Starting phenix.real_space_refine on Thu Feb 5 02:37:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be9_44474/02_2026/9be9_44474.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be9_44474/02_2026/9be9_44474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9be9_44474/02_2026/9be9_44474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be9_44474/02_2026/9be9_44474.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9be9_44474/02_2026/9be9_44474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be9_44474/02_2026/9be9_44474.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.026 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 99 5.16 5 C 8913 2.51 5 N 2391 2.21 5 O 2850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14253 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4399 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 25, 'TRANS': 526} Chain breaks: 6 Chain: "B" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4399 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 25, 'TRANS': 526} Chain breaks: 6 Chain: "C" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4399 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 25, 'TRANS': 526} Chain breaks: 6 Chain: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" 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: "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: "J" 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: "K" 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: "L" 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: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" 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: "U" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 3.74, per 1000 atoms: 0.26 Number of scatterers: 14253 At special positions: 0 Unit cell: (126.445, 130.625, 120.175, 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 99 16.00 O 2850 8.00 N 2391 7.00 C 8913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.05 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.04 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.01 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.01 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN M 4 " - " MAN M 5 " " MAN S 4 " - " MAN S 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA M 3 " - " MAN M 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " " BMA M 3 " - " MAN M 6 " " BMA S 3 " - " MAN S 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 701 " - " ASN A 187 " " NAG A 702 " - " ASN A 442 " " NAG A 703 " - " ASN A 448 " " NAG A 704 " - " ASN A 88 " " NAG A 705 " - " ASN A 160 " " NAG A 706 " - " ASN A 197 " " NAG A 707 " - " ASN A 230 " " NAG A 708 " - " ASN A 386 " " NAG A 709 " - " ASN A 392 " " NAG A 710 " - " ASN A 611 " " NAG B 701 " - " ASN B 187 " " NAG B 702 " - " ASN B 442 " " NAG B 703 " - " ASN B 448 " " NAG B 704 " - " ASN B 88 " " NAG B 705 " - " ASN B 160 " " NAG B 706 " - " ASN B 197 " " NAG B 707 " - " ASN B 230 " " NAG B 708 " - " ASN B 386 " " NAG B 709 " - " ASN B 392 " " NAG B 710 " - " ASN B 611 " " NAG C 701 " - " ASN C 187 " " NAG C 702 " - " ASN C 442 " " NAG C 703 " - " ASN C 448 " " NAG C 704 " - " ASN C 88 " " NAG C 705 " - " ASN C 160 " " NAG C 706 " - " ASN C 197 " " NAG C 707 " - " ASN C 230 " " NAG C 708 " - " ASN C 386 " " NAG C 709 " - " ASN C 392 " " NAG C 710 " - " ASN C 611 " " NAG D 1 " - " ASN A 156 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 289 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN B 156 " " NAG K 1 " - " ASN B 234 " " NAG L 1 " - " ASN B 241 " " NAG M 1 " - " ASN B 262 " " NAG N 1 " - " ASN B 289 " " NAG O 1 " - " ASN B 332 " " NAG P 1 " - " ASN C 156 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 241 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 289 " " NAG U 1 " - " ASN C 332 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 510.0 milliseconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3108 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 33 sheets defined 25.0% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.393A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.692A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.652A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 4.247A pdb=" N VAL A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 596 Processing helix chain 'A' and resid 618 through 626 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 647 Processing helix chain 'A' and resid 648 through 660 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.393A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 353 