=" O ILE H 611 " (cutoff:3.500A) Proline residue: H 618 - end of helix Processing helix chain 'H' and resid 626 through 638 removed outlier: 4.981A pdb=" N GLN H 630 " --> pdb=" O SER H 627 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP H 631 " --> pdb=" O CYS H 628 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU H 638 " --> pdb=" O PHE H 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 195 Processing helix chain 'J' and resid 198 through 223 Processing helix chain 'J' and resid 253 through 287 Proline residue: J 277 - end of helix Processing helix chain 'J' and resid 302 through 312 Processing helix chain 'J' and resid 336 through 343 Processing helix chain 'J' and resid 345 through 355 removed outlier: 3.909A pdb=" N TYR J 349 " --> pdb=" O ARG J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 382 Processing helix chain 'J' and resid 384 through 387 No H-bonds generated for 'chain 'J' and resid 384 through 387' Processing helix chain 'J' and resid 396 through 398 No H-bonds generated for 'chain 'J' and resid 396 through 398' Processing helix chain 'J' and resid 401 through 404 removed outlier: 3.736A pdb=" N ARG J 404 " --> pdb=" O PRO J 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 401 through 404' Processing helix chain 'J' and resid 407 through 410 No H-bonds generated for 'chain 'J' and resid 407 through 410' Processing helix chain 'J' and resid 412 through 425 removed outlier: 4.135A pdb=" N VAL J 417 " --> pdb=" O ARG J 413 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU J 424 " --> pdb=" O PHE J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 427 through 447 removed outlier: 4.101A pdb=" N TYR J 432 " --> pdb=" O ILE J 428 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASN J 443 " --> pdb=" O PHE J 439 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU J 444 " --> pdb=" O ARG J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 452 Processing helix chain 'J' and resid 461 through 464 No H-bonds generated for 'chain 'J' and resid 461 through 464' Processing helix chain 'J' and resid 472 through 491 removed outlier: 3.927A pdb=" N SER J 482 " --> pdb=" O ARG J 478 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR J 483 " --> pdb=" O ILE J 479 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA J 484 " --> pdb=" O ASN J 480 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA J 485 " --> pdb=" O ASP J 481 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER J 491 " --> pdb=" O SER J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 496 through 520 removed outlier: 3.741A pdb=" N LEU J 501 " --> pdb=" O ASN J 497 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 555 removed outlier: 3.701A pdb=" N SER J 554 " --> pdb=" O ALA J 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE J 555 " --> pdb=" O VAL J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 565 through 576 removed outlier: 4.083A pdb=" N PHE J 575 " --> pdb=" O ARG J 571 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 591 through 599 Processing helix chain 'J' and resid 603 through 623 removed outlier: 3.958A pdb=" N ILE J 614 " --> pdb=" O GLU J 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU J 615 " --> pdb=" O ILE J 611 " (cutoff:3.500A) Proline residue: J 618 - end of helix Processing helix chain 'J' and resid 626 through 638 removed outlier: 4.982A pdb=" N GLN J 630 " --> pdb=" O SER J 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP J 631 " --> pdb=" O CYS J 628 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU J 638 " --> pdb=" O PHE J 635 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 195 Processing helix chain 'L' and resid 198 through 223 Processing helix chain 'L' and resid 253 through 287 Proline residue: L 277 - end of helix Processing helix chain 'L' and resid 302 through 312 Processing helix chain 'L' and resid 336 through 343 Processing helix chain 'L' and resid 345 through 355 removed outlier: 3.907A pdb=" N TYR L 349 " --> pdb=" O ARG L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 382 Processing helix chain 'L' and resid 384 through 387 No H-bonds generated for 'chain 'L' and resid 384 through 387' Processing helix chain 'L' and resid 396 through 398 No H-bonds generated for 'chain 'L' and resid 396 through 398' Processing helix chain 'L' and resid 401 through 404 removed outlier: 3.738A pdb=" N ARG L 404 " --> pdb=" O PRO L 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 401 through 404' Processing helix chain 'L' and resid 407 through 410 No H-bonds generated for 'chain 'L' and resid 407 through 410' Processing helix chain 'L' and resid 412 through 425 removed outlier: 4.133A pdb=" N VAL L 417 " --> pdb=" O ARG L 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU L 424 " --> pdb=" O PHE L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 427 through 447 removed outlier: 4.101A pdb=" N TYR L 432 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN L 443 " --> pdb=" O PHE L 439 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU L 444 " --> pdb=" O ARG L 440 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 452 Processing helix chain 'L' and resid 461 through 464 No H-bonds generated for 'chain 'L' and resid 461 through 464' Processing helix chain 'L' and resid 472 through 491 removed outlier: 3.928A pdb=" N SER L 482 " --> pdb=" O ARG L 478 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR L 483 " --> pdb=" O ILE L 479 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA L 484 " --> pdb=" O ASN L 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA L 485 " --> pdb=" O ASP L 481 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER L 491 " --> pdb=" O SER L 487 " (cutoff:3.500A) Processing helix chain 'L' and resid 496 through 520 removed outlier: 3.740A pdb=" N LEU L 501 " --> pdb=" O ASN L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 538 through 555 removed outlier: 3.701A pdb=" N SER L 554 " --> pdb=" O ALA L 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE L 555 " --> pdb=" O VAL L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 565 through 576 removed outlier: 4.086A pdb=" N PHE L 575 " --> pdb=" O ARG L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 581 through 583 No H-bonds generated for 'chain 'L' and resid 581 through 583' Processing helix chain 'L' and resid 591 through 599 Processing helix chain 'L' and resid 603 through 623 removed outlier: 3.960A pdb=" N ILE L 614 " --> pdb=" O GLU L 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU L 615 " --> pdb=" O ILE L 611 " (cutoff:3.500A) Proline residue: L 618 - end of helix Processing helix chain 'L' and resid 626 through 638 removed outlier: 4.979A pdb=" N GLN L 630 " --> pdb=" O SER L 627 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP L 631 " --> pdb=" O CYS L 628 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU L 638 " --> pdb=" O PHE L 635 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 455 through 457 Processing sheet with id= B, first strand: chain 'B' and resid 640 through 643 Processing sheet with id= C, first strand: chain 'D' and resid 455 through 457 Processing sheet with id= D, first strand: chain 'D' and resid 640 through 643 Processing sheet with id= E, first strand: chain 'F' and resid 455 through 457 Processing sheet with id= F, first strand: chain 'F' and resid 640 through 643 Processing sheet with id= G, first strand: chain 'H' and resid 455 through 457 Processing sheet with id= H, first strand: chain 'H' and resid 640 through 643 Processing sheet with id= I, first strand: chain 'J' and resid 455 through 457 Processing sheet with id= J, first strand: chain 'J' and resid 640 through 643 Processing sheet with id= K, first strand: chain 'L' and resid 455 through 457 Processing sheet with id= L, first strand: chain 'L' and resid 640 through 643 1110 hydrogen bonds defined for protein. 