Starting phenix.real_space_refine on Thu Aug 8 07:12:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kxs_0782/08_2024/6kxs_0782.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kxs_0782/08_2024/6kxs_0782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kxs_0782/08_2024/6kxs_0782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kxs_0782/08_2024/6kxs_0782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kxs_0782/08_2024/6kxs_0782.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kxs_0782/08_2024/6kxs_0782.cif" } resolution = 3.4 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= 0.003 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 110 5.16 5 C 14169 2.51 5 N 3818 2.21 5 O 4402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 371": "OD1" <-> "OD2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A ASP 553": "OD1" <-> "OD2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C GLU 410": "OE1" <-> "OE2" Residue "C ASP 417": "OD1" <-> "OD2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 532": "OE1" <-> "OE2" Residue "C ASP 553": "OD1" <-> "OD2" Residue "D PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 371": "OD1" <-> "OD2" Residue "D TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "D PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 388": "OE1" <-> "OE2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E ASP 416": "OD1" <-> "OD2" Residue "E PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 526": "OE1" <-> "OE2" Residue "E GLU 549": "OE1" <-> "OE2" Residue "F PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 371": "OD1" <-> "OD2" Residue "F GLU 388": "OE1" <-> "OE2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "F ASP 453": "OD1" <-> "OD2" Residue "F PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 371": "OD1" <-> "OD2" Residue "G TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 398": "OE1" <-> "OE2" Residue "G ASP 416": "OD1" <-> "OD2" Residue "G PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 398": "OE1" <-> "OE2" Residue "H ASP 416": "OD1" <-> "OD2" Residue "H ASP 417": "OD1" <-> "OD2" Residue "H GLU 422": "OE1" <-> "OE2" Residue "H PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 451": "NH1" <-> "NH2" Residue "H GLU 468": "OE1" <-> "OE2" Residue "H ASP 483": "OD1" <-> "OD2" Residue "H TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 388": "OE1" <-> "OE2" Residue "K GLU 398": "OE1" <-> "OE2" Residue "K ASP 453": "OD1" <-> "OD2" Residue "K GLU 468": "OE1" <-> "OE2" Residue "K PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 483": "OD1" <-> "OD2" Residue "K TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 417": "OD1" <-> "OD2" Residue "L PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 120": "OE1" <-> "OE2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 9": "OE1" <-> "OE2" Residue "P TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 160": "OD1" <-> "OD2" Residue "P ASP 176": "OD1" <-> "OD2" Residue "P GLU 225": "OE1" <-> "OE2" Residue "P TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 285": "OD1" <-> "OD2" Residue "P TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 312": "OD1" <-> "OD2" Residue "P GLU 317": "OE1" <-> "OE2" Residue "P GLU 359": "OE1" <-> "OE2" Residue "P TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 384": "OE1" <-> "OE2" Residue "P PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 428": "OD1" <-> "OD2" Residue "P GLU 436": "OE1" <-> "OE2" Residue "P PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 492": "OD1" <-> "OD2" Residue "P TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 536": "OE1" <-> "OE2" Residue "P TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 22499 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1798 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 213} Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1764 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 208} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1723 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain breaks: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1785 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain breaks: 1 Chain: "K" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain breaks: 1 Chain: "L" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1773 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "P" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3875 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 472} Chain breaks: 6 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.58, per 1000 atoms: 0.56 Number of scatterers: 22499 At special positions: 0 Unit cell: (118.404, 189.612, 172.224, 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 110 16.00 O 4402 8.00 N 3818 7.00 C 14169 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.01 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.02 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.02 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.02 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.02 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.02 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.04 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.01 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.04 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.04 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.02 Simple disulfide: pdb=" SG CYS H 575 " - pdb=" SG CYS K 575 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.04 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Simple disulfide: pdb=" SG CYS L 575 " - pdb=" SG CYS J 14 " distance=2.04 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.07 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.05 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.01 Simple disulfide: pdb=" SG CYS P 38 " - pdb=" SG CYS P 46 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 202 " distance=2.02 Simple disulfide: pdb=" SG CYS P 239 " - pdb=" SG CYS P 307 " distance=2.03 Simple disulfide: pdb=" SG CYS P 253 " - pdb=" SG CYS P 