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.691A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 429' Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.652A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 540 removed outlier: 4.247A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 647 Processing helix chain 'B' and resid 648 through 660 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.393A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.692A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.652A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 540 removed outlier: 4.247A pdb=" N VAL C 539 " --> pdb=" O ILE C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 596 Processing helix chain 'C' and resid 618 through 626 Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 638 through 647 Processing helix chain 'C' and resid 648 through 660 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.329A pdb=" N VAL A 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.952A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.893A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 218 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.519A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 158 through 159 Processing sheet with id=AA8, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.383A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.592A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N VAL A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.174A pdb=" N VAL A 286 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.174A pdb=" N VAL A 286 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N VAL A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE A 468 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 303 through 308 Processing sheet with id=AB3, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.329A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.952A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.892A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 218 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.518A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 129 through 131 Processing sheet with id=AB8, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB9, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AC1, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.384A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.592A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N VAL B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.174A pdb=" N VAL B 286 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 271 through 273 removed outlier: 11.174A pdb=" N VAL B 286 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N VAL B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE B 468 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 303 through 308 Processing sheet with id=AC5, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.329A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.952A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.893A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS C 218 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.518A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AD1, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AD2, first strand: chain 'C' and resid 158 through 159 Processing sheet with id=AD3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.384A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.592A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.843A pdb=" N VAL C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.174A pdb=" N VAL C 286 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.174A pdb=" N VAL C 286 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 10.843A pdb=" N VAL C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE C 468 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 303 through 308 513 hydrogen bonds defined for protein. 