Starting phenix.real_space_refine on Thu Feb 5 20:38:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb5_40291/02_2026/8sb5_40291_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb5_40291/02_2026/8sb5_40291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sb5_40291/02_2026/8sb5_40291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb5_40291/02_2026/8sb5_40291.map" model { file = "/net/cci-nas-00/data/ceres_data/8sb5_40291/02_2026/8sb5_40291_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb5_40291/02_2026/8sb5_40291_neut.cif" } resolution = 3.9 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= -0.000 sd= 1.000 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 141 5.16 5 C 12620 2.51 5 N 3338 2.21 5 O 4106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s 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: 20205 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3607 Classifications: {'peptide': 461} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "H" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3614 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "M" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "O" 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" 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: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "W" 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.66, per 1000 atoms: 0.23 Number of scatterers: 20205 At special positions: 0 Unit cell: (156, 154.96, 134.16, 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 141 16.00 O 4106 8.00 N 3338 7.00 C 12620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 321 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS I 320 " distance=2.03 Simple disulfide: pdb=" SG CYS I 321 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.04 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 252 " - pdb=" SG CYS N 320 " distance=2.03 Simple disulfide: pdb=" SG CYS N 321 " - pdb=" SG CYS N 331 " 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 J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN J 10 " - " MAN J 11 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " " MAN V 10 " - " MAN V 11 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 10 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 10 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 985.7 milliseconds 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 46 sheets defined 20.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.472A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.957A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.494A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.562A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.285A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.760A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 311 through 315 removed outlier: 3.700A pdb=" N GLU D 315 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.472A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.674A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 4.453A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 596 Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.359A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 3.744A pdb=" N ILE G 642 " --> pdb=" O TYR G 638 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU G 647 " --> pdb=" O TYR G 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 311 through 315 Processing helix chain 'K' and resid 57 through 61 Processing helix chain 'K' and resid 68 through 72 Processing helix chain 'K' and resid 98 through 117 removed outlier: 4.522A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 387 through 390 Processing helix chain 'K' and resid 475 through 481 removed outlier: 3.712A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 534 Processing helix chain 'L' and resid 536 through 543 removed outlier: 4.471A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 596 removed outlier: 3.542A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA L 578 " --> pdb=" O LYS L 574 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.313A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 3.768A pdb=" N ILE L 642 " --> pdb=" O TYR L 638 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU L 647 " --> pdb=" O TYR L 643 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 311 through 315 removed outlier: 3.615A pdb=" N GLU N 315 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.599A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 removed outlier: 4.312A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.746A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.234A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.185A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.234A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 359 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 308 removed outlier: 5.450A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.505A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.811A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP C 50 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 93 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 98 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS C 116 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.811A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP C 50 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 93 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 253 Processing sheet with id=AB5, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.438A pdb=" N TRP