Starting phenix.real_space_refine on Sun Aug 24 13:41:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb5_40291/08_2025/8sb5_40291_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb5_40291/08_2025/8sb5_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_40291/08_2025/8sb5_40291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb5_40291/08_2025/8sb5_40291.map" model { file = "/net/cci-nas-00/data/ceres_data/8sb5_40291/08_2025/8sb5_40291_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb5_40291/08_2025/8sb5_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-2.0-5787/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: 4.75, per 1000 atoms: 0.24 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: 1.75 Conformation dependent library (CDL) restraints added in 844.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.80 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: 3.88 Time building geometry restraints manager: 2.29 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.430 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 aren 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 : 0.685 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: 0.8929 (mm) cc_final: 0.8614 (mm) REVERT: B 535 MET cc_start: 0.7560 (mmm) cc_final: 0.7324 (mmt) REVERT: D 271 HIS cc_start: 0.6171 (m-70) cc_final: 0.5957 (m-70) REVERT: H 27 TYR cc_start: 0.4325 (m-10) cc_final: 0.3870 (m-80) REVERT: M 6 GLN cc_start: 0.7203 (mt0) cc_final: 0.6878 (mt0) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.1395 time to fit residues: 80.2732 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 : 0.733 ------------------------------------------------------------------------------- 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 229 ASN K 258 GLN K 289 HIS ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.168900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157824 restraints weight = 28220.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.156757 restraints weight = 42699.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156483 restraints weight = 45350.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155744 restraints weight = 41531.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151198 restraints weight = 41110.002| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20752 Z= 0.186 Angle : 0.814 13.306 28376 Z= 0.402 Chirality : 0.048 0.235 3374 Planarity : 0.005 0.054 3469 Dihedral : 13.272 88.149 4119 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.79 % Favored : 95.01 % Rotamer: Outliers : 1.12 % Allowed : 7.79 % Favored : 91.09 % 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 aren not related in a simple way. whole: -1.27 (0.16), residues: 2463 helix: 0.05 (0.27), residues: 372 sheet: -0.65 (0.20), residues: 641 loop : -1.16 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 542 TYR 0.024 0.002 TYR D 281 PHE 0.026 0.002 PHE A 391 TRP 0.022 0.002 TRP K 35 HIS 0.007 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00416 (20633) covalent geometry : angle 0.77674 (28064) SS BOND : bond 0.00442 ( 45) SS BOND : angle 1.13663 ( 90) hydrogen bonds : bond 0.04859 ( 677) hydrogen bonds : angle 6.17203 ( 1920) link_ALPHA1-2 : bond 0.01121 ( 20) link_ALPHA1-2 : angle 2.92136 ( 60) link_ALPHA1-3 : bond 0.01076 ( 12) link_ALPHA1-3 : angle 1.73052 ( 36) link_ALPHA1-6 : bond 0.00433 ( 6) link_ALPHA1-6 : angle 1.69747 ( 18) link_BETA1-4 : bond 0.01323 ( 24) link_BETA1-4 : angle 3.51614 ( 72) link_NAG-ASN : bond 0.00707 ( 12) link_NAG-ASN : angle 2.18486 ( 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 322 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 298 time to evaluate : 0.759 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 112 TRP cc_start: 0.6884 (m-90) cc_final: 0.6536 (t-100) REVERT: A 374 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.8583 (t70) REVERT: B 542 ARG cc_start: 0.7235 (ttm170) cc_final: 0.6748 (ttm170) REVERT: H 115 ASP cc_start: 0.7017 (m-30) cc_final: 0.6774 (m-30) REVERT: K 112 TRP cc_start: 0.7450 (t-100) cc_final: 0.7240 (t-100) REVERT: K 500 ARG cc_start: 0.7612 (ptp-170) cc_final: 0.7403 (ptp-170) outliers start: 24 outliers final: 14 residues processed: 313 average time/residue: 0.1411 time to fit residues: 68.4971 Evaluate side-chains 267 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 295 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 295 VAL 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 K residue 295 VAL 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: 6.9990 chunk 4 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 289 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN F 374 HIS G 543 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.149264 restraints weight = 28720.