261 " distance=2.04 Simple disulfide: pdb=" SG CYS P 353 " - pdb=" SG CYS P 423 " distance=2.02 Simple disulfide: pdb=" SG CYS P 367 " - pdb=" SG CYS P 377 " distance=2.02 Simple disulfide: pdb=" SG CYS P 464 " - pdb=" SG CYS P 526 " distance=2.04 Simple disulfide: pdb=" SG CYS P 478 " - pdb=" SG CYS P 485 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 8.58 Conformation dependent library (CDL) restraints added in 3.9 seconds 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5456 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 72 sheets defined 8.6% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.248A pdb=" N LEU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 removed outlier: 3.594A pdb=" N SER A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.907A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.705A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 530 removed outlier: 3.603A pdb=" N THR B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.582A pdb=" N LEU C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 525 through 529 removed outlier: 3.551A pdb=" N ASN C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 525 through 529' Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.722A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 460 through 465 Processing helix chain 'D' and resid 525 through 531 removed outlier: 3.985A pdb=" N THR D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 removed outlier: 3.739A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 420 Processing helix chain 'E' and resid 462 through 467 removed outlier: 3.567A pdb=" N LEU E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 467' Processing helix chain 'E' and resid 525 through 529 Processing helix chain 'F' and resid 353 through 361 removed outlier: 4.167A pdb=" N THR F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 4.101A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 529 Processing helix chain 'G' and resid 353 through 359 Processing helix chain 'G' and resid 414 through 421 removed outlier: 3.634A pdb=" N TRP G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 466 removed outlier: 3.662A pdb=" N LEU G 466 " --> pdb=" O GLN G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 530 removed outlier: 3.733A pdb=" N THR G 530 " --> pdb=" O GLU G 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 360 Processing helix chain 'H' and resid 414 through 420 removed outlier: 4.009A pdb=" N SER H 420 " --> pdb=" O ASP H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 524 through 529 Processing helix chain 'K' and resid 414 through 419 removed outlier: 3.733A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 465 removed outlier: 3.636A pdb=" N LEU K 464 " --> pdb=" O ALA K 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 529 Processing helix chain 'L' and resid 353 through 358 Processing helix chain 'L' and resid 462 through 466 removed outlier: 3.661A pdb=" N ASN L 465 " --> pdb=" O GLU L 462 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU L 466 " --> pdb=" O GLN L 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 462 through 466' Processing helix chain 'L' and resid 526 through 530 removed outlier: 3.889A pdb=" N ASN L 529 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 141 Processing helix chain 'P' and resid 166 through 170 removed outlier: 4.307A pdb=" N THR P 170 " --> pdb=" O PRO P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 197 Processing helix chain 'P' and resid 298 through 302 removed outlier: 4.050A pdb=" N ALA P 302 " --> pdb=" O LYS P 299 " (cutoff:3.500A) Processing helix chain 'P' and resid 388 through 392 removed outlier: 3.502A pdb=" N GLU P 392 " --> pdb=" O ALA P 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 467 through 471 removed outlier: 3.566A pdb=" N SER P 471 " --> pdb=" O CYS P 468 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 350 removed outlier: 3.969A pdb=" N ASP A 371 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 383 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA5, first strand: chain 'A' and resid 567 through 569 removed outlier: 7.002A pdb=" N VAL A 567 " --> pdb=" O TYR J 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.778A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 424 through 428 Processing sheet with id=AA8, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.508A pdb=" N THR B 477 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 455 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.509A pdb=" N GLN B 493 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 550 " --> pdb=" O CYS B 536 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 506 through 507 Processing sheet with id=AB2, first strand: chain 'B' and resid 561 through 562 Processing sheet with id=AB3, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.659A pdb=" N THR C 366 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR C 366 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA C 411 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU C 368 " --> pdb=" O GLY C 409 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY C 409 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR C 370 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA C 407 " --> pdb=" O THR C 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.563A pdb=" N LEU C 437 " --> pdb=" O VAL C 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.669A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.710A pdb=" N GLN C 490 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 506 through 507 removed outlier: 3.533A pdb=" N MET C 506 " --> pdb=" O PHE C 516 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.503A pdb=" N ARG D 346 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 379 through 383 Processing sheet with id=AC1, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.602A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 485 through 489 Processing sheet with id=AC3, first strand: chain 'D' and resid 565 through 567 removed outlier: 7.230A pdb=" N LEU D 566 " --> pdb=" O VAL E 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.528A pdb=" N ILE E 350 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP E 371 " --> pdb=" O PHE E 405 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE E 405 " --> pdb=" O ASP E 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 380 through 383 removed outlier: 3.732A pdb=" N LEU E 437 " --> pdb=" O VAL E 428 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 453 through 455 removed outlier: 3.606A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 523 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 453 through 455 removed outlier: 3.606A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 523 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 485 through 489 Processing sheet with id=AC9, first strand: chain 'F' and resid 346 through 350 removed outlier: 3.528A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 372 through 373 removed outlier: 4.439A pdb=" N LEU F 372 " --> pdb=" O PHE F 405 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 379 through 383 removed outlier: 3.655A pdb=" N GLN F 439 " --> pdb=" O CYS F 426 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 455 removed outlier: 3.707A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 470 through 473 Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD6, first strand: chain 'F' and resid 565 through 566 removed outlier: 6.335A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 348 through 349 removed outlier: 3.759A pdb=" N ASP G 371 " --> pdb=" O PHE G 405 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE G 405 " --> pdb=" O ASP G 371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 379 through 383 removed outlier: 3.709A pdb=" N VAL G 428 " --> pdb=" O LEU G 437 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU G 437 " --> pdb=" O VAL G 428 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 453 through 457 Processing sheet with id=AE1, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.601A pdb=" N PHE G 479 " --> pdb=" O TYR G 515 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 493 through 494 removed outlier: 3.665A pdb=" N THR G 548 " --> pdb=" O VAL G 538 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 347 through 350 removed outlier: 3.901A pdb=" N ASP H 371 " --> pdb=" O PHE H 405 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE H 405 " --> pdb=" O ASP H 371 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 381 through 383 Processing sheet with id=AE5, first strand: chain 'H' and resid 453 through 454 removed outlier: 3.811A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 470 through 473 Processing sheet with id=AE7, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE8, first strand: chain 'H' and resid 506 through 507 Processing sheet with id=AE9, first strand: chain 'K' and resid 347 through 350 removed outlier: 3.927A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS K 367 " --> pdb=" O GLY K 409 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY K 409 " --> pdb=" O CYS K 367 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 382 through 384 removed outlier: 3.721A pdb=" N VAL K 428 " --> pdb=" O LEU K 437 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.869A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.869A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL K 476 " --> pdb=" O ALA K 517 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 493 through 494 removed outlier: 3.540A pdb=" N ARG K 550 " --> pdb=" O CYS K 536 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR K 548 " --> pdb=" O VAL K 538 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 346 through 350 removed outlier: 6.040A pdb=" N PHE L 405 " --> pdb=" O ASP L 371 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 381 through 383 Processing sheet with id=AF7, first strand: chain 'L' and resid 453 through 457 removed outlier: 5.233A pdb=" N THR L 471 " --> pdb=" O VAL L 523 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL L 523 " --> pdb=" O THR L 471 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N THR L 473 " --> pdb=" O LEU L 521 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU L 521 " --> pdb=" O THR L 473 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU L 475 " --> pdb=" O SER L 519 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER L 519 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR L 477 " --> pdb=" O ALA L 517 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA L 517 " --> pdb=" O THR L 477 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE L 479 " --> pdb=" O TYR L 515 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 453 through 457 removed outlier: 5.233A pdb=" N THR L 471 " --> pdb=" O VAL L 523 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL L 523 " --> pdb=" O THR L 471 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N THR L 473 " --> pdb=" O LEU L 521 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU L 521 " --> pdb=" O THR L 473 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU L 475 " --> pdb=" O SER L 519 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER L 519 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR L 477 " --> pdb=" O ALA L 517 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA L 517 " --> pdb=" O THR L 477 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE L 479 " --> pdb=" O TYR L 515 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 485 through 489 Processing sheet with id=AG1, first strand: chain 'L' and resid 561 through 562 removed outlier: 8.259A pdb=" N LEU L 561 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 567 through 568 removed outlier: 7.040A pdb=" N VAL L 567 " --> pdb=" O VAL J 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'J' and resid 112 through 113 Processing sheet with id=AG4, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.636A pdb=" N SER P 12 " --> pdb=" O GLU P 108 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER P 110 " --> pdb=" O SER P 12 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG P 89 " --> pdb=" O GLN P 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE P 47 " --> pdb=" O ARG P 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 18 through 23 Processing sheet with id=AG6, first strand: chain 'P' and resid 122 through 125 removed outlier: 6.232A pdb=" N TYR P 122 " --> pdb=" O GLN P 218 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU P 220 " --> pdb=" O TYR P 122 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL P 124 " --> pdb=" O LEU P 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'P' and resid 129 through 133 Processing sheet with id=AG8, first strand: chain 'P' and resid 155 through 159 removed outlier: 5.716A pdb=" N LEU P 157 " --> pdb=" O LYS P 149 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS P 149 " --> pdb=" O LEU P 157 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.627A pdb=" N VAL P 227 " --> pdb=" O PHE P 327 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASN P 329 " --> pdb=" O VAL P 227 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU P 229 " --> pdb=" O ASN P 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'P' and resid 234 through 238 Processing sheet with id=AH2, first strand: chain 'P' and resid 250 through 253 removed outlier: 3.672A pdb=" N CYS P 307 " --> pdb=" O GLN P 322 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 340 through 344 removed outlier: 4.288A pdb=" N THR P 433 " --> pdb=" O CYS P 423 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 348 through 354 Processing sheet with id=AH5, first strand: chain 'P' and resid 365 through 367 removed outlier: 4.655A pdb=" N VAL P 381 " --> pdb=" O TRP P 366 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 464 through 466 Processing sheet with id=AH7, first strand: chain 'P' and resid 474 through 475 Processing sheet with id=AH8, first strand: chain 'P' and resid 477 through 478 removed outlier: 4.449A pdb=" N TRP P 477 " --> pdb=" O LEU P 488 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU P 488 " --> pdb=" O TRP P 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'P' and resid 524 through 525 603 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.47 Time building geometry restraints manager: 9.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3770 1.30 - 1.44: 6374 1.44 - 1.57: 12757 1.57 - 1.70: 4 1.70 - 1.83: 141 Bond restraints: 23046 Sorted by residual: bond pdb=" CB ASN L 563 " pdb=" CG ASN L 563 " ideal model delta sigma weight residual 1.516 1.371 0.145 2.50e-02 1.60e+03 3.37e+01 bond pdb=" CB VAL L 567 " pdb=" CG2 VAL L 567 " ideal model delta sigma weight residual 1.521 1.351 0.170 3.30e-02 9.18e+02 2.65e+01 bond pdb=" C ALA B 542 " pdb=" N LEU B 543 " ideal model delta sigma weight residual 1.328 1.254 0.074 1.45e-02 4.76e+03 2.60e+01 bond pdb=" C ALA D 542 " pdb=" N LEU D 543 " ideal model delta sigma weight residual 1.331 1.256 0.075 1.48e-02 4.57e+03 2.55e+01 bond pdb=" CA SER L 565 " pdb=" C SER L 565 " ideal model delta sigma weight residual 1.527 1.467 0.060 1.20e-02 6.94e+03 2.53e+01 ... (remaining 23041 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.70: 629 104.70 - 112.85: 12440 112.85 - 121.00: 11012 121.00 - 129.15: 7187 129.15 - 137.31: 225 Bond angle restraints: 31493 Sorted by residual: angle pdb=" C PRO G 507 " pdb=" N GLU G 508 " pdb=" CA GLU G 508 " ideal model delta sigma weight residual 120.39 132.06 -11.67 1.39e+00 5.18e-01 7.04e+01 angle pdb=" N VAL P 448 " pdb=" CA VAL P 448 " pdb=" C VAL P 448 " ideal model delta sigma weight residual 109.19 103.52 5.67 8.20e-01 1.49e+00 4.78e+01 angle pdb=" C LYS J 13 " pdb=" N CYS J 14 " pdb=" CA CYS J 14 " ideal model delta sigma weight residual 123.93 134.29 -10.36 1.54e+00 4.22e-01 4.53e+01 angle pdb=" C ARG P 99 " pdb=" CA ARG P 99 " pdb=" CB ARG P 99 " ideal model delta sigma weight residual 111.22 103.00 8.22 1.24e+00 6.50e-01 4.40e+01 angle pdb=" C GLY L 573 " pdb=" N THR L 574 " pdb=" CA THR L 574 " ideal model delta sigma weight residual 122.08 112.62 9.46 1.53e+00 4.27e-01 3.82e+01 ... (remaining 31488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12219 17.87 - 35.73: 1579 35.73 - 53.60: 278 53.60 - 71.46: 37 71.46 - 89.33: 27 Dihedral angle restraints: 14140 sinusoidal: 5745 harmonic: 8395 Sorted by residual: dihedral pdb=" CA GLY K 531 " pdb=" C GLY K 531 " pdb=" N GLU K 532 " pdb=" CA GLU K 532 " ideal model delta harmonic sigma weight residual -180.00 -135.05 -44.95 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CB CYS P 253 " pdb=" SG CYS P 253 " pdb=" SG CYS P 261 " pdb=" CB CYS P 261 " ideal model delta sinusoidal sigma weight residual -86.00 -6.97 -79.03 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CB CYS P 38 " pdb=" SG CYS P 38 " pdb=" SG CYS P 46 " pdb=" CB CYS P 46 " ideal model delta sinusoidal sigma weight residual 93.00 16.60 76.40 1 1.00e+01 1.00e-02 7.34e+01 ... (remaining 14137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 3592 0.208 - 0.415: 95 0.415 - 0.623: 1 0.623 - 0.830: 2 0.830 - 1.038: 1 Chirality restraints: 3691 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.74e+02 chirality pdb=" C1 NAG G 601 " pdb=" ND2 ASN G 563 " pdb=" C2 NAG G 601 " pdb=" O5 NAG G 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.69e+01 chirality pdb=" C1 NAG F 601 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG F 601 " pdb=" O5 NAG F 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.52e+01 ... (remaining 3688 not shown) Planarity restraints: 4037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 558 " -0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO F 559 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO F 559 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 559 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 113 " -0.063 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO J 114 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO J 114 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 114 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 27 " 0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO J 28 