1404 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: 2.37 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4467 1.35 - 1.48: 3759 1.48 - 1.61: 6165 1.61 - 1.74: 0 1.74 - 1.87: 132 Bond restraints: 14523 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" CB ASN C 611 " pdb=" CG ASN C 611 " ideal model delta sigma weight residual 1.516 1.591 -0.075 2.50e-02 1.60e+03 9.00e+00 bond pdb=" CB ASN B 611 " pdb=" CG ASN B 611 " ideal model delta sigma weight residual 1.516 1.591 -0.075 2.50e-02 1.60e+03 8.96e+00 ... (remaining 14518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 17520 1.58 - 3.16: 1801 3.16 - 4.73: 287 4.73 - 6.31: 72 6.31 - 7.89: 15 Bond angle restraints: 19695 Sorted by residual: angle pdb=" CA ASN C 611 " pdb=" CB ASN C 611 " pdb=" CG ASN C 611 " ideal model delta sigma weight residual 112.60 117.08 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" CA ASN B 611 " pdb=" CB ASN B 611 " pdb=" CG ASN B 611 " ideal model delta sigma weight residual 112.60 117.07 -4.47 1.00e+00 1.00e+00 2.00e+01 angle pdb=" CA ASN A 611 " pdb=" CB ASN A 611 " pdb=" CG ASN A 611 " ideal model delta sigma weight residual 112.60 117.07 -4.47 1.00e+00 1.00e+00 2.00e+01 angle pdb=" N HIS B 249 " pdb=" CA HIS B 249 " pdb=" C HIS B 249 " ideal model delta sigma weight residual 110.53 105.73 4.80 1.32e+00 5.74e-01 1.32e+01 angle pdb=" N HIS A 249 " pdb=" CA HIS A 249 " pdb=" C HIS A 249 " ideal model delta sigma weight residual 110.53 105.73 4.80 1.32e+00 5.74e-01 1.32e+01 ... (remaining 19690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 9432 21.29 - 42.58: 258 42.58 - 63.87: 69 63.87 - 85.16: 36 85.16 - 106.45: 18 Dihedral angle restraints: 9813 sinusoidal: 5016 harmonic: 4797 Sorted by residual: dihedral pdb=" O4 BMA S 3 " pdb=" C4 BMA S 3 " pdb=" C5 BMA S 3 " pdb=" O5 BMA S 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.74 106.45 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.73 106.44 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.69 106.40 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 9810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1672 0.062 - 0.123: 634 0.123 - 0.185: 94 0.185 - 0.246: 24 0.246 - 0.307: 6 Chirality restraints: 2430 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2427 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 384 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.61e+00 pdb=" C TYR B 384 " -0.054 2.00e-02 2.50e+03 pdb=" O TYR B 384 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS B 385 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 384 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C TYR C 384 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR C 384 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS C 385 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 384 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C TYR A 384 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR A 384 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS A 385 " 0.018 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1992 2.76 - 3.30: 13024 3.30 - 3.83: 22703 3.83 - 4.37: 26749 4.37 - 4.90: 45989 Nonbonded interactions: 110457 Sorted by model distance: nonbonded pdb=" OE2 GLU A 647 " pdb=" NH1 ARG C 542 " model vdw 2.229 3.120 nonbonded pdb=" NH1 ARG B 542 " pdb=" OE2 GLU C 647 " model vdw 2.229 3.120 nonbonded pdb=" NH1 ARG A 542 " pdb=" OE2 GLU B 647 " model vdw 2.229 3.120 nonbonded pdb=" O4 MAN M 4 " pdb=" O6 MAN M 4 " model vdw 2.298 3.040 nonbonded pdb=" O4 MAN S 4 " pdb=" O6 MAN S 4 " model vdw 2.298 3.040 ... (remaining 110452 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.830 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 14634 Z= 0.328 Angle : 1.131 16.839 19995 Z= 0.608 Chirality : 0.064 0.307 2430 Planarity : 0.006 0.046 2406 Dihedral : 12.028 106.449 6606 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.20 % Allowed : 0.61 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1614 helix: 0.92 (0.26), residues: 324 sheet: 0.63 (0.23), residues: 450 loop : 0.07 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.021 0.003 TYR C 191 PHE 0.022 0.003 PHE C 383 TRP 0.027 0.003 TRP B 479 HIS 0.017 0.003 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00699 (14523) covalent geometry : angle 1.07017 (19695) SS BOND : bond 0.00896 ( 33) SS BOND : angle 3.32788 ( 66) hydrogen bonds : bond 0.12940 ( 495) hydrogen bonds : angle 6.59983 ( 1404) link_ALPHA1-2 : bond 0.00378 ( 3) link_ALPHA1-2 : angle 1.47445 ( 9) link_ALPHA1-3 : bond 0.00406 ( 3) link_ALPHA1-3 : angle 1.76904 ( 9) link_ALPHA1-6 : bond 0.00453 ( 3) link_ALPHA1-6 : angle 1.30403 ( 9) link_BETA1-4 : bond 0.01220 ( 21) link_BETA1-4 : angle 4.62230 ( 63) link_NAG-ASN : bond 0.00587 ( 48) link_NAG-ASN : angle 2.48620 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 352 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8740 (mmm) cc_final: 0.8510 (mmt) REVERT: A 631 TRP cc_start: 0.8262 (t-100) cc_final: 0.8031 (t-100) REVERT: B 475 MET cc_start: 0.8702 (mmm) cc_final: 0.8486 (mmt) REVERT: C 100 MET cc_start: 0.7809 (mtp) cc_final: 0.7472 (mtt) REVERT: C 215 ILE cc_start: 0.8553 (mt) cc_final: 0.8063 (mt) outliers start: 3 outliers final: 3 residues processed: 355 average time/residue: 0.1391 time to fit residues: 69.7302 Evaluate side-chains 151 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 611 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0040 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 374 HIS A 652 GLN B 195 ASN B 240 ASN B 287 HIS B 374 HIS B 425 ASN B 650 GLN B 652 GLN C 72 HIS C 195 ASN C 240 ASN C 287 HIS C 374 HIS C 425 ASN C 652 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109103 restraints weight = 24129.