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148142 restraints weight = 41910.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147813 restraints weight = 44758.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147077 restraints weight = 41547.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146997 restraints weight = 41319.648| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20752 Z= 0.264 Angle : 0.846 12.832 28376 Z= 0.420 Chirality : 0.049 0.213 3374 Planarity : 0.005 0.059 3469 Dihedral : 12.180 91.333 4119 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.01 % Favored : 93.79 % Rotamer: Outliers : 2.80 % Allowed : 10.96 % Favored : 86.24 % 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 aren not related in a simple way. whole: -1.31 (0.16), residues: 2463 helix: 0.13 (0.26), residues: 378 sheet: -0.79 (0.19), residues: 656 loop : -1.17 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 542 TYR 0.027 0.003 TYR N 319 PHE 0.032 0.003 PHE K 391 TRP 0.034 0.003 TRP K 35 HIS 0.022 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00616 (20633) covalent geometry : angle 0.80701 (28064) SS BOND : bond 0.00765 ( 45) SS BOND : angle 1.76508 ( 90) hydrogen bonds : bond 0.04869 ( 677) hydrogen bonds : angle 5.92598 ( 1920) link_ALPHA1-2 : bond 0.01089 ( 20) link_ALPHA1-2 : angle 2.87979 ( 60) link_ALPHA1-3 : bond 0.01097 ( 12) link_ALPHA1-3 : angle 1.58210 ( 36) link_ALPHA1-6 : bond 0.00372 ( 6) link_ALPHA1-6 : angle 1.94683 ( 18) link_BETA1-4 : bond 0.01270 ( 24) link_BETA1-4 : angle 3.36865 ( 72) link_NAG-ASN : bond 0.01020 ( 12) link_NAG-ASN : angle 2.78775 ( 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 323 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 263 time to evaluate : 0.543 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 395 TYR cc_start: 0.6252 (t80) cc_final: 0.5915 (t80) REVERT: B 647 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7914 (mm-30) REVERT: F 374 HIS cc_start: 0.9265 (OUTLIER) cc_final: 0.8602 (t-170) REVERT: F 434 MET cc_start: 0.8567 (ttp) cc_final: 0.8257 (ttp) REVERT: I 305 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6304 (tp) REVERT: K 112 TRP cc_start: 0.7661 (t-100) cc_final: 0.7306 (t-100) REVERT: K 374 HIS cc_start: 0.9069 (OUTLIER) cc_final: 0.8396 (t-170) REVERT: K 423 ILE cc_start: 0.9225 (mm) cc_final: 0.9020 (mm) REVERT: K 481 SER cc_start: 0.9289 (p) cc_final: 0.9073 (t) REVERT: K 500 ARG cc_start: 0.7691 (ptp-170) cc_final: 0.7445 (ptp-170) REVERT: L 520 LEU cc_start: 0.5846 (mt) cc_final: 0.5598 (mp) REVERT: L 542 ARG cc_start: 0.8520 (ttm110) cc_final: 0.7794 (ttp80) outliers start: 60 outliers final: 30 residues processed: 305 average time/residue: 0.1179 time to fit residues: 57.0854 Evaluate side-chains 276 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 112 TRP Chi-restraints excluded: chain A residue 292 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 44 VAL Chi-restraints excluded: chain F residue 47 GLU 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 G residue 529 THR Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain G residue 580 VAL 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 N residue 279 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 219 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 177 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.173693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157071 restraints weight = 31014.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155811 restraints weight = 43382.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.155389 restraints weight = 45950.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154743 restraints weight = 42726.