3168 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: 6.47 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6129 1.33 - 1.45: 4312 1.45 - 1.57: 12209 1.57 - 1.69: 84 1.69 - 1.80: 108 Bond restraints: 22842 Sorted by residual: bond pdb=" C1 LMN B 801 " pdb=" O5 LMN B 801 " ideal model delta sigma weight residual 1.403 1.548 -0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" C1 LMN L 801 " pdb=" O5 LMN L 801 " ideal model delta sigma weight residual 1.403 1.547 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C1 LMN J 801 " pdb=" O5 LMN J 801 " ideal model delta sigma weight residual 1.403 1.547 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C1 LMN H 801 " pdb=" O5 LMN H 801 " ideal model delta sigma weight residual 1.403 1.547 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C1 LMN F 801 " pdb=" O5 LMN F 801 " ideal model delta sigma weight residual 1.403 1.546 -0.143 2.00e-02 2.50e+03 5.13e+01 ... (remaining 22837 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.92: 540 106.92 - 113.72: 13155 113.72 - 120.51: 9696 120.51 - 127.31: 7388 127.31 - 134.10: 289 Bond angle restraints: 31068 Sorted by residual: angle pdb=" CBJ LMN B 802 " pdb=" CBL LMN B 802 " pdb=" CBR LMN B 802 " ideal model delta sigma weight residual 112.20 133.40 -21.20 3.00e+00 1.11e-01 4.99e+01 angle pdb=" CBJ LMN F 802 " pdb=" CBL LMN F 802 " pdb=" CBR LMN F 802 " ideal model delta sigma weight residual 112.20 133.34 -21.14 3.00e+00 1.11e-01 4.97e+01 angle pdb=" CBJ LMN J 802 " pdb=" CBL LMN J 802 " pdb=" CBR LMN J 802 " ideal model delta sigma weight residual 112.20 133.30 -21.10 3.00e+00 1.11e-01 4.95e+01 angle pdb=" CBJ LMN D 802 " pdb=" CBL LMN D 802 " pdb=" CBR LMN D 802 " ideal model delta sigma weight residual 112.20 133.26 -21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" CBJ LMN H 802 " pdb=" CBL LMN H 802 " pdb=" CBR LMN H 802 " ideal model delta sigma weight residual 112.20 133.24 -21.04 3.00e+00 1.11e-01 4.92e+01 ... (remaining 31063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.53: 13332 29.53 - 59.05: 456 59.05 - 88.58: 180 88.58 - 118.10: 114 118.10 - 147.63: 66 Dihedral angle restraints: 14148 sinusoidal: 6564 harmonic: 7584 Sorted by residual: dihedral pdb=" CBH LMN H 801 " pdb=" CBJ LMN H 801 " pdb=" CBL LMN H 801 " pdb=" CBR LMN H 801 " ideal model delta sinusoidal sigma weight residual 181.02 33.39 147.63 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CBH LMN B 801 " pdb=" CBJ LMN B 801 " pdb=" CBL LMN B 801 " pdb=" CBR LMN B 801 " ideal model delta sinusoidal sigma weight residual 181.02 33.45 147.57 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CBH LMN D 801 " pdb=" CBJ LMN D 801 " pdb=" CBL LMN D 801 " pdb=" CBR LMN D 801 " ideal model delta sinusoidal sigma weight residual 181.02 33.47 147.55 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 14145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2384 0.045 - 0.090: 926 0.090 - 0.136: 211 0.136 - 0.181: 24 0.181 - 0.226: 13 Chirality restraints: 3558 Sorted by residual: chirality pdb=" CCQ LMN D 801 " pdb=" CCF LMN D 801 " pdb=" CCH LMN D 801 " pdb=" OCB LMN D 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CCQ LMN F 801 " pdb=" CCF LMN F 801 " pdb=" CCH LMN F 801 " pdb=" OCB LMN F 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CCQ LMN L 801 " pdb=" CCF LMN L 801 " pdb=" CCH LMN L 801 " pdb=" OCB LMN L 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3555 not shown) Planarity restraints: 3678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 617 " 0.031 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO L 618 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 618 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 618 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 617 " -0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO J 618 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 618 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 618 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 617 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO F 618 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 618 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 618 " -0.026 5.00e-02 4.00e+02 ... (remaining 3675 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4932 2.77 - 3.30: 21422 3.30 - 3.83: 37072 3.83 - 4.37: 45249 4.37 - 4.90: 76701 Nonbonded interactions: 185376 Sorted by model distance: nonbonded pdb=" OAN LMN B 802 " pdb=" OBZ LMN B 802 " model vdw 2.237 2.440 nonbonded pdb=" OAN LMN D 802 " pdb=" OBZ LMN D 802 " model vdw 2.237 2.440 nonbonded pdb=" OAN LMN F 802 " pdb=" OBZ LMN F 802 " model vdw 2.238 2.440 nonbonded pdb=" OAN LMN J 802 " pdb=" OBZ LMN J 802 " model vdw 2.238 2.440 nonbonded pdb=" OAN LMN L 802 " pdb=" OBZ LMN L 802 " model vdw 2.238 2.440 ... (remaining 185371 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 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.740 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: 3.930 Check model and map are aligned: 0.300 Set scattering table: 0.210 Process input model: 58.070 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.011 0.145 22842 Z= 0.736 Angle : 0.950 21.201 31068 Z= 0.413 Chirality : 0.049 0.226 3558 Planarity : 0.004 0.046 3678 Dihedral : 22.603 147.628 9228 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.60 % Allowed : 6.23 % Favored : 91.17 % 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: -2.14 (0.15), residues: 2496 helix: -1.08 (0.11), residues: 1818 sheet: None (None), residues: 0 loop : -1.94 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 280 HIS 0.004 0.001 HIS J 473 PHE 0.013 0.002 PHE J 386 TYR 0.027 0.002 TYR D 600 ARG 0.005 0.001 ARG F 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 470 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 282 MET cc_start: 0.8800 (tpp) cc_final: 0.8456 (tpp) REVERT: B 310 LEU cc_start: 0.7990 (tp) cc_final: 0.7739 (mp) REVERT: B 366 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 391 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 440 ARG cc_start: 0.7523 (ttt180) cc_final: 0.7318 (tmt170) REVERT: B 548 LEU cc_start: 0.7143 (mt) cc_final: 0.6862 (mt) REVERT: B 559 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7253 (mm-30) REVERT: B 586 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8281 (p0) REVERT: D 282 MET cc_start: 0.8586 (tpp) cc_final: 0.8275 (tpp) REVERT: D 284 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6542 (mt-10) REVERT: D 