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111560 restraints weight = 17703.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113330 restraints weight = 14061.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114154 restraints weight = 11866.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115342 restraints weight = 10696.768| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14634 Z= 0.160 Angle : 0.770 16.797 19995 Z= 0.373 Chirality : 0.050 0.385 2430 Planarity : 0.005 0.052 2406 Dihedral : 9.155 81.814 3396 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.10 % Favored : 96.72 % Rotamer: Outliers : 2.58 % Allowed : 8.76 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1614 helix: 2.14 (0.27), residues: 330 sheet: -0.36 (0.21), residues: 471 loop : -0.12 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 419 TYR 0.010 0.002 TYR C 302 PHE 0.015 0.002 PHE A 382 TRP 0.016 0.001 TRP B 479 HIS 0.010 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00344 (14523) covalent geometry : angle 0.68801 (19695) SS BOND : bond 0.00241 ( 33) SS BOND : angle 1.75143 ( 66) hydrogen bonds : bond 0.04871 ( 495) hydrogen bonds : angle 5.78713 ( 1404) link_ALPHA1-2 : bond 0.00428 ( 3) link_ALPHA1-2 : angle 1.79473 ( 9) link_ALPHA1-3 : bond 0.00972 ( 3) link_ALPHA1-3 : angle 1.81960 ( 9) link_ALPHA1-6 : bond 0.00843 ( 3) link_ALPHA1-6 : angle 1.42771 ( 9) link_BETA1-4 : bond 0.01542 ( 21) link_BETA1-4 : angle 4.35809 ( 63) link_NAG-ASN : bond 0.00500 ( 48) link_NAG-ASN : angle 2.69600 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7265 (pt0) cc_final: 0.7008 (pt0) REVERT: A 475 MET cc_start: 0.8791 (mmm) cc_final: 0.8542 (mmt) REVERT: B 475 MET cc_start: 0.8757 (mmm) cc_final: 0.8275 (mmt) REVERT: C 100 MET cc_start: 0.7916 (mtp) cc_final: 0.7451 (mtt) REVERT: C 434 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7796 (ttt) outliers start: 38 outliers final: 19 residues processed: 193 average time/residue: 0.1118 time to fit residues: 33.2850 Evaluate side-chains 131 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 465 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 39 optimal weight: 0.0470 chunk 41 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 374 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 650 GLN C 66 HIS C 374 HIS C 655 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107322 restraints weight = 24337.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109608 restraints weight = 18154.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111134 restraints weight = 14664.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112315 restraints weight = 12630.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113023 restraints weight = 11269.772| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14634 Z= 0.150 Angle : 0.688 16.980 19995 Z= 0.330 Chirality : 0.048 0.378 2430 Planarity : 0.004 0.049 2406 Dihedral : 8.570 76.854 3390 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 2.72 % Allowed : 9.50 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.21), residues: 1614 helix: 2.47 (0.28), residues: 327 sheet: -0.42 (0.21), residues: 480 loop : -0.30 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 419 TYR 0.018 0.001 TYR A 486 PHE 0.015 0.002 PHE A 382 TRP 0.014 0.001 TRP B 479 HIS 0.021 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00331 (14523) covalent geometry : angle 0.61269 (19695) SS BOND : bond 0.00244 ( 33) SS BOND : angle 1.83243 ( 66) hydrogen bonds : bond 0.04258 ( 495) hydrogen bonds : angle 5.45861 ( 1404) link_ALPHA1-2 : bond 0.00454 ( 3) link_ALPHA1-2 : angle 1.55662 ( 9) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 1.58862 ( 9) link_ALPHA1-6 : bond 0.00846 ( 3) link_ALPHA1-6 : angle 1.61434 ( 9) link_BETA1-4 : bond 0.01533 ( 21) link_BETA1-4 : angle 4.22643 ( 63) link_NAG-ASN : bond 0.00571 ( 48) link_NAG-ASN : angle 2.12293 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.8737 (mmm) cc_final: 0.8415 (mmt) REVERT: B 213 ILE cc_start: 0.8902 (mm) cc_final: 0.8581 (pt) REVERT: B 475 MET cc_start: 0.8805 (mmm) cc_final: 0.8251 (mmt) REVERT: C 100 MET cc_start: 0.7875 (mtp) cc_final: 0.7586 (mtt) REVERT: C 213 ILE cc_start: 0.8830 (mm) cc_final: 0.8433 (pt) REVERT: C 442 ASN cc_start: 0.6528 (OUTLIER) cc_final: 0.6308 (m-40) outliers start: 40 outliers final: 24 residues processed: 163 average time/residue: 0.1109 time to fit residues: 28.2177 Evaluate side-chains 136 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 655 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104910 restraints weight = 24442.