D 267 " --> pdb=" O MET D 279 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR D 281 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL D 265 " --> pdb=" O TYR D 281 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.438A pdb=" N TRP D 267 " --> pdb=" O MET D 279 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR D 281 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL D 265 " --> pdb=" O TYR D 281 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 494 through 499 Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.241A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.751A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS F 218 " --> pdb=" O PHE F 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 176 removed outlier: 4.581A pdb=" N ASN F 156 " --> pdb=" O SER F 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.775A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.306A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.186A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.186A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.599A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.306A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 359 " --> pdb=" O TYR F 395 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.457A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.735A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL H 93 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS H 116 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.735A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL H 93 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 248 through 253 Processing sheet with id=AD2, first strand: chain 'I' and resid 277 through 281 removed outlier: 6.478A pdb=" N TRP I 267 " --> pdb=" O MET I 279 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR I 281 " --> pdb=" O VAL I 265 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 265 " --> pdb=" O TYR I 281 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 277 through 281 removed outlier: 6.478A pdb=" N TRP I 267 " --> pdb=" O MET I 279 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR I 281 " --> pdb=" O VAL I 265 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 265 " --> pdb=" O TYR I 281 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 494 through 499 Processing sheet with id=AD5, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.590A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU K 84 " --> pdb=" O THR K 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 55 through 56 Processing sheet with id=AD7, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'K' and resid 169 through 176 removed outlier: 4.361A pdb=" N ASN K 156 " --> pdb=" O SER K 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 259 through 261 removed outlier: 3.787A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.926A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 12.215A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 259 through 261 removed outlier: 3.787A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.926A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 12.215A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 302 through 308 removed outlier: 5.409A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 394 through 395 removed outlier: 3.623A pdb=" N ILE K 359 " --> pdb=" O TYR K 395 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.905A pdb=" N ASN M 59 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP M 50 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL M 93 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS M 116 " --> pdb=" O THR M 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.905A pdb=" N ASN M 59 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP M 50 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL M 93 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 248 through 253 Processing sheet with id=AE9, first strand: chain 'N' and resid 277 through 281 removed outlier: 6.593A pdb=" N TRP N 267 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR N 281 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL N 265 " --> pdb=" O TYR N 281 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 277 through 281 removed outlier: 6.593A pdb=" N TRP N 267 " --> pdb=" O MET N 279 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR N 281 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL N 265 " --> pdb=" O TYR N 281 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 1920 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: 3.84 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4671 1.33 - 1.45: 4828 1.45 - 1.58: 10932 1.58 - 1.70: 10 1.70 - 1.82: 192 Bond restraints: 20633 Sorted by residual: bond pdb=" C1 BMA X 3 " pdb=" C2 BMA X 3 " ideal model delta sigma weight residual 1.519 1.607 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 BMA T 3 " pdb=" C2 BMA T 3 " ideal model delta sigma weight residual 1.519 1.604 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 BMA P 3 " pdb=" C2 BMA P 3 " ideal model delta sigma weight residual 1.519 1.601 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 MAN V 9 " pdb=" C2 MAN V 9 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C2 MAN V 8 " pdb=" O2 MAN V 8 " ideal model delta sigma weight residual 1.407 1.472 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 20628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 26971 2.20 - 4.40: 847 4.40 - 6.60: 191 6.60 - 8.80: 45 8.80 - 11.00: 10 Bond angle restraints: 28064 Sorted by residual: angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.70 -11.00 1.80e+00 3.09e-01 3.73e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 132.61 -10.91 1.80e+00 3.09e-01 3.67e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 132.60 -10.90 1.80e+00 3.09e-01 3.67e+01 angle pdb=" C ASN F 403 " pdb=" N SER F 404 " pdb=" CA SER F 404 " ideal model delta sigma weight residual 121.70 130.99 -9.29 1.80e+00 3.09e-01 2.66e+01 angle pdb=" C ASN K 403 " pdb=" N SER K 404 " pdb=" CA SER K 404 " ideal model delta sigma weight residual 121.70 130.87 -9.17 1.80e+00 3.09e-01 2.60e+01 ... (remaining 28059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 12348 22.74 - 45.48: 661 45.48 - 68.22: 89 68.22 - 90.96: 99 90.96 - 113.69: 48 Dihedral angle restraints: 13245 sinusoidal: 6091 harmonic: 7154 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -149.71 63.71 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS K 119 " pdb=" SG CYS K 119 " pdb=" SG CYS K 205 " pdb=" CB CYS K 205 " ideal model delta sinusoidal sigma weight residual -86.00 -148.18 62.18 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -146.87 60.87 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 13242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2785 0.066 - 0.131: 492 0.131 - 0.197: 83 0.197 - 0.262: 3 0.262 - 0.328: 11 Chirality restraints: 3374 Sorted by residual: chirality pdb=" CA THR A 123 " pdb=" N THR A 123 " pdb=" C THR A 123 " pdb=" CB THR A 123 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3371 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG M 84 " -0.364 9.50e-02 1.11e+02 1.63e-01 1.78e+01 pdb=" NE ARG M 84 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG M 84 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG M 84 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG M 84 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 596 " 0.028 2.00e-02 2.50e+03 1.91e-02 9.16e+00 pdb=" CG TRP L 596 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP L 596 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP L 596 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP L 596 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 596 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP L 596 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 596 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 596 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 596 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 596 " 0.024 2.00e-02 2.50e+03 1.69e-02 7.12e+00 pdb=" CG TRP B 596 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 596 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 596 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 596 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 596 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 596 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 596 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 596 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 596 " 0.001 2.00e-02 2.50e+03 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 386 2.66 - 3.22: 19495 3.22 - 3.78: 29478 3.78 - 4.34: 41440 4.34 - 4.90: 69021 Nonbonded interactions: 159820 Sorted by model distance: nonbonded pdb=" OG1 THR M 28 " pdb=" OD2 ASP M 31 " model vdw 2.103 3.040 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR B 606 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASN K 463 " pdb=" OG1 THR K 465 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR G 529 " pdb=" O ASP G 624 " model vdw 2.143 3.040 nonbonded pdb=" OG SER I 295 " pdb=" OG1 THR I 306 " model vdw 2.160 3.040 ... (remaining 159815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'F' and (resid 32 through 443 or resid 445 through 505)) selection = (chain 'K' and (resid 32 through 443 or resid 445 through 505)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.500 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 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 : 0.006 0.114 20752 Z= 0.286 Angle : 1.058 14.732 28376 Z= 0.521 Chirality : 0.055 0.328 3374 Planarity : 0.006 0.163 3469 Dihedral : 17.058 113.694 8534 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.20 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.51 (0.16), residues: 2463 helix: -0.60 (0.26), residues: 399 sheet: -0.72 (0.20), residues: 614 loop : -1.24 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 84 TYR 0.032 0.003 TYR K 395 PHE 0.010 0.001 PHE A 376 TRP 0.051 0.003 TRP L 596 HIS 0.012 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00602 (20633) covalent geometry : angle 0.99624 (28064) SS BOND : bond 0.00318 ( 45) SS BOND : angle 1.45326 ( 90) hydrogen bonds : bond 0.22082 ( 677) hydrogen bonds : angle 9.05040 ( 1920) link_ALPHA1-2 : bond 0.01397 ( 20) link_ALPHA1-2 : angle 4.71896 ( 60) link_ALPHA1-3 : bond 0.00937 ( 12) link_ALPHA1-3 : angle 3.09838 ( 36) link_ALPHA1-6 : bond 0.00514 ( 6) link_ALPHA1-6 : angle 2.84282 ( 18) link_BETA1-4 : bond 0.01158 ( 24) link_BETA1-4 : angle 4.83187 ( 72) link_NAG-ASN : bond 0.00648 ( 12) link_NAG-ASN : angle 2.58635 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 ILE cc_start: 0.8944 (mm) cc_final: 0.8619 (mm) REVERT: B 535 MET cc_start: 0.7558 (mmm) cc_final: 0.7320 (mmt) REVERT: D 271 HIS cc_start: 0.6170 (m-70) cc_final: 0.5954 (m-70) REVERT: F 99 ASP cc_start: 0.7787 (p0) cc_final: 0.7583 (p0) REVERT: H 27 TYR cc_start: 0.4329 (m-10) cc_final: 0.3875 (m-80) REVERT: M 6 GLN cc_start: 0.7196 (mt0) cc_final: 0.6863 (mt0) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.1351 time to fit residues: 78.2935 Evaluate side-chains 287 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 289 HIS A 374 HIS C 43 GLN F 33 ASN F 229 ASN F 289 HIS G 577 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 229 ASN K 258 GLN K 289 HIS N 270 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.168978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157905 restraints weight = 28128.