310 LEU cc_start: 0.7930 (tp) cc_final: 0.7681 (mm) REVERT: D 366 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7724 (tt) REVERT: D 367 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7469 (m-70) REVERT: D 380 ASN cc_start: 0.8331 (m-40) cc_final: 0.8060 (m110) REVERT: D 391 GLN cc_start: 0.7475 (tm-30) cc_final: 0.6923 (tm130) REVERT: D 440 ARG cc_start: 0.7409 (ttt180) cc_final: 0.7060 (tmt170) REVERT: D 548 LEU cc_start: 0.6569 (mt) cc_final: 0.6342 (mp) REVERT: D 559 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7401 (mm-30) REVERT: F 280 TRP cc_start: 0.7706 (t-100) cc_final: 0.7246 (t60) REVERT: F 367 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7644 (m-70) REVERT: F 391 GLN cc_start: 0.7616 (tm-30) cc_final: 0.6925 (tm130) REVERT: F 548 LEU cc_start: 0.6607 (mt) cc_final: 0.6178 (mp) REVERT: F 641 ILE cc_start: 0.8322 (tt) cc_final: 0.7947 (tp) REVERT: F 651 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8501 (p) REVERT: H 282 MET cc_start: 0.8805 (tpp) cc_final: 0.8442 (tpp) REVERT: H 310 LEU cc_start: 0.7985 (tp) cc_final: 0.7719 (mp) REVERT: H 366 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7937 (tt) REVERT: H 391 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7400 (tm-30) REVERT: H 440 ARG cc_start: 0.7454 (ttt180) cc_final: 0.7242 (tmt170) REVERT: H 548 LEU cc_start: 0.7238 (mt) cc_final: 0.6989 (mt) REVERT: H 559 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7326 (mm-30) REVERT: H 586 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8218 (p0) REVERT: H 587 MET cc_start: 0.8348 (mtp) cc_final: 0.8119 (mtm) REVERT: J 280 TRP cc_start: 0.7420 (t-100) cc_final: 0.7201 (t60) REVERT: J 282 MET cc_start: 0.8787 (tpp) cc_final: 0.8481 (tpp) REVERT: J 284 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6713 (mt-10) REVERT: J 367 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7391 (m-70) REVERT: J 391 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7280 (tm-30) REVERT: J 440 ARG cc_start: 0.7304 (ttt180) cc_final: 0.7017 (tmt170) REVERT: J 559 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7472 (mm-30) REVERT: J 586 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8382 (p0) REVERT: L 280 TRP cc_start: 0.7725 (t-100) cc_final: 0.7207 (t60) REVERT: L 391 GLN cc_start: 0.7585 (tm-30) cc_final: 0.6968 (tm130) REVERT: L 440 ARG cc_start: 0.7324 (ttt180) cc_final: 0.6950 (tmt170) REVERT: L 548 LEU cc_start: 0.6743 (mt) cc_final: 0.6395 (mp) REVERT: L 559 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7226 (mm-30) REVERT: L 571 ARG cc_start: 0.7762 (tpt170) cc_final: 0.7422 (tpt170) REVERT: L 651 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8547 (p) outliers start: 60 outliers final: 7 residues processed: 524 average time/residue: 1.3654 time to fit residues: 812.2707 Evaluate side-chains 321 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 303 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain F residue 367 HIS Chi-restraints excluded: chain F residue 651 SER Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 482 SER Chi-restraints excluded: chain H residue 586 ASN Chi-restraints excluded: chain H residue 651 SER Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 586 ASN Chi-restraints excluded: chain L residue 651 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 0.0470 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 228 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 443 ASN D 179 ASN D 443 ASN F 209 GLN H 179 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 ASN J 179 ASN J 209 GLN J 443 ASN L 281 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22842 Z= 0.163 Angle : 0.663 9.723 31068 Z= 0.286 Chirality : 0.049 0.460 3558 Planarity : 0.004 0.039 3678 Dihedral : 18.319 125.337 4372 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.55 % Allowed : 14.24 % Favored : 82.21 % 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: -0.14 (0.16), residues: 2496 helix: 0.33 (0.12), residues: 1866 sheet: None (None), residues: 0 loop : -1.06 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J 269 HIS 0.003 0.001 HIS J 473 PHE 0.022 0.001 PHE L 438 TYR 0.017 0.001 TYR H 600 ARG 0.005 0.000 ARG L 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 354 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.8821 (t80) cc_final: 0.8503 (t80) REVERT: B 282 MET cc_start: 0.8834 (tpp) cc_final: 0.8406 (tpp) REVERT: B 366 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7696 (tt) REVERT: B 368 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7797 (ptm160) REVERT: B 391 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7484 (tm-30) REVERT: B 548 LEU cc_start: 0.7043 (mt) cc_final: 0.6765 (mt) REVERT: D 284 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6444 (mt-10) REVERT: D 310 LEU cc_start: 0.7941 (tp) cc_final: 0.7581 (mm) REVERT: D 344 MET cc_start: 0.8756 (mtp) cc_final: 0.8384 (mtp) REVERT: D 366 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7727 (tt) REVERT: D 391 GLN cc_start: 0.7449 (tm-30) cc_final: 0.7093 (tm-30) REVERT: D 559 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7426 (mm-30) REVERT: F 260 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6402 (pp) REVERT: F 280 TRP cc_start: 0.7612 (t-100) cc_final: 0.7088 (t60) REVERT: F 366 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7774 (tt) REVERT: F 391 GLN cc_start: 0.7504 (tm-30) cc_final: 0.6873 (tm130) REVERT: F 548 LEU cc_start: 0.6396 (mt) cc_final: 0.6121 (mp) REVERT: H 191 TYR cc_start: 0.8808 (t80) cc_final: 0.8498 (t80) REVERT: H 282 MET cc_start: 0.8835 (tpp) cc_final: 0.8401 (tpp) REVERT: H 366 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7688 (tt) REVERT: H 368 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7843 (ptm160) REVERT: H 391 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7482 (tm-30) REVERT: H 500 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7765 (mmm160) REVERT: H 548 LEU cc_start: 0.6876 (mt) cc_final: 0.6611 (mt) REVERT: J 260 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5955 (pp) REVERT: J 280 TRP cc_start: 0.7550 (t-100) cc_final: 0.7185 (t60) REVERT: J 282 MET cc_start: 0.8880 (tpp) cc_final: 0.8572 (tpp) REVERT: J 284 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6559 (mt-10) REVERT: J 344 MET cc_start: 0.8737 (mtp) cc_final: 0.8418 (mtp) REVERT: J 367 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7492 (m-70) REVERT: J 391 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7264 (tm-30) REVERT: J 559 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7430 (mm-30) REVERT: J 648 TYR cc_start: 0.7493 (m-80) cc_final: 0.7078 (m-80) REVERT: L 280 TRP cc_start: 0.7537 (t-100) cc_final: 0.7042 (t60) REVERT: L 368 ARG cc_start: 0.7254 (ttt90) cc_final: 0.6777 (ttm-80) REVERT: L 391 GLN cc_start: 0.7580 (tm-30) cc_final: 0.6941 (tm130) REVERT: L 431 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7674 (tp) REVERT: L 548 LEU cc_start: 0.6352 (mt) cc_final: 0.6112 (mt) REVERT: L 586 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8201 (p0) outliers start: 82 outliers final: 9 residues processed: 408 average time/residue: 1.4029 time to fit residues: 651.3856 