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO J 28 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO J 28 " 0.050 5.00e-02 4.00e+02 ... (remaining 4034 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1877 2.71 - 3.25: 19931 3.25 - 3.80: 34960 3.80 - 4.35: 41541 4.35 - 4.90: 73598 Nonbonded interactions: 171907 Sorted by model distance: nonbonded pdb=" O THR L 533 " pdb=" OG1 THR L 551 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASP P 230 " pdb=" OG SER P 332 " model vdw 2.172 3.040 nonbonded pdb=" O THR A 473 " pdb=" OG1 THR A 473 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR L 383 " pdb=" OG1 THR L 425 " model vdw 2.217 3.040 nonbonded pdb=" O SER L 565 " pdb=" OG SER L 565 " model vdw 2.221 3.040 ... (remaining 171902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 58.840 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.018 0.175 23046 Z= 1.177 Angle : 1.438 13.767 31493 Z= 0.800 Chirality : 0.088 1.038 3691 Planarity : 0.011 0.097 4026 Dihedral : 15.959 89.331 8570 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 15.20 % Favored : 84.41 % Rotamer: Outliers : 3.30 % Allowed : 16.95 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.73 (0.13), residues: 2823 helix: -4.59 (0.13), residues: 227 sheet: -2.61 (0.14), residues: 1065 loop : -3.35 (0.13), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP P 37 HIS 0.015 0.003 HIS C 518 PHE 0.053 0.006 PHE D 479 TYR 0.047 0.005 TYR P 228 ARG 0.026 0.001 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 313 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 LEU cc_start: 0.1936 (OUTLIER) cc_final: 0.0865 (tt) REVERT: C 450 HIS cc_start: 0.8081 (m-70) cc_final: 0.7513 (m170) REVERT: G 364 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7707 (mtpp) REVERT: G 498 GLU cc_start: 0.6432 (tm-30) cc_final: 0.6150 (tm-30) REVERT: H 562 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7393 (p90) REVERT: K 493 GLN cc_start: 0.7746 (pm20) cc_final: 0.7511 (mp10) REVERT: K 514 ARG cc_start: 0.7327 (mmt90) cc_final: 0.6921 (mpt180) REVERT: J 34 GLU cc_start: 0.7523 (mp0) cc_final: 0.7266 (mt-10) REVERT: P 262 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7353 (p0) outliers start: 84 outliers final: 52 residues processed: 392 average time/residue: 0.4048 time to fit residues: 230.8371 Evaluate side-chains 306 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 251 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 556 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain K residue 551 THR Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 563 ASN Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 262 ASP Chi-restraints excluded: chain P residue 267 THR Chi-restraints excluded: chain P residue 367 CYS Chi-restraints excluded: chain P residue 379 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 221 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 256 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 400 HIS A 402 ASN B 465 ASN B 487 GLN B 545 ASN C 463 GLN D 385 GLN D 419 ASN D 439 GLN D 463 GLN E 419 ASN E 430 HIS E 545 ASN F 490 GLN F 518 HIS ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 GLN G 518 HIS H 463 GLN H 487 GLN H 518 HIS K 402 ASN K 450 HIS ** K 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 490 GLN L 419 ASN L 463 GLN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN P 97 ASN ** P 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 329 ASN P 373 GLN P 482 ASN P 486 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23046 Z= 0.224 Angle : 0.718 13.293 31493 Z= 0.368 Chirality : 0.049 0.405 3691 Planarity : 0.006 0.082 4026 Dihedral : 8.317 59.242 3409 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.51 % Allowed : 19.03 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.14), residues: 2823 helix: -3.98 (0.18), residues: 238 sheet: -2.08 (0.14), residues: 1078 loop : -2.79 (0.14), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 418 HIS 0.008 0.001 HIS E 393 PHE 0.016 0.002 PHE B 479 TYR 0.020 0.002 TYR J 117 ARG 0.005 0.001 ARG H 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 309 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 537 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8529 (t) REVERT: C 368 LEU cc_start: 0.1653 (OUTLIER) cc_final: 0.0599 (tt) REVERT: C 515 TYR cc_start: 0.8451 (m-80) cc_final: 0.8206 (m-10) REVERT: C 528 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.7670 (t-100) REVERT: D 528 TRP cc_start: 0.8311 (OUTLIER) cc_final: 0.8108 (t-100) REVERT: H 562 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7106 (p90) outliers start: 115 outliers final: 79 residues processed: 409 average time/residue: 0.3748 time to fit residues: 228.9753 Evaluate side-chains 333 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 249 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 TRP Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 528 TRP Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 526 GLU Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 555 SER Chi-restraints excluded: chain H residue 556 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain H residue 575 CYS Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 267 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain P residue 367 CYS Chi-restraints excluded: chain P residue 373 GLN Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 431 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 256 optimal weight: 0.9980 chunk 277 optimal weight: 20.0000 chunk 228 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 205 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN D 450 HIS ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 HIS ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 385 GLN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 373 GLN P 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23046 Z= 0.272 Angle : 0.692 10.689 31493 Z= 0.353 Chirality : 0.049 0.454 3691 Planarity : 0.006 0.073 4026 Dihedral : 7.781 59.353 3385 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 5.97 % Allowed : 20.13 