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.156837 restraints weight = 44064.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156098 restraints weight = 47610.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155188 restraints weight = 45132.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155325 restraints weight = 43376.648| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20752 Z= 0.187 Angle : 0.814 13.240 28376 Z= 0.405 Chirality : 0.048 0.238 3374 Planarity : 0.005 0.055 3469 Dihedral : 13.734 89.651 4119 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.79 % Favored : 94.97 % Rotamer: Outliers : 0.89 % Allowed : 7.65 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.28 (0.17), residues: 2463 helix: 0.02 (0.27), residues: 372 sheet: -0.67 (0.20), residues: 645 loop : -1.16 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 298 TYR 0.022 0.002 TYR D 281 PHE 0.028 0.002 PHE A 391 TRP 0.027 0.002 TRP K 35 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00418 (20633) covalent geometry : angle 0.77575 (28064) SS BOND : bond 0.00424 ( 45) SS BOND : angle 1.04420 ( 90) hydrogen bonds : bond 0.05098 ( 677) hydrogen bonds : angle 6.33089 ( 1920) link_ALPHA1-2 : bond 0.01170 ( 20) link_ALPHA1-2 : angle 3.09045 ( 60) link_ALPHA1-3 : bond 0.01117 ( 12) link_ALPHA1-3 : angle 1.63827 ( 36) link_ALPHA1-6 : bond 0.00386 ( 6) link_ALPHA1-6 : angle 1.78352 ( 18) link_BETA1-4 : bond 0.01378 ( 24) link_BETA1-4 : angle 3.54583 ( 72) link_NAG-ASN : bond 0.00681 ( 12) link_NAG-ASN : angle 2.20938 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 298 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8522 (t70) REVERT: A 423 ILE cc_start: 0.9249 (mm) cc_final: 0.8941 (mt) REVERT: B 542 ARG cc_start: 0.7208 (ttm170) cc_final: 0.6745 (ttm170) REVERT: D 301 ASN cc_start: 0.5451 (t0) cc_final: 0.5246 (t0) REVERT: F 99 ASP cc_start: 0.7670 (p0) cc_final: 0.7439 (p0) REVERT: H 115 ASP cc_start: 0.6945 (m-30) cc_final: 0.6725 (m-30) REVERT: K 500 ARG cc_start: 0.7537 (ptp-170) cc_final: 0.7323 (ptp-170) outliers start: 19 outliers final: 12 residues processed: 309 average time/residue: 0.1488 time to fit residues: 71.5957 Evaluate side-chains 269 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 256 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN B 651 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 HIS ** N 270 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.165139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.152515 restraints weight = 28520.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146024 restraints weight = 41286.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.143483 restraints weight = 33719.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143022 restraints weight = 42888.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.143061 restraints weight = 40567.766| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20752 Z= 0.217 Angle : 0.801 12.785 28376 Z= 0.398 Chirality : 0.048 0.212 3374 Planarity : 0.005 0.059 3469 Dihedral : 12.247 89.089 4119 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.28 % Favored : 94.52 % Rotamer: Outliers : 2.29 % Allowed : 10.54 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.21 (0.17), residues: 2463 helix: 0.19 (0.27), residues: 375 sheet: -0.70 (0.19), residues: 656 loop : -1.11 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 542 TYR 0.032 0.002 TYR A 486 PHE 0.035 0.002 PHE A 391 TRP 0.031 0.002 TRP K 35 HIS 0.016 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00502 (20633) covalent geometry : angle 0.76247 (28064) SS BOND : bond 0.00487 ( 45) SS BOND : angle 1.67922 ( 90) hydrogen bonds : bond 0.04639 ( 677) hydrogen bonds : angle 5.82886 ( 1920) link_ALPHA1-2 : bond 0.01075 ( 20) link_ALPHA1-2 : angle 2.85755 ( 60) link_ALPHA1-3 : bond 0.01097 ( 12) link_ALPHA1-3 : angle 1.54972 ( 36) link_ALPHA1-6 : bond 0.00398 ( 6) link_ALPHA1-6 : angle 1.88426 ( 18) link_BETA1-4 : bond 0.01302 ( 24) link_BETA1-4 : angle 3.33366 ( 72) link_NAG-ASN : bond 0.00833 ( 12) link_NAG-ASN : angle 2.46005 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7910 (p0) cc_final: 0.7451 (t0) REVERT: A 423 ILE cc_start: 0.9264 (mm) cc_final: 0.9037 (mt) REVERT: B 595 ILE cc_start: 0.9258 (pt) cc_final: 0.8937 (pt) REVERT: D 301 ASN cc_start: 0.5853 (t0) cc_final: 0.5646 (t0) REVERT: F 45 TRP cc_start: 0.7981 (m-10) cc_final: 0.7766 (m-10) REVERT: F 99 ASP cc_start: 0.7712 (p0) cc_final: 0.7493 (p0) REVERT: G 542 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7540 (ttm170) REVERT: H 81 MET cc_start: 0.7678 (tmm) cc_final: 0.7399 (tmm) REVERT: I 305 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.6159 (tp) REVERT: K 374 HIS cc_start: 0.8994 (OUTLIER) cc_final: 0.8445 (t-170) REVERT: K 423 ILE cc_start: 0.9195 (mm) cc_final: 0.8990 (mm) REVERT: K 481 SER cc_start: 0.9230 (p) cc_final: 0.9004 (t) REVERT: L 520 LEU cc_start: 0.5671 (mt) cc_final: 0.5439 (mp) REVERT: L 542 ARG cc_start: 0.8351 (ttm110) cc_final: 0.8026 (ttm170) REVERT: M 81 MET cc_start: 0.7664 (tmm) cc_final: 0.7297 (tmm) outliers start: 49 outliers final: 24 residues processed: 302 average time/residue: 0.1455 time to fit residues: 69.6960 Evaluate side-chains 273 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 51 MET Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 219 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 177 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN G 543 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 616 ASN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.173940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157511 restraints weight = 31082.