Evaluate side-chains 307 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 287 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 585 ASP Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 519 ILE Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 482 SER Chi-restraints excluded: chain J residue 585 ASP Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 585 ASP Chi-restraints excluded: chain L residue 586 ASN Chi-restraints excluded: chain L residue 611 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN D 209 GLN F 443 ASN H 209 GLN J 179 ASN J 209 GLN J 443 ASN ** L 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 22842 Z= 0.328 Angle : 0.657 8.600 31068 Z= 0.303 Chirality : 0.050 0.429 3558 Planarity : 0.005 0.066 3678 Dihedral : 14.949 136.765 4352 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.24 % Allowed : 13.85 % Favored : 80.91 % 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: 0.36 (0.16), residues: 2496 helix: 0.66 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -0.69 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 269 HIS 0.007 0.002 HIS B 588 PHE 0.023 0.002 PHE H 384 TYR 0.020 0.002 TYR D 600 ARG 0.009 0.001 ARG D 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 332 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.8949 (t80) cc_final: 0.8630 (t80) REVERT: B 282 MET cc_start: 0.8784 (tpp) cc_final: 0.8479 (tpp) REVERT: B 284 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: B 366 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7596 (tt) REVERT: B 368 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7775 (ptm160) REVERT: B 437 ASN cc_start: 0.8483 (m-40) cc_final: 0.8043 (m110) REVERT: B 548 LEU cc_start: 0.6928 (mt) cc_final: 0.6682 (mt) REVERT: B 559 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7564 (mm-30) REVERT: B 586 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8398 (p0) REVERT: D 284 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6460 (mt-10) REVERT: D 366 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7523 (tt) REVERT: D 368 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7011 (ttm170) REVERT: D 421 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7946 (tp) REVERT: D 559 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7347 (mm-30) REVERT: F 280 TRP cc_start: 0.7930 (t-100) cc_final: 0.7364 (t60) REVERT: F 366 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7764 (tt) REVERT: F 391 GLN cc_start: 0.7437 (tm-30) cc_final: 0.6846 (tm130) REVERT: F 548 LEU cc_start: 0.6498 (mt) cc_final: 0.6275 (mt) REVERT: H 191 TYR cc_start: 0.8958 (t80) cc_final: 0.8641 (t80) REVERT: H 282 MET cc_start: 0.8785 (tpp) cc_final: 0.8481 (tpp) REVERT: H 284 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: H 366 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7618 (tt) REVERT: H 368 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7812 (ptm160) REVERT: H 380 ASN cc_start: 0.8076 (m-40) cc_final: 0.7860 (m110) REVERT: H 390 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6387 (pp20) REVERT: H 452 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8107 (mt) REVERT: H 559 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7658 (mm-30) REVERT: H 586 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8394 (p0) REVERT: J 280 TRP cc_start: 0.7647 (t-100) cc_final: 0.7196 (t60) REVERT: J 284 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6651 (mt-10) REVERT: J 310 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7495 (mm) REVERT: J 367 HIS cc_start: 0.7811 (OUTLIER) cc_final: 0.7564 (m-70) REVERT: J 391 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7341 (tm-30) REVERT: J 431 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.6959 (mp) REVERT: J 548 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6763 (mp) REVERT: J 559 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7381 (mm-30) REVERT: J 586 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8159 (p0) REVERT: L 280 TRP cc_start: 0.7872 (t-100) cc_final: 0.7310 (t60) REVERT: L 366 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7825 (tt) REVERT: L 368 ARG cc_start: 0.7262 (ttt90) cc_final: 0.6780 (ttm-80) REVERT: L 391 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7030 (tm130) REVERT: L 431 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7822 (tp) REVERT: L 587 MET cc_start: 0.8415 (mtm) cc_final: 0.8100 (mtm) outliers start: 121 outliers final: 49 residues processed: 422 average time/residue: 1.3227 time to fit residues: 637.0344 Evaluate side-chains 365 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 295 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 585 ASP Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 284 GLU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 431 ILE Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 586 ASN Chi-restraints excluded: chain H residue 627 SER Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 310 LEU Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain J residue 548 LEU Chi-restraints excluded: chain J residue 585 ASP Chi-restraints excluded: chain J residue 586 ASN Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain J residue 627 SER Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 482 SER Chi-restraints excluded: chain L residue 585 ASP Chi-restraints excluded: chain L residue 586 ASN Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 153 optimal weight: 0.1980 chunk 230 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN H 209 GLN J 179 ASN J 209 GLN J 443 ASN ** L 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22842 Z= 0.193 Angle : 0.577 8.247 31068 Z= 0.263 Chirality : 0.046 0.393 3558 Planarity : 0.004 0.046 3678 Dihedral : 13.160 140.651 4352 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.42 % Allowed : 16.88 % Favored : 78.70 % 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: 0.89 (0.16), residues: 2496 helix: 0.96 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : -0.20 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 269 HIS 0.004 0.001 HIS J 473 PHE 0.018 0.001 PHE D 442 TYR 0.023 0.001 TYR B 648 ARG 0.009 0.000 ARG J 570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 330 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.8866 (t80) cc_final: 0.8524 (t80) REVERT: B 281 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7208 (mm110) REVERT: B 282 MET cc_start: 0.8860 (tpp) cc_final: 0.8411 (tpp) REVERT: B 366 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7611 (tt) REVERT: B 368 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7899 (ptm160) REVERT: B 548 LEU cc_start: 0.6979 (mt) cc_final: 0.6744 (mt) REVERT: B 559 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7555 (mm-30) REVERT: D 284 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6331 (mt-10) REVERT: D 366 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7539 (tt) REVERT: D 559 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7350 (mm-30) REVERT: F 280 TRP cc_start: 0.7865 (t-100) cc_final: 0.7245 (t60) REVERT: F 366 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7631 (tt) REVERT: F 368 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7520 (ptm160) REVERT: F 548 LEU cc_start: 0.6463 (mt) cc_final: 0.6236 (mt) REVERT: H 191 TYR cc_start: 0.8857 (t80) cc_final: 0.8529 (t80) REVERT: H 281 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7306 (mm110) REVERT: H 282 MET cc_start: 0.8850 (tpp) cc_final: 0.8398 (tpp) REVERT: H 366 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7625 (tt) REVERT: H 390 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6204 (pp20) REVERT: H 452 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8081 (mt) REVERT: H 559 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7568 (mm-30) REVERT: J 280 TRP cc_start: 0.7672 (t-100) cc_final: 0.7255 (t60) REVERT: J 281 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7189 (tp-100) REVERT: J 284 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6613 (mt-10) REVERT: J 367 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.7602 (m-70) REVERT: J 431 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.6852 (mp) REVERT: J 444 GLU cc_start: 0.7184 (mp0) cc_final: 0.6970 (mp0) REVERT: J 453 SER cc_start: 0.8209 (t) cc_final: 0.7897 (p) REVERT: J 559 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7354 (mm-30) REVERT: L 269 TRP cc_start: 0.6898 (t60) cc_final: 0.6648 (t60) REVERT: L 280 TRP cc_start: 0.7871 (t-100) cc_final: 0.7254 (t60) REVERT: L 366 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7712 (tt) REVERT: L 368 ARG cc_start: 0.7146 (ttt90) cc_final: 0.6666 (ttm-80) REVERT: L 413 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7346 (mtp-110) REVERT: L 548 LEU cc_start: 0.5999 (mt) cc_final: 0.5795 (mp) REVERT: L 587 MET cc_start: 0.8256 (mtm) cc_final: 0.8037 (mtm) outliers start: 102 outliers final: 41 residues processed: 405 average time/residue: 1.3237 time to fit residues: 611.3957 Evaluate side-chains 349 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 295 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 585 ASP Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain L residue 585 ASP Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN H 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22842 Z= 0.186 Angle : 0.556 10.097 31068 Z= 0.256 Chirality : 0.044 0.354 3558 Planarity : 0.004 0.054 3678 Dihedral : 12.412 142.882 4352 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.68 % Allowed : 16.54 % Favored : 78.79 % 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: 1.15 (0.17), residues: 2496 helix: 1.14 (0.12), residues: 1830 sheet: None (None), residues: 0 loop : -0.10 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 269 HIS 0.005 0.001 HIS H 588 PHE 0.026 0.001 PHE B 442 TYR 0.015 0.001 TYR B 600 ARG 0.008 0.000 ARG D 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 335 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.8835 (t80) cc_final: 0.8494 (t80) REVERT: B 281 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7285 (mm110) REVERT: B 282 MET cc_start: 0.8872 (tpp) cc_final: 0.8429 (tpp) REVERT: B 284 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: B 366 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7582 (tt) REVERT: B 413 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6657 (mtm110) REVERT: B 548 LEU cc_start: 0.6899 (mt) cc_final: 0.6664 (mt) REVERT: B 586 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8252 (p0) REVERT: D 217 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7967 (mt) REVERT: D 304 ARG cc_start: 0.8080 (tpp-160) cc_final: 0.7865 (tpp-160) REVERT: D 366 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7491 (tt) REVERT: D 478 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.7416 (ptt90) REVERT: D 559 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7395 (mm-30) REVERT: D 586 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8091 (p0) REVERT: F 280 TRP cc_start: 0.7860 (t-100) cc_final: 0.7218 (t60) REVERT: F 366 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7653 (tt) REVERT: F 413 ARG cc_start: 0.7718 (mtp180) cc_final: 0.7395 (mtm180) REVERT: F 421 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7841 (mp) REVERT: F 548 LEU cc_start: 0.6506 (mt) cc_final: 0.6300 (mt) REVERT: H 191 TYR cc_start: 0.8844 (t80) cc_final: 0.8508 (t80) REVERT: H 281 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7342 (mm110) REVERT: H 282 MET cc_start: 0.8868 (tpp) cc_final: 0.8420 (tpp) REVERT: H 284 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: H 366 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7546 (tt) REVERT: H 390 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6222 (pp20) REVERT: H 453 SER cc_start: 0.8238 (t) cc_final: 0.7860 (p) REVERT: H 559 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7542 (mm-30) REVERT: H 586 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8184 (p0) REVERT: H 623 PHE cc_start: 0.7458 (m-10) cc_final: 0.7226 (m-80) REVERT: J 280 TRP cc_start: 0.7705 (t-100) cc_final: 0.7141 (t60) REVERT: J 431 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.6873 (mp) REVERT: J 453 SER cc_start: 0.8231 (t) cc_final: 0.7924 (p) REVERT: J 548 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6791 (mp) REVERT: J 559 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7330 (mm-30) REVERT: J 586 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8072 (p0) REVERT: L 280 TRP cc_start: 0.7827 (t-100) cc_final: 0.7205 (t60) REVERT: L 366 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7692 (tt) REVERT: L 368 ARG cc_start: 0.7206 (ttt90) cc_final: 0.6738 (ttm-80) REVERT: L 413 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7412 (mtm180) REVERT: L 421 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7653 (mp) REVERT: L 453 SER cc_start: 0.7906 (t) cc_final: 0.7673 (p) REVERT: L 587 MET cc_start: 0.8298 (mtm) cc_final: 0.8084 (mtm) outliers start: 108 outliers final: 47 residues processed: 418 average time/residue: 1.2739 time to fit residues: 610.1652 Evaluate side-chains 372 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 305 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 585 ASP Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 284 GLU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 586 ASN Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 368 ARG Chi-restraints excluded: chain J residue 405 LYS Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain J residue 482 SER Chi-restraints excluded: chain J residue 548 LEU Chi-restraints excluded: chain J residue 586 ASN Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain L residue 585 ASP Chi-restraints excluded: chain L residue 586 ASN Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN H 209 GLN L 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22842 Z= 0.164 Angle : 0.540 11.889 31068 Z= 0.248 Chirality : 0.042 0.365 3558 Planarity : 0.004 0.045 3678 Dihedral : 12.089 142.717 4350 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.33 % Allowed : 17.53 % Favored : 78.14 % 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: 1.43 (0.17), residues: 2496 helix: 1.36 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -0.01 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 269 HIS 0.004 0.001 HIS B 588 PHE 0.023 0.001 PHE L 438 