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107217 restraints weight = 18191.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108786 restraints weight = 14671.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109618 restraints weight = 12610.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110682 restraints weight = 11443.002| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 14634 Z= 0.175 Angle : 0.694 17.023 19995 Z= 0.329 Chirality : 0.049 0.379 2430 Planarity : 0.004 0.056 2406 Dihedral : 8.208 72.832 3390 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.60 % Rotamer: Outliers : 2.78 % Allowed : 9.44 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1614 helix: 2.22 (0.28), residues: 345 sheet: -0.28 (0.23), residues: 447 loop : -0.47 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 419 TYR 0.027 0.002 TYR A 302 PHE 0.017 0.002 PHE B 382 TRP 0.015 0.001 TRP C 479 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00407 (14523) covalent geometry : angle 0.61756 (19695) SS BOND : bond 0.00532 ( 33) SS BOND : angle 1.86964 ( 66) hydrogen bonds : bond 0.04023 ( 495) hydrogen bonds : angle 5.35564 ( 1404) link_ALPHA1-2 : bond 0.00319 ( 3) link_ALPHA1-2 : angle 1.51399 ( 9) link_ALPHA1-3 : bond 0.00912 ( 3) link_ALPHA1-3 : angle 1.82118 ( 9) link_ALPHA1-6 : bond 0.00881 ( 3) link_ALPHA1-6 : angle 1.68344 ( 9) link_BETA1-4 : bond 0.01466 ( 21) link_BETA1-4 : angle 4.16965 ( 63) link_NAG-ASN : bond 0.00516 ( 48) link_NAG-ASN : angle 2.22529 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.599 Fit side-chains REVERT: A 475 MET cc_start: 0.8859 (mmm) cc_final: 0.8492 (mmt) REVERT: B 475 MET cc_start: 0.8858 (mmm) cc_final: 0.8433 (mmt) REVERT: C 100 MET cc_start: 0.7906 (mtp) cc_final: 0.7680 (mtt) REVERT: C 213 ILE cc_start: 0.8910 (mm) cc_final: 0.8528 (pt) REVERT: C 442 ASN cc_start: 0.6776 (OUTLIER) cc_final: 0.6553 (m-40) REVERT: C 475 MET cc_start: 0.8360 (mmt) cc_final: 0.8092 (mmt) outliers start: 41 outliers final: 28 residues processed: 148 average time/residue: 0.1091 time to fit residues: 25.3359 Evaluate side-chains 133 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 492 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 0.0470 chunk 122 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 374 HIS B 374 HIS B 425 ASN C 195 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105065 restraints weight = 24330.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107304 restraints weight = 18244.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108860 restraints weight = 14795.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109675 restraints weight = 12751.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.110635 restraints weight = 11583.813| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14634 Z= 0.149 Angle : 0.674 17.170 19995 Z= 0.318 Chirality : 0.048 0.375 2430 Planarity : 0.004 0.052 2406 Dihedral : 8.074 70.090 3390 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 2.99 % Allowed : 9.91 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1614 helix: 2.19 (0.28), residues: 351 sheet: 0.03 (0.24), residues: 408 loop : -0.52 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 419 TYR 0.029 0.002 TYR B 302 PHE 0.015 0.002 PHE A 382 TRP 0.014 0.001 TRP C 479 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00338 (14523) covalent geometry : angle 0.59337 (19695) SS BOND : bond 0.00246 ( 33) SS BOND : angle 2.30603 ( 66) hydrogen bonds : bond 0.03799 ( 495) hydrogen bonds : angle 5.26163 ( 1404) link_ALPHA1-2 : bond 0.00419 ( 3) link_ALPHA1-2 : angle 1.47447 ( 9) link_ALPHA1-3 : bond 0.00927 ( 3) link_ALPHA1-3 : angle 1.71573 ( 9) link_ALPHA1-6 : bond 0.00915 ( 3) link_ALPHA1-6 : angle 1.74615 ( 9) link_BETA1-4 : bond 0.01487 ( 21) link_BETA1-4 : angle 4.12400 ( 63) link_NAG-ASN : bond 0.00553 ( 48) link_NAG-ASN : angle 2.12417 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 120 time to evaluate : 0.553 Fit side-chains REVERT: A 104 MET cc_start: 0.8438 (ttm) cc_final: 0.8210 (ttp) REVERT: A 475 MET cc_start: 0.8859 (mmm) cc_final: 0.8415 (mmt) REVERT: B 419 ARG cc_start: 0.7279 (mtp180) cc_final: 0.7050 (mtp180) REVERT: B 475 MET cc_start: 0.8788 (mmm) cc_final: 0.8296 (mmt) REVERT: C 100 MET cc_start: 0.7864 (mtp) cc_final: 0.7617 (mtt) REVERT: C 281 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8263 (p) REVERT: C 442 ASN cc_start: 0.6753 (OUTLIER) cc_final: 0.6518 (m-40) outliers start: 44 outliers final: 30 residues processed: 156 average time/residue: 0.1091 time to fit residues: 26.6044 Evaluate side-chains 134 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 492 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 88 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 425 ASN B 655 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105385 restraints weight = 24396.