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156454 restraints weight = 40821.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156120 restraints weight = 45044.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.155459 restraints weight = 40054.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.155534 restraints weight = 40148.717| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20752 Z= 0.190 Angle : 0.763 13.186 28376 Z= 0.379 Chirality : 0.047 0.236 3374 Planarity : 0.005 0.060 3469 Dihedral : 10.913 85.007 4119 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.24 % Favored : 94.56 % Rotamer: Outliers : 2.19 % Allowed : 12.55 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.03 (0.17), residues: 2463 helix: 0.59 (0.27), residues: 369 sheet: -0.50 (0.20), residues: 627 loop : -1.10 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 579 TYR 0.022 0.002 TYR A 486 PHE 0.023 0.002 PHE K 391 TRP 0.022 0.002 TRP G 571 HIS 0.015 0.002 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00434 (20633) covalent geometry : angle 0.72730 (28064) SS BOND : bond 0.00820 ( 45) SS BOND : angle 1.62596 ( 90) hydrogen bonds : bond 0.04146 ( 677) hydrogen bonds : angle 5.48587 ( 1920) link_ALPHA1-2 : bond 0.00975 ( 20) link_ALPHA1-2 : angle 2.61443 ( 60) link_ALPHA1-3 : bond 0.01102 ( 12) link_ALPHA1-3 : angle 1.58679 ( 36) link_ALPHA1-6 : bond 0.00348 ( 6) link_ALPHA1-6 : angle 1.87014 ( 18) link_BETA1-4 : bond 0.01259 ( 24) link_BETA1-4 : angle 3.12685 ( 72) link_NAG-ASN : bond 0.00748 ( 12) link_NAG-ASN : angle 2.25758 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.7957 (p0) cc_final: 0.7467 (t0) REVERT: A 423 ILE cc_start: 0.9233 (mm) cc_final: 0.9009 (mt) REVERT: B 542 ARG cc_start: 0.7485 (ttm170) cc_final: 0.7061 (ttm170) REVERT: B 595 ILE cc_start: 0.9288 (pt) cc_final: 0.8973 (pt) REVERT: B 647 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8084 (mm-30) REVERT: F 99 ASP cc_start: 0.7800 (p0) cc_final: 0.7585 (p0) REVERT: F 434 MET cc_start: 0.8604 (ttp) cc_final: 0.8017 (ttp) REVERT: G 542 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7569 (ttm170) REVERT: K 298 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8544 (ttp-110) REVERT: K 377 ASN cc_start: 0.8313 (t0) cc_final: 0.8112 (t0) REVERT: K 423 ILE cc_start: 0.9215 (mm) cc_final: 0.8983 (mm) REVERT: K 481 SER cc_start: 0.9264 (p) cc_final: 0.8994 (t) REVERT: K 500 ARG cc_start: 0.7658 (ptp-170) cc_final: 0.7450 (ptp-170) REVERT: L 520 LEU cc_start: 0.6027 (mt) cc_final: 0.5808 (mp) REVERT: M 81 MET cc_start: 0.7553 (tmm) cc_final: 0.7346 (tmm) outliers start: 47 outliers final: 28 residues processed: 301 average time/residue: 0.1503 time to fit residues: 70.7571 Evaluate side-chains 273 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 26 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS A 417 GLN B 540 GLN D 301 ASN F 352 HIS F 374 HIS F 422 GLN G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 352 HIS K 374 HIS K 422 GLN L 616 ASN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.168421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.151691 restraints weight = 31104.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150350 restraints weight = 46938.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150207 restraints weight = 51096.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149593 restraints weight = 42288.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149701 restraints weight = 41561.169| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 20752 Z= 0.302 Angle : 0.866 13.509 28376 Z= 0.429 Chirality : 0.049 0.241 3374 Planarity : 0.005 0.060 3469 Dihedral : 10.911 90.521 4119 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.31 % Favored : 92.49 % Rotamer: Outliers : 3.45 % Allowed : 13.43 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.23 (0.17), residues: 2463 helix: 0.41 (0.27), residues: 381 sheet: -0.69 (0.20), residues: 645 loop : -1.22 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 542 TYR 0.022 0.003 TYR F 486 PHE 0.026 0.003 PHE D 323 TRP 0.025 0.003 TRP G 571 HIS 0.010 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00710 (20633) covalent geometry : angle 0.83139 (28064) SS BOND : bond 0.00724 ( 45) SS BOND : angle 1.66188 ( 90) hydrogen bonds : bond 0.04489 ( 677) hydrogen bonds : angle 5.73631 ( 1920) link_ALPHA1-2 : bond 0.01004 ( 20) link_ALPHA1-2 : angle 2.55794 ( 60) link_ALPHA1-3 : bond 0.01036 ( 12) link_ALPHA1-3 : angle 1.67209 ( 36) link_ALPHA1-6 : bond 0.00318 ( 6) link_ALPHA1-6 : angle 1.90522 ( 18) link_BETA1-4 : bond 0.01274 ( 24) link_BETA1-4 : angle 3.25760 ( 72) link_NAG-ASN : bond 0.01161 ( 12) link_NAG-ASN : angle 2.93562 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 257 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 TYR cc_start: 0.6215 (t80) cc_final: 0.5941 (t80) REVERT: B 542 ARG cc_start: 0.7660 (ttm170) cc_final: 0.6758 (ttm170) REVERT: B 595 ILE cc_start: 0.9328 (pt) cc_final: 0.9024 (pt) REVERT: B 647 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8151 (mm-30) REVERT: C 80 TYR cc_start: 0.7346 (m-80) cc_final: 0.7140 (m-10) REVERT: F 112 TRP cc_start: 0.7754 (t-100) cc_final: 0.7502 (t-100) REVERT: F 374 HIS cc_start: 0.9333 (OUTLIER) cc_final: 0.8637 (t-170) REVERT: F 481 SER cc_start: 0.9385 (p) cc_final: 0.9124 (t) REVERT: G 542 ARG cc_start: 0.7708 (ttm170) cc_final: 0.7354 (ttm170) REVERT: I 305 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6176 (tp) REVERT: K 298 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8626 (ttp-170) REVERT: K 423 ILE cc_start: 0.9224 (mm) cc_final: 0.8858 (mm) outliers start: 74 outliers final: 55 residues processed: 315 average time/residue: 0.1498 time to fit residues: 73.9224 Evaluate side-chains 300 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 70 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN F 374 HIS G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 HIS ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.173781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157838 restraints weight = 30713.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156814 restraints weight = 42414.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156295 restraints weight = 44293.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155869 restraints weight = 40281.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155875 restraints weight = 39711.234| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20752 Z= 0.154 Angle : 0.732 12.984 28376 Z= 0.365 Chirality : 0.046 0.213 3374 Planarity : 0.004 0.056 3469 Dihedral : 9.998 81.728 4119 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.28 % Favored : 94.52 % Rotamer: Outliers : 2.61 % Allowed : 14.79 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.88 (0.17), residues: 2463 helix: 0.83 (0.27), residues: 375 sheet: -0.38 (0.21), residues: 586 loop : -1.05 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 293 TYR 0.039 0.002 TYR F 486 PHE 0.017 0.001 PHE A 391 TRP 0.021 0.002 TRP G 571 HIS 0.014 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00346 (20633) covalent geometry : angle 0.69997 (28064) SS BOND : bond 0.00668 ( 45) SS BOND : angle 1.47309 ( 90) hydrogen bonds : bond 0.03825 ( 677) hydrogen bonds : angle 5.30776 ( 1920) link_ALPHA1-2 : bond 0.00905 ( 20) link_ALPHA1-2 : angle 2.39614 ( 60) link_ALPHA1-3 : bond 0.01062 ( 12) link_ALPHA1-3 : angle 1.49112 ( 36) link_ALPHA1-6 : bond 0.00374 ( 6) link_ALPHA1-6 : angle 1.81691 ( 18) link_BETA1-4 : bond 0.01143 ( 24) link_BETA1-4 : angle 2.93653 ( 72) link_NAG-ASN : bond 0.00584 ( 12) link_NAG-ASN : angle 2.03033 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.7477 (ttm170) cc_final: 0.6681 (ttm170) REVERT: B 595 ILE cc_start: 0.9288 (pt) cc_final: 0.9025 (pt) REVERT: B 647 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8111 (mm-30) REVERT: C 47 TRP cc_start: 0.8256 (t60) cc_final: 0.7901 (t60) REVERT: F 481 SER cc_start: 0.9308 (p) cc_final: 0.9100 (t) REVERT: G 542 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7641 (ttm170) REVERT: H 47 TRP cc_start: 0.8062 (t60) cc_final: 0.7651 (t60) REVERT: I 305 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.6014 (tp) REVERT: K 423 ILE cc_start: 0.9164 (mm) cc_final: 0.8904 (mm) outliers start: 56 outliers final: 37 residues processed: 301 average time/residue: 0.1485 time to fit residues: 70.5602 Evaluate side-chains 279 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 70 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 11 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 0.0470 chunk 154 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.173281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156938 restraints weight = 31014.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155696 restraints weight = 46556.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156033 restraints weight = 47742.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155684 restraints weight = 38478.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155823 restraints weight = 38485.315| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20752 Z= 0.172 Angle : 0.735 12.873 28376 Z= 0.365 Chirality : 0.046 0.205 3374 Planarity : 0.004 0.055 3469 Dihedral : 9.666 79.575 4119 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.01 % Favored : 93.83 % Rotamer: Outliers : 2.85 % Allowed : 15.44 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.76 (0.17), residues: 2463 helix: 0.98 (0.27), residues: 375 sheet: -0.20 (0.21), residues: 571 loop : -1.03 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 579 TYR 0.031 0.002 TYR F 486 PHE 0.013 0.002 PHE A 391 TRP 0.031 0.002 TRP B 596 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00393 (20633) covalent geometry : angle 0.70488 (28064) SS BOND : bond 0.00556 ( 45) SS BOND : angle 1.32158 ( 90) hydrogen bonds : bond 0.03731 ( 677) hydrogen bonds : angle 5.21741 ( 1920) link_ALPHA1-2 : bond 0.00883 ( 20) link_ALPHA1-2 : angle 2.32056 ( 60) link_ALPHA1-3 : bond 0.01039 ( 12) link_ALPHA1-3 : angle 1.44899 ( 36) link_ALPHA1-6 : bond 0.00379 ( 6) link_ALPHA1-6 : angle 1.77992 ( 18) link_BETA1-4 : bond 0.01130 ( 24) link_BETA1-4 : angle 2.97518 ( 72) link_NAG-ASN : bond 0.00708 ( 12) link_NAG-ASN : angle 2.05284 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.7521 (ttm170) cc_final: 0.6716 (ttm170) REVERT: B 595 ILE cc_start: 0.9333 (pt) cc_final: 0.9086 (pt) REVERT: B 647 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8211 (mm-30) REVERT: C 47 TRP cc_start: 0.8255 (t60) cc_final: 0.7999 (t60) REVERT: F 481 SER cc_start: 0.9341 (p) cc_final: 0.9102 (t) REVERT: G 542 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7681 (ttm170) REVERT: H 47 TRP cc_start: 0.8071 (t60) cc_final: 0.7596 (t60) REVERT: H 81 MET cc_start: 0.7396 (tmm) cc_final: 0.7128 (tmm) REVERT: I 305 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5977 (tp) REVERT: K 423 ILE cc_start: 0.9179 (mm) cc_final: 0.8934 (mm) REVERT: K 434 MET cc_start: 0.8641 (ttp) cc_final: 0.8438 (ttp) outliers start: 61 outliers final: 44 residues processed: 308 average time/residue: 0.1488 time to fit residues: 72.3775 Evaluate side-chains 292 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 50 TRP Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 182 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 0.0050 chunk 90 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.173064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157740 restraints weight = 31096.