TYR 0.014 0.001 TYR H 600 ARG 0.008 0.000 ARG F 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 329 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.8818 (t80) cc_final: 0.8468 (t80) REVERT: B 281 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7396 (mm110) REVERT: B 282 MET cc_start: 0.8876 (tpp) cc_final: 0.8404 (tpp) REVERT: B 284 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: B 413 ARG cc_start: 0.6999 (mtp180) cc_final: 0.6568 (mtm110) REVERT: B 586 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8179 (p0) REVERT: D 366 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7492 (tt) REVERT: D 368 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6964 (ttm-80) REVERT: D 431 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7601 (mm) REVERT: D 478 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.7424 (ptt90) REVERT: D 559 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7343 (mm-30) REVERT: F 280 TRP cc_start: 0.7840 (t-100) cc_final: 0.7211 (t60) REVERT: F 366 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7630 (tt) REVERT: F 413 ARG cc_start: 0.7707 (mtp180) cc_final: 0.7404 (mtm180) REVERT: H 191 TYR cc_start: 0.8822 (t80) cc_final: 0.8495 (t80) REVERT: H 281 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7301 (mm110) REVERT: H 282 MET cc_start: 0.8879 (tpp) cc_final: 0.8408 (tpp) REVERT: H 284 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: H 366 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7522 (tt) REVERT: H 390 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6234 (pp20) REVERT: H 623 PHE cc_start: 0.7442 (m-10) cc_final: 0.7195 (m-80) REVERT: J 280 TRP cc_start: 0.7668 (t-100) cc_final: 0.7130 (t60) REVERT: J 281 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7163 (tp-100) REVERT: J 366 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7632 (tt) REVERT: J 431 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.6856 (mp) REVERT: J 453 SER cc_start: 0.8229 (t) cc_final: 0.7889 (p) REVERT: J 478 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7434 (ptt90) REVERT: J 559 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7324 (mm-30) REVERT: L 280 TRP cc_start: 0.7812 (t-100) cc_final: 0.7197 (t60) REVERT: L 366 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7673 (tt) REVERT: L 368 ARG cc_start: 0.7203 (ttt90) cc_final: 0.6748 (ttm-80) REVERT: L 413 ARG cc_start: 0.7720 (mtp180) cc_final: 0.7411 (mtm180) outliers start: 100 outliers final: 49 residues processed: 403 average time/residue: 1.3372 time to fit residues: 615.7761 Evaluate side-chains 368 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 302 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 284 GLU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 366 LEU Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 482 SER Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN H 209 GLN L 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22842 Z= 0.206 Angle : 0.551 9.935 31068 Z= 0.257 Chirality : 0.043 0.350 3558 Planarity : 0.004 0.043 3678 Dihedral : 12.184 143.995 4350 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.68 % Allowed : 17.84 % Favored : 77.49 % 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: 1.39 (0.17), residues: 2496 helix: 1.29 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : 0.11 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 269 HIS 0.005 0.001 HIS B 588 PHE 0.027 0.001 PHE B 442 TYR 0.032 0.001 TYR J 648 ARG 0.006 0.000 ARG F 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 322 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.8865 (t80) cc_final: 0.8513 (t80) REVERT: B 281 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7311 (mm110) REVERT: B 282 MET cc_start: 0.8861 (tpp) cc_final: 0.8391 (tpp) REVERT: B 284 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: B 413 ARG cc_start: 0.6946 (mtp180) cc_final: 0.6527 (mtm110) REVERT: B 437 ASN cc_start: 0.8387 (m-40) cc_final: 0.8177 (m110) REVERT: B 586 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8297 (p0) REVERT: B 587 MET cc_start: 0.8625 (mmm) cc_final: 0.8306 (mtt) REVERT: D 217 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7908 (mt) REVERT: D 366 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7546 (tt) REVERT: D 431 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.6944 (mp) REVERT: D 478 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.7437 (ptt90) REVERT: D 559 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7347 (mm-30) REVERT: D 586 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8099 (p0) REVERT: F 280 TRP cc_start: 0.7858 (t-100) cc_final: 0.7222 (t60) REVERT: F 366 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7654 (tt) REVERT: F 413 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7377 (mtm180) REVERT: F 421 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7856 (mp) REVERT: F 548 LEU cc_start: 0.6081 (mt) cc_final: 0.5850 (mp) REVERT: H 191 TYR cc_start: 0.8849 (t80) cc_final: 0.8499 (t80) REVERT: H 281 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7300 (mm110) REVERT: H 282 MET cc_start: 0.8849 (tpp) cc_final: 0.8401 (tpp) REVERT: H 284 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: H 390 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6218 (pp20) REVERT: H 413 ARG cc_start: 0.7069 (mtp180) cc_final: 0.6774 (mtm180) REVERT: H 453 SER cc_start: 0.8357 (t) cc_final: 0.7977 (p) REVERT: H 586 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8250 (p0) REVERT: J 280 TRP cc_start: 0.7692 (t-100) cc_final: 0.7123 (t60) REVERT: J 281 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7171 (tp-100) REVERT: J 366 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7581 (tt) REVERT: J 431 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.6898 (mp) REVERT: J 453 SER cc_start: 0.8258 (t) cc_final: 0.7910 (p) REVERT: J 478 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7451 (ptt90) REVERT: J 548 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6757 (mp) REVERT: J 559 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7333 (mm-30) REVERT: J 586 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8027 (p0) REVERT: L 280 TRP cc_start: 0.7834 (t-100) cc_final: 0.7211 (t60) REVERT: L 366 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7654 (tt) REVERT: L 368 ARG cc_start: 0.7217 (ttt90) cc_final: 0.6758 (ttm-80) REVERT: L 413 ARG cc_start: 0.7692 (mtp180) cc_final: 0.7382 (mtm180) REVERT: L 421 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7714 (mp) REVERT: L 453 SER cc_start: 0.7909 (t) cc_final: 0.7676 (p) outliers start: 108 outliers final: 62 residues processed: 400 average time/residue: 1.3480 time to fit residues: 615.9857 Evaluate side-chains 389 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 305 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 284 GLU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 519 ILE Chi-restraints excluded: chain H residue 586 ASN Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 366 LEU Chi-restraints excluded: chain J residue 390 GLU Chi-restraints excluded: chain J residue 405 LYS Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 