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106659 restraints weight = 18663.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107151 restraints weight = 15885.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107831 restraints weight = 14384.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108064 restraints weight = 13955.334| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14634 Z= 0.142 Angle : 0.668 17.100 19995 Z= 0.313 Chirality : 0.048 0.375 2430 Planarity : 0.004 0.051 2406 Dihedral : 7.986 68.189 3390 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.97 % Favored : 95.91 % Rotamer: Outliers : 3.12 % Allowed : 10.73 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1614 helix: 2.20 (0.28), residues: 351 sheet: 0.06 (0.24), residues: 408 loop : -0.55 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 419 TYR 0.024 0.001 TYR A 302 PHE 0.015 0.002 PHE B 382 TRP 0.012 0.001 TRP C 479 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00319 (14523) covalent geometry : angle 0.58946 (19695) SS BOND : bond 0.00260 ( 33) SS BOND : angle 2.24203 ( 66) hydrogen bonds : bond 0.03718 ( 495) hydrogen bonds : angle 5.25572 ( 1404) link_ALPHA1-2 : bond 0.00409 ( 3) link_ALPHA1-2 : angle 1.44093 ( 9) link_ALPHA1-3 : bond 0.00919 ( 3) link_ALPHA1-3 : angle 1.73302 ( 9) link_ALPHA1-6 : bond 0.00923 ( 3) link_ALPHA1-6 : angle 1.76509 ( 9) link_BETA1-4 : bond 0.01438 ( 21) link_BETA1-4 : angle 4.08034 ( 63) link_NAG-ASN : bond 0.00512 ( 48) link_NAG-ASN : angle 2.07759 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.559 Fit side-chains REVERT: A 475 MET cc_start: 0.8810 (mmm) cc_final: 0.8409 (mmt) REVERT: B 419 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6974 (mtp180) REVERT: B 475 MET cc_start: 0.8762 (mmm) cc_final: 0.8270 (mmt) REVERT: C 281 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8325 (p) outliers start: 46 outliers final: 32 residues processed: 156 average time/residue: 0.1072 time to fit residues: 26.2342 Evaluate side-chains 139 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 655 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 655 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 52 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.125043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103117 restraints weight = 24500.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104975 restraints weight = 19187.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105795 restraints weight = 15292.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106474 restraints weight = 14074.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106658 restraints weight = 12878.167| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14634 Z= 0.173 Angle : 0.694 17.132 19995 Z= 0.323 Chirality : 0.049 0.377 2430 Planarity : 0.004 0.057 2406 Dihedral : 8.016 67.374 3390 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 2.78 % Allowed : 12.29 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1614 helix: 2.15 (0.28), residues: 351 sheet: -0.03 (0.24), residues: 414 loop : -0.67 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 419 TYR 0.034 0.002 TYR A 302 PHE 0.015 0.002 PHE A 317 TRP 0.014 0.001 TRP C 479 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00403 (14523) covalent geometry : angle 0.61866 (19695) SS BOND : bond 0.00331 ( 33) SS BOND : angle 2.14078 ( 66) hydrogen bonds : bond 0.03795 ( 495) hydrogen bonds : angle 5.29067 ( 1404) link_ALPHA1-2 : bond 0.00486 ( 3) link_ALPHA1-2 : angle 1.43879 ( 9) link_ALPHA1-3 : bond 0.00862 ( 3) link_ALPHA1-3 : angle 1.84817 ( 9) link_ALPHA1-6 : bond 0.00885 ( 3) link_ALPHA1-6 : angle 1.73942 ( 9) link_BETA1-4 : bond 0.01444 ( 21) link_BETA1-4 : angle 4.08674 ( 63) link_NAG-ASN : bond 0.00481 ( 48) link_NAG-ASN : angle 2.14139 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.589 Fit side-chains REVERT: A 213 ILE cc_start: 0.8997 (mm) cc_final: 0.8596 (pt) REVERT: A 475 MET cc_start: 0.8842 (mmm) cc_final: 0.8455 (mmt) REVERT: B 419 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6900 (mtp180) REVERT: B 475 MET cc_start: 0.8817 (mmm) cc_final: 0.8312 (mmt) outliers start: 41 outliers final: 34 residues processed: 148 average time/residue: 0.1135 time to fit residues: 26.1328 Evaluate side-chains 140 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 492 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 374 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101465 restraints weight = 24660.