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.14), residues: 2823 helix: -3.53 (0.21), residues: 244 sheet: -1.76 (0.15), residues: 1064 loop : -2.55 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 418 HIS 0.007 0.001 HIS H 400 PHE 0.015 0.002 PHE B 479 TYR 0.019 0.002 TYR P 228 ARG 0.005 0.000 ARG K 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 267 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 LEU cc_start: 0.1691 (OUTLIER) cc_final: 0.1021 (tp) REVERT: C 450 HIS cc_start: 0.8081 (m-70) cc_final: 0.7458 (m-70) REVERT: C 515 TYR cc_start: 0.8457 (m-80) cc_final: 0.8199 (m-10) REVERT: C 528 TRP cc_start: 0.8098 (OUTLIER) cc_final: 0.7534 (t60) REVERT: D 528 TRP cc_start: 0.8381 (OUTLIER) cc_final: 0.8004 (t-100) REVERT: H 562 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.6783 (p90) REVERT: K 537 VAL cc_start: 0.8771 (p) cc_final: 0.8527 (m) REVERT: L 449 LEU cc_start: 0.5182 (OUTLIER) cc_final: 0.4924 (pp) REVERT: P 262 ASP cc_start: 0.7645 (p0) cc_final: 0.7378 (p0) outliers start: 152 outliers final: 111 residues processed: 395 average time/residue: 0.3393 time to fit residues: 206.7656 Evaluate side-chains 363 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 247 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 528 TRP Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 528 TRP Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 474 CYS Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 393 HIS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 555 SER Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain H residue 575 CYS Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 535 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 449 LEU Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 484 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 267 THR Chi-restraints excluded: chain P residue 268 LEU Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain P residue 300 GLU Chi-restraints excluded: chain P residue 367 CYS Chi-restraints excluded: chain P residue 373 GLN Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 509 VAL Chi-restraints excluded: chain P residue 512 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.5980 chunk 192 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 122 optimal weight: 0.3980 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 ASN B 545 ASN ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 GLN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 373 GLN P 482 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23046 Z= 0.177 Angle : 0.628 9.386 31493 Z= 0.317 Chirality : 0.046 0.399 3691 Planarity : 0.005 0.069 4026 Dihedral : 6.995 56.996 3379 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.34 % Allowed : 21.51 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.96 (0.15), residues: 2823 helix: -3.01 (0.26), residues: 231 sheet: -1.33 (0.15), residues: 1048 loop : -2.27 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 418 HIS 0.006 0.001 HIS H 400 PHE 0.013 0.001 PHE B 479 TYR 0.019 0.001 TYR F 534 ARG 0.005 0.000 ARG K 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 282 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 570 ASP cc_start: 0.7151 (t0) cc_final: 0.6942 (t0) REVERT: C 368 LEU cc_start: 0.1434 (OUTLIER) cc_final: 0.0822 (tp) REVERT: C 450 HIS cc_start: 0.8073 (m-70) cc_final: 0.7447 (m-70) REVERT: C 515 TYR cc_start: 0.8432 (m-80) cc_final: 0.8180 (m-10) REVERT: C 528 TRP cc_start: 0.8051 (OUTLIER) cc_final: 0.7671 (t-100) REVERT: D 528 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.8134 (t-100) REVERT: F 561 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6599 (mp) REVERT: G 489 MET cc_start: 0.7354 (mtm) cc_final: 0.7061 (mtt) REVERT: K 537 VAL cc_start: 0.8631 (p) cc_final: 0.8419 (m) REVERT: L 449 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4957 (pp) REVERT: P 262 ASP cc_start: 0.7617 (p0) cc_final: 0.7191 (p0) outliers start: 136 outliers final: 98 residues processed: 400 average time/residue: 0.3543 time to fit residues: 216.4937 Evaluate side-chains 359 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 256 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 528 TRP Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 528 TRP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 532 GLU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 524 SER Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 474 CYS Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 393 HIS Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain H residue 575 CYS Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 THR Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 535 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 427 THR Chi-restraints excluded: chain L residue 449 LEU Chi-restraints excluded: chain L residue 484 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 268 LEU Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain P residue 341 VAL Chi-restraints excluded: chain P residue 373 GLN Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 509 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 244 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 545 ASN C 463 GLN ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 GLN K 518 HIS J 36 ASN ** P 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 373 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 23046 Z= 0.430 Angle : 0.731 8.387 31493 Z= 0.374 Chirality : 0.052 0.533 3691 Planarity : 0.006 0.068 4026 Dihedral : 7.491 59.488 3370 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 6.51 % Allowed : 22.25 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.98 (0.15), residues: 2823 helix: -2.86 (0.27), residues: 233 sheet: -1.44 (0.15), residues: 1069 loop : -2.24 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 37 HIS 0.007 0.001 HIS C 518 PHE 0.020 0.002 PHE A 479 TYR 0.026 0.002 TYR P 228 ARG 0.004 0.001 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 261 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 570 ASP cc_start: 0.7198 (t0) cc_final: 