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.156588 restraints weight = 49914.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156729 restraints weight = 46513.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156392 restraints weight = 41559.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156404 restraints weight = 38648.810| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20752 Z= 0.176 Angle : 0.729 12.566 28376 Z= 0.364 Chirality : 0.046 0.207 3374 Planarity : 0.004 0.056 3469 Dihedral : 9.322 77.878 4119 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 2.85 % Allowed : 15.49 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.71 (0.17), residues: 2463 helix: 0.91 (0.27), residues: 387 sheet: -0.15 (0.21), residues: 575 loop : -0.98 (0.17), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 298 TYR 0.030 0.002 TYR F 486 PHE 0.015 0.002 PHE K 376 TRP 0.025 0.002 TRP G 596 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00402 (20633) covalent geometry : angle 0.69938 (28064) SS BOND : bond 0.00608 ( 45) SS BOND : angle 1.37691 ( 90) hydrogen bonds : bond 0.03720 ( 677) hydrogen bonds : angle 5.19629 ( 1920) link_ALPHA1-2 : bond 0.00862 ( 20) link_ALPHA1-2 : angle 2.22320 ( 60) link_ALPHA1-3 : bond 0.00973 ( 12) link_ALPHA1-3 : angle 1.43144 ( 36) link_ALPHA1-6 : bond 0.00384 ( 6) link_ALPHA1-6 : angle 1.74638 ( 18) link_BETA1-4 : bond 0.01097 ( 24) link_BETA1-4 : angle 2.88184 ( 72) link_NAG-ASN : bond 0.00693 ( 12) link_NAG-ASN : angle 2.01476 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 TYR cc_start: 0.6451 (t80) cc_final: 0.6139 (t80) REVERT: B 542 ARG cc_start: 0.7523 (ttm170) cc_final: 0.6696 (ttm170) REVERT: B 595 ILE cc_start: 0.9280 (pt) cc_final: 0.9018 (pt) REVERT: B 647 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8149 (mm-30) REVERT: G 542 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7677 (ttm170) REVERT: H 47 TRP cc_start: 0.8103 (t60) cc_final: 0.7575 (t60) REVERT: H 81 MET cc_start: 0.7275 (tmm) cc_final: 0.7033 (tmm) REVERT: I 305 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5958 (tp) REVERT: K 423 ILE cc_start: 0.9182 (mm) cc_final: 0.8915 (mm) REVERT: K 434 MET cc_start: 0.8633 (ttp) cc_final: 0.8410 (ttp) outliers start: 61 outliers final: 50 residues processed: 298 average time/residue: 0.1551 time to fit residues: 72.4493 Evaluate side-chains 294 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 424 ILE Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 50 TRP Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 10 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN G 540 GLN G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 GLN ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.151723 restraints weight = 28232.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.150621 restraints weight = 44794.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.150313 restraints weight = 47279.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149710 restraints weight = 40996.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149506 restraints weight = 42213.531| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20752 Z= 0.198 Angle : 0.752 12.590 28376 Z= 0.375 Chirality : 0.047 0.204 3374 Planarity : 0.005 0.056 3469 Dihedral : 9.233 78.003 4119 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.37 % Favored : 93.50 % Rotamer: Outliers : 2.99 % Allowed : 16.04 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.72 (0.17), residues: 2463 helix: 0.92 (0.27), residues: 387 sheet: -0.17 (0.21), residues: 575 loop : -1.00 (0.17), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 166 TYR 0.029 0.002 TYR F 486 PHE 0.015 0.002 PHE K 376 TRP 0.038 0.002 TRP B 596 HIS 0.007 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00458 (20633) covalent geometry : angle 0.72371 (28064) SS BOND : bond 0.00608 ( 45) SS BOND : angle 1.41748 ( 90) hydrogen bonds : bond 0.03773 ( 677) hydrogen bonds : angle 5.22478 ( 1920) link_ALPHA1-2 : bond 0.00862 ( 20) link_ALPHA1-2 : angle 2.18221 ( 60) link_ALPHA1-3 : bond 0.00958 ( 12) link_ALPHA1-3 : angle 1.42339 ( 36) link_ALPHA1-6 : bond 0.00395 ( 6) link_ALPHA1-6 : angle 1.73423 ( 18) link_BETA1-4 : bond 0.01037 ( 24) link_BETA1-4 : angle 2.88374 ( 72) link_NAG-ASN : bond 0.00778 ( 12) link_NAG-ASN : angle 2.13104 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.7018 (m-30) cc_final: 0.6634 (t0) REVERT: A 395 TYR cc_start: 0.6324 (t80) cc_final: 0.6033 (t80) REVERT: B 542 ARG cc_start: 0.7592 (ttm170) cc_final: 0.6546 (ttm170) REVERT: B 595 ILE cc_start: 0.9308 (pt) cc_final: 0.9060 (pt) REVERT: B 647 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8203 (mm-30) REVERT: G 542 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7670 (ttm170) REVERT: H 47 TRP cc_start: 0.8208 (t60) cc_final: 0.7581 (t60) REVERT: H 81 MET cc_start: 0.7306 (tmm) cc_final: 0.7077 (tmm) REVERT: I 305 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6029 (tp) REVERT: K 423 ILE cc_start: 0.9149 (mm) cc_final: 0.8899 (mm) outliers start: 64 outliers final: 55 residues processed: 302 average time/residue: 0.1465 time to fit residues: 70.0497 Evaluate side-chains 303 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain K residue 424 ILE Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 50 TRP Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 239 optimal weight: 0.0870 chunk 23 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN D 292 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 GLN ** 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 = 0.3911 r_free = 0.3911 target = 0.169987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.159650 restraints weight = 27823.