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102603 restraints weight = 19387.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103366 restraints weight = 17038.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103906 restraints weight = 15183.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104228 restraints weight = 14307.032| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14634 Z= 0.191 Angle : 0.712 17.054 19995 Z= 0.332 Chirality : 0.049 0.378 2430 Planarity : 0.004 0.058 2406 Dihedral : 7.914 65.786 3390 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.46 % Favored : 95.35 % Rotamer: Outliers : 3.05 % Allowed : 12.02 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.21), residues: 1614 helix: 2.09 (0.28), residues: 351 sheet: -0.21 (0.24), residues: 399 loop : -0.76 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 419 TYR 0.023 0.002 TYR B 302 PHE 0.016 0.002 PHE B 376 TRP 0.017 0.002 TRP C 479 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00450 (14523) covalent geometry : angle 0.64088 (19695) SS BOND : bond 0.00348 ( 33) SS BOND : angle 1.87386 ( 66) hydrogen bonds : bond 0.03864 ( 495) hydrogen bonds : angle 5.35392 ( 1404) link_ALPHA1-2 : bond 0.00430 ( 3) link_ALPHA1-2 : angle 1.38163 ( 9) link_ALPHA1-3 : bond 0.00821 ( 3) link_ALPHA1-3 : angle 1.92300 ( 9) link_ALPHA1-6 : bond 0.00858 ( 3) link_ALPHA1-6 : angle 1.66848 ( 9) link_BETA1-4 : bond 0.01416 ( 21) link_BETA1-4 : angle 4.09566 ( 63) link_NAG-ASN : bond 0.00422 ( 48) link_NAG-ASN : angle 2.18309 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.573 Fit side-chains REVERT: A 213 ILE cc_start: 0.9036 (mm) cc_final: 0.8651 (pt) REVERT: A 475 MET cc_start: 0.8875 (mmm) cc_final: 0.8414 (mmt) REVERT: B 419 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6853 (mtp180) REVERT: B 475 MET cc_start: 0.8795 (mmm) cc_final: 0.8344 (mmt) outliers start: 45 outliers final: 35 residues processed: 149 average time/residue: 0.1046 time to fit residues: 24.6456 Evaluate side-chains 137 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 492 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 137 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 374 HIS A 422 GLN B 66 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 655 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.102370 restraints weight = 24471.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104231 restraints weight = 19833.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105279 restraints weight = 16033.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105748 restraints weight = 14254.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105866 restraints weight = 13396.312| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14634 Z= 0.143 Angle : 0.685 17.208 19995 Z= 0.318 Chirality : 0.048 0.373 2430 Planarity : 0.004 0.056 2406 Dihedral : 7.734 63.647 3390 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.72 % Rotamer: Outliers : 2.58 % Allowed : 12.97 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1614 helix: 2.12 (0.28), residues: 351 sheet: -0.10 (0.24), residues: 408 loop : -0.73 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 419 TYR 0.025 0.001 TYR A 302 PHE 0.017 0.002 PHE A 382 TRP 0.015 0.001 TRP C 479 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00323 (14523) covalent geometry : angle 0.61338 (19695) SS BOND : bond 0.00303 ( 33) SS BOND : angle 1.91885 ( 66) hydrogen bonds : bond 0.03665 ( 495) hydrogen bonds : angle 5.26782 ( 1404) link_ALPHA1-2 : bond 0.00489 ( 3) link_ALPHA1-2 : angle 1.36633 ( 9) link_ALPHA1-3 : bond 0.00898 ( 3) link_ALPHA1-3 : angle 1.77538 ( 9) link_ALPHA1-6 : bond 0.00889 ( 3) link_ALPHA1-6 : angle 1.70412 ( 9) link_BETA1-4 : bond 0.01498 ( 21) link_BETA1-4 : angle 4.07107 ( 63) link_NAG-ASN : bond 0.00457 ( 48) link_NAG-ASN : angle 2.06340 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ILE cc_start: 0.9020 (mm) cc_final: 0.8619 (pt) REVERT: A 475 MET cc_start: 0.8811 (mmm) cc_final: 0.8365 (mmt) REVERT: B 122 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8983 (tt) REVERT: B 419 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6877 (mtp180) REVERT: B 475 MET cc_start: 0.8790 (mmm) cc_final: 0.8256 (mmt) outliers start: 38 outliers final: 31 residues processed: 143 average time/residue: 0.1033 time to fit residues: 23.4397 Evaluate side-chains 135 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain C residue 655 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 159 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 422 GLN A 655 GLN B 422 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101897 restraints weight = 24725.