0.6906 (t0) REVERT: C 368 LEU cc_start: 0.1293 (OUTLIER) cc_final: 0.0717 (tp) REVERT: C 450 HIS cc_start: 0.8123 (m-70) cc_final: 0.7608 (m170) REVERT: C 515 TYR cc_start: 0.8508 (m-80) cc_final: 0.8211 (m-10) REVERT: C 528 TRP cc_start: 0.8132 (OUTLIER) cc_final: 0.7422 (t60) REVERT: D 348 PHE cc_start: 0.4141 (OUTLIER) cc_final: 0.3726 (t80) REVERT: D 528 TRP cc_start: 0.8407 (OUTLIER) cc_final: 0.7621 (t60) REVERT: E 566 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7582 (tt) REVERT: F 561 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6546 (mp) REVERT: L 449 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.4988 (pp) REVERT: J 125 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6618 (tp30) REVERT: P 101 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7109 (mt) REVERT: P 262 ASP cc_start: 0.7701 (p0) cc_final: 0.7447 (p0) outliers start: 166 outliers final: 135 residues processed: 405 average time/residue: 0.3483 time to fit residues: 216.4914 Evaluate side-chains 392 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 248 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 528 TRP Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 348 PHE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 528 TRP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 524 SER Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 474 CYS Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 393 HIS Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 526 GLU Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 555 SER Chi-restraints excluded: chain H residue 556 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain H residue 575 CYS Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 THR Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 535 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 427 THR Chi-restraints excluded: chain L residue 449 LEU Chi-restraints excluded: chain L residue 484 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 253 CYS Chi-restraints excluded: chain P residue 267 THR Chi-restraints excluded: chain P residue 268 LEU Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain P residue 300 GLU Chi-restraints excluded: chain P residue 341 VAL Chi-restraints excluded: chain P residue 367 CYS Chi-restraints excluded: chain P residue 373 GLN Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 509 VAL Chi-restraints excluded: chain P residue 512 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 160 optimal weight: 0.2980 chunk 67 optimal weight: 20.0000 chunk 272 optimal weight: 0.0670 chunk 226 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 GLN B 439 GLN B 545 ASN ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 545 ASN ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 373 GLN P 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23046 Z= 0.183 Angle : 0.627 9.174 31493 Z= 0.318 Chirality : 0.046 0.412 3691 Planarity : 0.005 0.068 4026 Dihedral : 6.826 58.551 3367 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 6.08 % Allowed : 23.59 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.65 (0.15), residues: 2823 helix: -2.71 (0.27), residues: 239 sheet: -1.13 (0.16), residues: 1064 loop : -2.06 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 418 HIS 0.006 0.001 HIS H 400 PHE 0.014 0.001 PHE D 479 TYR 0.027 0.001 TYR F 534 ARG 0.005 0.000 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 277 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 LEU cc_start: 0.1332 (OUTLIER) cc_final: 0.0802 (tp) REVERT: C 450 HIS cc_start: 0.8116 (m-70) cc_final: 0.7491 (m-70) REVERT: C 515 TYR cc_start: 0.8458 (m-80) cc_final: 0.8171 (m-10) REVERT: C 528 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.7622 (t-100) REVERT: D 528 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.8065 (t-100) REVERT: F 561 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6519 (mp) REVERT: G 489 MET cc_start: 0.7330 (mtm) cc_final: 0.7017 (mtt) REVERT: K 537 VAL cc_start: 0.8505 (p) cc_final: 0.8222 (m) REVERT: L 449 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4928 (pp) REVERT: L 528 TRP cc_start: 0.7583 (OUTLIER) cc_final: 0.7275 (m100) REVERT: P 129 THR cc_start: 0.4158 (OUTLIER) cc_final: 0.3869 (t) REVERT: P 262 ASP cc_start: 0.7510 (p0) cc_final: 0.7272 (p0) REVERT: P 529 LYS cc_start: 0.6375 (tptt) cc_final: 0.5547 (tptt) outliers start: 155 outliers final: 123 residues processed: 405 average time/residue: 0.3664 time to fit residues: 229.8884 Evaluate side-chains 391 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 261 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 528 TRP Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 528 TRP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 428 VAL Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 524 SER Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 474 CYS Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 393 HIS Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 526 GLU Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 555 SER Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain H residue 575 CYS Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 THR Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 535 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 427 THR Chi-restraints excluded: chain L residue 449 LEU Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 484 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 528 TRP Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 267 THR Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain P residue 367 CYS Chi-restraints excluded: chain P residue 373 GLN Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 509 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 199 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 229 optimal weight: 0.2980 chunk 152 optimal weight: 2.9990 chunk 271 optimal weight: 0.0870 chunk 170 optimal weight: 5.9990 chunk 165 optimal weight: 0.4980 chunk 125 optimal weight: 9.