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158484 restraints weight = 38184.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158501 restraints weight = 38599.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157932 restraints weight = 35006.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.157811 restraints weight = 36447.014| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20752 Z= 0.133 Angle : 0.705 12.375 28376 Z= 0.353 Chirality : 0.045 0.209 3374 Planarity : 0.004 0.059 3469 Dihedral : 8.495 71.452 4119 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.79 % Favored : 95.09 % Rotamer: Outliers : 2.43 % Allowed : 16.74 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.55 (0.17), residues: 2463 helix: 1.16 (0.27), residues: 381 sheet: -0.05 (0.21), residues: 575 loop : -0.90 (0.17), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 166 TYR 0.025 0.002 TYR A 486 PHE 0.012 0.001 PHE A 391 TRP 0.045 0.002 TRP G 596 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00294 (20633) covalent geometry : angle 0.68051 (28064) SS BOND : bond 0.00524 ( 45) SS BOND : angle 1.31957 ( 90) hydrogen bonds : bond 0.03449 ( 677) hydrogen bonds : angle 5.00411 ( 1920) link_ALPHA1-2 : bond 0.00808 ( 20) link_ALPHA1-2 : angle 2.08564 ( 60) link_ALPHA1-3 : bond 0.00985 ( 12) link_ALPHA1-3 : angle 1.33500 ( 36) link_ALPHA1-6 : bond 0.00464 ( 6) link_ALPHA1-6 : angle 1.64923 ( 18) link_BETA1-4 : bond 0.00986 ( 24) link_BETA1-4 : angle 2.60533 ( 72) link_NAG-ASN : bond 0.00398 ( 12) link_NAG-ASN : angle 1.57304 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.6821 (m-30) cc_final: 0.6513 (t0) REVERT: B 542 ARG cc_start: 0.7314 (ttm170) cc_final: 0.6416 (ttm170) REVERT: C 105 TYR cc_start: 0.8610 (m-80) cc_final: 0.8311 (m-80) REVERT: G 593 LEU cc_start: 0.8184 (mt) cc_final: 0.7693 (tt) REVERT: H 47 TRP cc_start: 0.8165 (t60) cc_final: 0.7613 (t60) REVERT: I 305 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5863 (tp) REVERT: K 167 ASP cc_start: 0.7026 (m-30) cc_final: 0.6264 (t0) REVERT: K 423 ILE cc_start: 0.9122 (mm) cc_final: 0.8896 (mm) REVERT: K 434 MET cc_start: 0.8513 (ttp) cc_final: 0.8275 (ttp) REVERT: M 47 TRP cc_start: 0.8170 (t60) cc_final: 0.7825 (t60) outliers start: 52 outliers final: 41 residues processed: 308 average time/residue: 0.1413 time to fit residues: 68.3890 Evaluate side-chains 295 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain C residue 50 TRP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 320 CYS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 347 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 201 CYS Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 244 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 424 ILE Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 50 TRP Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 126 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 76 optimal weight: 0.0020 chunk 187 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS F 195 ASN F 258 GLN F 374 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 HIS K 105 HIS ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149599 restraints weight = 28232.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149203 restraints weight = 28849.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149140 restraints weight = 29176.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149072 restraints weight = 30065.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149058 restraints weight = 29218.714| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20752 Z= 0.141 Angle : 0.705 12.504 28376 Z= 0.353 Chirality : 0.045 0.226 3374 Planarity : 0.005 0.105 3469 Dihedral : 8.190 69.909 4119 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.44 % Favored : 94.40 % Rotamer: Outliers : 2.61 % Allowed : 16.74 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.45 (0.17), residues: 2463 helix: 1.51 (0.28), residues: 363 sheet: 0.03 (0.22), residues: 571 loop : -0.90 (0.17), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 542 TYR 0.028 0.002 TYR A 486 PHE 0.011 0.001 PHE F 376 TRP 0.065 0.002 TRP H 36 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00317 (20633) covalent geometry : angle 0.68131 (28064) SS BOND : bond 0.00629 ( 45) SS BOND : angle 1.33323 ( 90) hydrogen bonds : bond 0.03454 ( 677) hydrogen bonds : angle 4.95820 ( 1920) link_ALPHA1-2 : bond 0.00793 ( 20) link_ALPHA1-2 : angle 2.04839 ( 60) link_ALPHA1-3 : bond 0.00978 ( 12) link_ALPHA1-3 : angle 1.31502 ( 36) link_ALPHA1-6 : bond 0.00501 ( 6) link_ALPHA1-6 : angle 1.60217 ( 18) link_BETA1-4 : bond 0.00936 ( 24) link_BETA1-4 : angle 2.56407 ( 72) link_NAG-ASN : bond 0.00487 ( 12) link_NAG-ASN : angle 1.67357 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.37 seconds wall clock time: 54 minutes 16.84 seconds (3256.84 seconds total)