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103709 restraints weight = 19229.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104306 restraints weight = 15412.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104988 restraints weight = 14405.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.105505 restraints weight = 13257.538| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14634 Z= 0.166 Angle : 0.703 17.144 19995 Z= 0.327 Chirality : 0.049 0.378 2430 Planarity : 0.004 0.054 2406 Dihedral : 7.669 63.259 3390 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.58 % Favored : 95.23 % Rotamer: Outliers : 2.51 % Allowed : 13.44 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.21), residues: 1614 helix: 2.04 (0.28), residues: 351 sheet: -0.13 (0.24), residues: 408 loop : -0.78 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 419 TYR 0.025 0.001 TYR A 302 PHE 0.023 0.002 PHE B 53 TRP 0.014 0.001 TRP C 479 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00384 (14523) covalent geometry : angle 0.63520 (19695) SS BOND : bond 0.00298 ( 33) SS BOND : angle 1.86765 ( 66) hydrogen bonds : bond 0.03740 ( 495) hydrogen bonds : angle 5.27796 ( 1404) link_ALPHA1-2 : bond 0.00488 ( 3) link_ALPHA1-2 : angle 1.34309 ( 9) link_ALPHA1-3 : bond 0.00855 ( 3) link_ALPHA1-3 : angle 1.85605 ( 9) link_ALPHA1-6 : bond 0.00869 ( 3) link_ALPHA1-6 : angle 1.65958 ( 9) link_BETA1-4 : bond 0.01475 ( 21) link_BETA1-4 : angle 4.06516 ( 63) link_NAG-ASN : bond 0.00488 ( 48) link_NAG-ASN : angle 2.03651 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.8825 (mmm) cc_final: 0.8334 (mmt) REVERT: B 122 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8993 (tt) REVERT: B 320 MET cc_start: 0.7116 (mmm) cc_final: 0.6693 (mmm) REVERT: B 419 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6874 (mtp180) REVERT: B 475 MET cc_start: 0.8769 (mmm) cc_final: 0.8209 (mmt) REVERT: C 434 MET cc_start: 0.7831 (ttt) cc_final: 0.7581 (ttp) outliers start: 37 outliers final: 31 residues processed: 133 average time/residue: 0.1045 time to fit residues: 22.0380 Evaluate side-chains 133 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 655 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 492 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 77 optimal weight: 0.0470 chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 240 ASN B 619 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.125259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102863 restraints weight = 24509.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105094 restraints weight = 19447.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106123 restraints weight = 15751.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106576 restraints weight = 13739.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106672 restraints weight = 12989.268| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14634 Z= 0.132 Angle : 0.678 17.144 19995 Z= 0.314 Chirality : 0.048 0.373 2430 Planarity : 0.004 0.051 2406 Dihedral : 7.500 61.745 3390 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.40 % Favored : 95.42 % Rotamer: Outliers : 2.24 % Allowed : 13.51 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1614 helix: 2.01 (0.28), residues: 351 sheet: -0.11 (0.24), residues: 408 loop : -0.80 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 419 TYR 0.021 0.001 TYR A 302 PHE 0.023 0.002 PHE B 53 TRP 0.025 0.001 TRP A 112 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00296 (14523) covalent geometry : angle 0.61021 (19695) SS BOND : bond 0.00265 ( 33) SS BOND : angle 1.68264 ( 66) hydrogen bonds : bond 0.03608 ( 495) hydrogen bonds : angle 5.22866 ( 1404) link_ALPHA1-2 : bond 0.00494 ( 3) link_ALPHA1-2 : angle 1.34413 ( 9) link_ALPHA1-3 : bond 0.00898 ( 3) link_ALPHA1-3 : angle 1.75593 ( 9) link_ALPHA1-6 : bond 0.00893 ( 3) link_ALPHA1-6 : angle 1.66970 ( 9) link_BETA1-4 : bond 0.01478 ( 21) link_BETA1-4 : angle 4.04041 ( 63) link_NAG-ASN : bond 0.00485 ( 48) link_NAG-ASN : angle 1.98419 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2063.01 seconds wall clock time: 36 minutes 55.82 seconds (2215.82 seconds total)