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 545 ASN ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 487 GLN L 395 ASN J 29 ASN ** P 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 373 GLN P 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23046 Z= 0.224 Angle : 0.638 8.940 31493 Z= 0.323 Chirality : 0.047 0.445 3691 Planarity : 0.005 0.066 4026 Dihedral : 6.760 58.948 3367 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 6.24 % Allowed : 23.74 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.46 (0.15), residues: 2823 helix: -2.60 (0.28), residues: 238 sheet: -1.02 (0.16), residues: 1081 loop : -1.93 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 418 HIS 0.006 0.001 HIS H 400 PHE 0.014 0.001 PHE B 479 TYR 0.024 0.001 TYR F 534 ARG 0.008 0.000 ARG K 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 259 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 LEU cc_start: 0.1174 (OUTLIER) cc_final: 0.0689 (tp) REVERT: C 515 TYR cc_start: 0.8442 (m-80) cc_final: 0.8152 (m-10) REVERT: C 528 TRP cc_start: 0.8094 (OUTLIER) cc_final: 0.7613 (t-100) REVERT: D 528 TRP cc_start: 0.8321 (OUTLIER) cc_final: 0.8024 (t-100) REVERT: F 561 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6561 (mp) REVERT: G 489 MET cc_start: 0.7358 (mtm) cc_final: 0.7054 (mtt) REVERT: K 463 GLN cc_start: 0.7827 (tm-30) cc_final: 0.6894 (tm-30) REVERT: K 537 VAL cc_start: 0.8439 (p) cc_final: 0.8158 (m) REVERT: L 449 LEU cc_start: 0.5291 (OUTLIER) cc_final: 0.4962 (pp) REVERT: L 528 TRP cc_start: 0.7534 (OUTLIER) cc_final: 0.7245 (m100) REVERT: J 125 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6568 (tp30) REVERT: P 129 THR cc_start: 0.4226 (OUTLIER) cc_final: 0.3914 (t) REVERT: P 262 ASP cc_start: 0.7577 (p0) cc_final: 0.7337 (p0) outliers start: 159 outliers final: 136 residues processed: 392 average time/residue: 0.3428 time to fit residues: 206.3767 Evaluate side-chains 391 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 247 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 528 TRP Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 528 TRP Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 367 CYS Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 524 SER Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 474 CYS Chi-restraints excluded: chain G residue 518 HIS Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain H residue 393 HIS Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 526 GLU Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 541 GLU Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 555 SER Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain H residue 575 CYS Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 390 VAL Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 404 THR Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 477 THR Chi-restraints excluded: chain K residue 535 THR Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 574 THR Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 427 THR Chi-restraints excluded: chain L residue 449 LEU Chi-restraints excluded: chain L residue 476 VAL Chi-restraints excluded: chain L residue 484 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 528 TRP Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 547 VAL Chi-restraints excluded: chain L residue 548 THR Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 67 THR Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 188 VAL Chi-restraints excluded: chain P residue 220 LEU Chi-restraints excluded: chain P residue 267 THR Chi-restraints excluded: chain P residue 268 LEU Chi-restraints excluded: chain P residue 295 THR Chi-restraints excluded: chain P residue 367 CYS Chi-restraints excluded: chain P residue 373 GLN Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 405 THR Chi-restraints excluded: chain P residue 431 TRP Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 509 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.573 > 50: distance: 8 - 106: 34.214 distance: 11 - 103: 4.732 distance: 20 - 91: 29.267 distance: 23 - 88: 12.937 distance: 33 - 78: 26.402 distance: 53 - 58: 16.920 distance: 58 - 59: 14.628 distance: 59 - 60: 22.501 distance: 59 - 62: 12.509 distance: 60 - 61: 25.966 distance: 60 - 67: 6.356 distance: 62 - 63: 18.327 distance: 63 - 64: 23.751 distance: 64 - 65: 4.677 distance: 65 - 66: 14.511 distance: 67 - 68: 7.224 distance: 67 - 207: 22.131 distance: 68 - 69: 17.413 distance: 68 - 71: 15.108 distance: 69 - 70: 24.274 distance: 69 - 75: 8.814 distance: 70 - 204: 32.137 distance: 71 - 72: 15.609 distance: 72 - 73: 13.298 distance: 72 - 74: 14.059 distance: 75 - 76: 17.945 distance: 76 - 77: 10.539 distance: 76 - 79: 26.100 distance: 77 - 82: 12.173 distance: 79 - 80: 12.426 distance: 79 - 81: 12.974 distance: 82 - 83: 38.490 distance: 83 - 84: 32.985 distance: 83 - 86: 31.238 distance: 84 - 85: 41.322 distance: 84 - 88: 22.107 distance: 86 - 87: 21.762 distance: 87 - 224: 15.033 distance: 88 - 89: 20.553 distance: 89 - 90: 20.323 distance: 89 - 92: 19.589 distance: 90 - 91: 30.088 distance: 90 - 96: 9.446 distance: 92 - 93: 18.476 distance: 93 - 94: 10.576 distance: 93 - 95: 28.100 distance: 96 - 97: 21.678 distance: 97 - 98: 31.646 distance: 97 - 100: 13.091 distance: 98 - 99: 31.117 distance: 98 - 103: 17.980 distance: 100 - 101: 25.863 distance: 100 - 102: 29.101 distance: 103 - 104: 9.530 distance: 104 - 105: 16.742 distance: 104 - 107: 46.113 distance: 105 - 106: 31.529 distance: 105 - 110: 30.470 distance: 107 - 108: 4.252 distance: 107 - 109: 14.538 distance: 110 - 111: 20.458 distance: 111 - 112: 22.132 distance: 111 - 114: 5.804 distance: 112 - 113: 26.856 distance: 112 - 118: 10.727 distance: 114 - 115: 25.869 distance: 115 - 116: 19.105 distance: 115 - 117: 27.149 distance: 118 - 119: 17.689 distance: 119 - 120: 4.281 distance: 120 - 121: 14.648 distance: 120 - 126: 5.491 distance: 122 - 123: 12.299 distance: 123 - 124: 13.856 distance: 123 - 125: 17.701 distance: 126 - 127: 10.576 distance: 127 - 128: 8.264 distance: 127 - 130: 13.589 distance: 128 - 129: 12.048 distance: 128 - 133: 7.886 distance: 130 - 131: 12.091 distance: 130 - 132: 12.255