482 SER Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 548 LEU Chi-restraints excluded: chain J residue 585 ASP Chi-restraints excluded: chain J residue 586 ASN Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN F 205 HIS H 209 GLN ** J 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22842 Z= 0.262 Angle : 0.586 12.080 31068 Z= 0.275 Chirality : 0.045 0.365 3558 Planarity : 0.004 0.042 3678 Dihedral : 12.462 147.710 4350 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.81 % Allowed : 17.88 % Favored : 77.32 % 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: 1.29 (0.16), residues: 2496 helix: 1.22 (0.12), residues: 1812 sheet: None (None), residues: 0 loop : 0.08 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 269 HIS 0.006 0.001 HIS H 588 PHE 0.022 0.002 PHE L 438 TYR 0.043 0.002 TYR J 648 ARG 0.011 0.001 ARG H 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 320 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.8906 (t80) cc_final: 0.8529 (t80) REVERT: B 281 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7289 (mm110) REVERT: B 282 MET cc_start: 0.8851 (tpp) cc_final: 0.8398 (tpp) REVERT: B 284 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: B 413 ARG cc_start: 0.7068 (mtp180) cc_final: 0.6609 (mtm180) REVERT: B 453 SER cc_start: 0.8251 (t) cc_final: 0.7896 (p) REVERT: B 586 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8276 (p0) REVERT: D 366 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7632 (tt) REVERT: D 368 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6984 (ttm-80) REVERT: D 431 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.6915 (mp) REVERT: D 478 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7448 (ptt90) REVERT: D 559 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7361 (mm-30) REVERT: D 586 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8096 (p0) REVERT: F 280 TRP cc_start: 0.8000 (t-100) cc_final: 0.7327 (t60) REVERT: F 365 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6710 (tp) REVERT: F 366 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7641 (tt) REVERT: F 413 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7320 (mtm180) REVERT: F 421 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7848 (mp) REVERT: H 191 TYR cc_start: 0.8907 (t80) cc_final: 0.8541 (t80) REVERT: H 281 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7314 (mm110) REVERT: H 282 MET cc_start: 0.8833 (tpp) cc_final: 0.8371 (tpp) REVERT: H 284 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: H 366 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7587 (tt) REVERT: H 390 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6200 (pp20) REVERT: H 413 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6813 (mtm110) REVERT: H 453 SER cc_start: 0.8408 (t) cc_final: 0.8008 (p) REVERT: H 579 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8214 (ttp) REVERT: H 586 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8261 (p0) REVERT: J 281 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7273 (tp-100) REVERT: J 366 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7632 (tt) REVERT: J 431 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.6867 (mp) REVERT: J 453 SER cc_start: 0.8288 (t) cc_final: 0.7934 (p) REVERT: J 478 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.7457 (ptt90) REVERT: J 548 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6694 (mp) REVERT: J 559 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7311 (mm-30) REVERT: J 586 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8078 (p0) REVERT: L 280 TRP cc_start: 0.7981 (t-100) cc_final: 0.7321 (t60) REVERT: L 281 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7520 (mm-40) REVERT: L 366 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7657 (tt) REVERT: L 368 ARG cc_start: 0.7239 (ttt90) cc_final: 0.6741 (ttm-80) REVERT: L 413 ARG cc_start: 0.7687 (mtp180) cc_final: 0.7382 (mtm180) REVERT: L 421 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7725 (mp) REVERT: L 453 SER cc_start: 0.7941 (t) cc_final: 0.7702 (p) outliers start: 111 outliers final: 61 residues processed: 401 average time/residue: 1.2936 time to fit residues: 594.1032 Evaluate side-chains 393 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 306 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 284 GLU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain H residue 586 ASN Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 366 LEU Chi-restraints excluded: chain J residue 390 GLU Chi-restraints excluded: chain J residue 405 LYS Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 520 THR Chi-restraints excluded: chain J residue 548 LEU Chi-restraints excluded: chain J residue 586 ASN Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain L residue 586 ASN Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 177 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN L 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22842 Z= 0.208 Angle : 0.562 12.219 31068 Z= 0.263 Chirality : 0.044 0.384 3558 Planarity : 0.004 0.048 3678 Dihedral : 12.300 146.990 4350 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.33 % Allowed : 18.61 % Favored : 77.06 % 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: 1.36 (0.16), residues: 2496 helix: 1.28 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : 0.09 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 269 HIS 0.005 0.001 HIS H 588 PHE 0.025 0.001 PHE J 442 TYR 0.018 0.001 TYR H 648 ARG 0.014 0.000 ARG H 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 317 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.8847 (t80) cc_final: 0.8504 (t80) REVERT: B 281 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7318 (mm110) REVERT: B 282 MET cc_start: 0.8851 (tpp) cc_final: 0.8375 (tpp) REVERT: B 284 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: B 413 ARG cc_start: 0.7065 (mtp180) cc_final: 0.6507 (mtm110) REVERT: B 453 SER cc_start: 0.8216 (t) cc_final: 0.7890 (p) REVERT: B 586 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8284 (p0) REVERT: B 587 MET cc_start: 0.8647 (mmm) cc_final: 0.8343 (mtt) REVERT: D 366 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7593 (tt) REVERT: D 368 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7008 (ttm-80) REVERT: D 431 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.6890 (mp) REVERT: D 478 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7430 (ptt90) REVERT: D 559 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7363 (mm-30) REVERT: D 586 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.8027 (p0) REVERT: F 280 TRP cc_start: 0.7915 (t-100) cc_final: 0.7282 (t60) REVERT: F 365 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6716 (tp) REVERT: F 366 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7761 (tt) REVERT: F 413 ARG cc_start: 0.7666 (mtp180) cc_final: 0.7316 (mtm180) REVERT: F 421 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7846 (mp) REVERT: F 548 LEU cc_start: 0.6112 (mt) cc_final: 0.5895 (mp) REVERT: H 191 TYR cc_start: 0.8843 (t80) cc_final: 0.8505 (t80) REVERT: H 281 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7315 (mm110) REVERT: H 282 MET cc_start: 0.8851 (tpp) cc_final: 0.8377 (tpp) REVERT: H 284 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: H 390 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6218 (pp20) REVERT: H 413 ARG cc_start: 0.7053 (mtp180) cc_final: 0.6759 (mtm110) REVERT: H 453 SER cc_start: 0.8377 (t) cc_final: 0.7987 (p) REVERT: H 586 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8262 (p0) REVERT: J 281 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7280 (tp-100) REVERT: J 431 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.6914 (mp) REVERT: J 453 SER cc_start: 0.8283 (t) cc_final: 0.7923 (p) REVERT: J 478 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.7437 (ptt90) REVERT: J 548 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6730 (mp) REVERT: J 559 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7294 (mm-30) REVERT: J 586 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8029 (p0) REVERT: L 280 TRP cc_start: 0.7890 (t-100) cc_final: 0.7276 (t60) REVERT: L 281 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7460 (mm110) REVERT: L 366 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7663 (tt) REVERT: L 399 ARG cc_start: 0.7429 (mtm180) cc_final: 0.7161 (mmm-85) REVERT: L 413 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7381 (mtm180) REVERT: L 421 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7713 (mp) REVERT: L 453 SER cc_start: 0.7929 (t) cc_final: 0.7679 (p) outliers start: 100 outliers final: 59 residues processed: 388 average time/residue: 1.3569 time to fit residues: 600.2236 Evaluate side-chains 394 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 312 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 284 GLU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 431 ILE Chi-restraints excluded: chain H residue 586 ASN Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 390 GLU Chi-restraints excluded: chain J residue 405 LYS Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 548 LEU Chi-restraints excluded: chain J residue 586 ASN Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain L residue 586 ASN Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 251 optimal weight: 0.0870 chunk 231 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22842 Z= 0.152 Angle : 0.537 12.574 31068 Z= 0.249 Chirality : 0.042 0.358 3558 Planarity : 0.004 0.043 3678 Dihedral : 12.028 144.262 4350 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.99 % Allowed : 20.04 % Favored : 76.97 % 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: 1.63 (0.17), residues: 2496 helix: 1.56 (0.12), residues: 1812 sheet: None (None), residues: 0 loop : -0.07 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP D 269 HIS 0.003 0.001 HIS H 588 PHE 0.036 0.001 PHE B 442 TYR 0.013 0.001 TYR L 600 ARG 0.005 0.000 ARG D 570 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 317 time to evaluate : 2.477 Fit side-chains REVERT: B 191 TYR cc_start: 0.8824 (t80) cc_final: 0.8511 (t80) REVERT: B 282 MET cc_start: 0.8866 (tpp) cc_final: 0.8428 (tpp) REVERT: B 308 ARG cc_start: 0.7313 (mmm-85) cc_final: 0.6989 (mtp85) REVERT: B 413 ARG cc_start: 0.6924 (mtp180) cc_final: 0.6618 (mtm110) REVERT: B 586 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8152 (p0) REVERT: B 587 MET cc_start: 0.8655 (mmm) cc_final: 0.8241 (mtt) REVERT: D 366 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7537 (tt) REVERT: D 431 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7540 (mm) REVERT: D 478 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7439 (ptt90) REVERT: D 559 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7337 (mm-30) REVERT: F 280 TRP cc_start: 0.7902 (t-100) cc_final: 0.7240 (t60) REVERT: F 365 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6611 (tp) REVERT: F 366 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7652 (tt) REVERT: F 368 ARG cc_start: 0.8392 (ptm160) cc_final: 0.8152 (ptm-80) REVERT: F 413 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7280 (mtm180) REVERT: F 421 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7759 (mp) REVERT: F 570 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7751 (mtp85) REVERT: H 191 TYR cc_start: 0.8818 (t80) cc_final: 0.8511 (t80) REVERT: H 282 MET cc_start: 0.8883 (tpp) cc_final: 0.8438 (tpp) REVERT: H 390 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6210 (pp20) REVERT: H 413 ARG cc_start: 0.7010 (mtp180) cc_final: 0.6722 (mtm110) REVERT: H 453 SER cc_start: 0.8122 (t) cc_final: 0.7769 (p) REVERT: J 280 TRP cc_start: 0.7651 (t-100) cc_final: 0.7101 (t60) REVERT: J 281 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7213 (tp-100) REVERT: J 431 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.6861 (mp) REVERT: J 453 SER cc_start: 0.8197 (t) cc_final: 0.7858 (p) REVERT: J 478 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7454 (ptt90) REVERT: J 559 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7326 (mm-30) REVERT: L 280 TRP cc_start: 0.7814 (t-100) cc_final: 0.7195 (t60) REVERT: L 281 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7444 (mm110) REVERT: L 366 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7634 (tt) REVERT: L 413 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7320 (mtm180) REVERT: L 421 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7694 (mp) REVERT: L 431 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7656 (pp) REVERT: L 453 SER cc_start: 0.7971 (t) cc_final: 0.7702 (p) outliers start: 69 outliers final: 45 residues processed: 366 average time/residue: 1.3535 time to fit residues: 564.0899 Evaluate side-chains 364 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 304 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain F residue 519 ILE Chi-restraints excluded: chain F residue 560 THR Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 390 GLU Chi-restraints excluded: chain H residue 519 ILE Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 390 GLU Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 560 THR Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 184 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 200 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN H 209 GLN ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.161235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125213 restraints weight = 25646.053| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.89 r_work: 0.3165 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22842 Z= 0.183 Angle : 0.556 12.383 31068 Z= 0.259 Chirality : 0.043 0.364 3558 Planarity : 0.004 0.043 3678 Dihedral : 12.060 144.297 4350 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.99 % Allowed : 20.13 % Favored : 76.88 % 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: 1.62 (0.17), residues: 2496 helix: 1.51 (0.12), residues: 1812 sheet: None (None), residues: 0 loop : 0.04 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 269 HIS 0.005 0.001 HIS H 588 PHE 0.031 0.001 PHE J 442 TYR 0.014 0.001 TYR H 600 ARG 0.005 0.000 ARG D 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9041.54 seconds wall clock time: 162 minutes 42.76 seconds (9762.76 seconds total)