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154895 restraints weight = 40055.222| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 20752 Z= 0.181 Angle : 0.768 13.959 28376 Z= 0.381 Chirality : 0.047 0.241 3374 Planarity : 0.004 0.056 3469 Dihedral : 10.892 85.431 4119 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.24 % Favored : 94.56 % Rotamer: Outliers : 2.43 % Allowed : 12.41 % Favored : 85.17 % 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 aren not related in a simple way. whole: -1.08 (0.17), residues: 2463 helix: 0.50 (0.27), residues: 372 sheet: -0.54 (0.20), residues: 631 loop : -1.13 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 579 TYR 0.017 0.002 TYR D 268 PHE 0.023 0.002 PHE K 391 TRP 0.022 0.002 TRP G 571 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00414 (20633) covalent geometry : angle 0.73026 (28064) SS BOND : bond 0.00792 ( 45) SS BOND : angle 1.86898 ( 90) hydrogen bonds : bond 0.04154 ( 677) hydrogen bonds : angle 5.53495 ( 1920) link_ALPHA1-2 : bond 0.00969 ( 20) link_ALPHA1-2 : angle 2.60996 ( 60) link_ALPHA1-3 : bond 0.01039 ( 12) link_ALPHA1-3 : angle 1.55383 ( 36) link_ALPHA1-6 : bond 0.00362 ( 6) link_ALPHA1-6 : angle 1.87875 ( 18) link_BETA1-4 : bond 0.01179 ( 24) link_BETA1-4 : angle 3.11227 ( 72) link_NAG-ASN : bond 0.00722 ( 12) link_NAG-ASN : angle 2.25348 ( 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: 52 poor density : 261 time to evaluate : 0.735 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: symmetry clash REVERT: A 99 ASP cc_start: 0.7962 (p0) cc_final: 0.7467 (t0) REVERT: B 542 ARG cc_start: 0.7450 (ttm170) cc_final: 0.6953 (ttm170) REVERT: F 298 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8343 (ttp-170) REVERT: K 112 TRP cc_start: 0.7393 (t-100) cc_final: 0.6674 (t-100) REVERT: K 423 ILE cc_start: 0.9193 (mm) cc_final: 0.8968 (mm) REVERT: K 481 SER cc_start: 0.9274 (p) cc_final: 0.9073 (t) REVERT: M 81 MET cc_start: 0.7449 (tmm) cc_final: 0.7122 (tmm) outliers start: 52 outliers final: 33 residues processed: 303 average time/residue: 0.1436 time to fit residues: 67.9740 Evaluate side-chains 273 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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 A residue 481 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 98 THR 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 295 VAL Chi-restraints excluded: chain F residue 298 ARG 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 H residue 98 THR Chi-restraints excluded: chain H residue 103 SER 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 245 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain N residue 259 VAL 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: 1.9990 chunk 223 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS F 352 HIS F 374 HIS F 422 GLN G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 352 HIS ** K 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152213 restraints weight = 31062.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.151157 restraints weight = 41973.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151316 restraints weight = 42492.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150784 restraints weight = 37452.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150333 restraints weight = 39441.310| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 20752 Z= 0.296 Angle : 0.860 13.189 28376 Z= 0.426 Chirality : 0.049 0.238 3374 Planarity : 0.005 0.058 3469 Dihedral : 10.891 90.231 4119 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.51 % Favored : 92.29 % Rotamer: Outliers : 3.40 % Allowed : 14.04 % Favored : 82.56 % 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 aren not related in a simple way. whole: -1.23 (0.17), residues: 2463 helix: 0.34 (0.27), residues: 384 sheet: -0.63 (0.20), residues: 639 loop : -1.23 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 579 TYR 0.024 0.003 TYR F 486 PHE 0.025 0.003 PHE D 323 TRP 0.024 0.003 TRP G 571 HIS 0.021 0.003 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00696 (20633) covalent geometry : angle 0.82521 (28064) SS BOND : bond 0.00757 ( 45) SS BOND : angle 1.64637 ( 90) hydrogen bonds : bond 0.04513 ( 677) hydrogen bonds : angle 5.73559 ( 1920) link_ALPHA1-2 : bond 0.01007 ( 20) link_ALPHA1-2 : angle 2.55941 ( 60) link_ALPHA1-3 : bond 0.01038 ( 12) link_ALPHA1-3 : angle 1.66168 ( 36) link_ALPHA1-6 : bond 0.00329 ( 6) link_ALPHA1-6 : angle 1.91124 ( 18) link_BETA1-4 : bond 0.01274 ( 24) link_BETA1-4 : angle 3.24839 ( 72) link_NAG-ASN : bond 0.01129 ( 12) link_NAG-ASN : angle 2.92904 ( 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 319 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 246 time to evaluate : 0.766 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 395 TYR cc_start: 0.6190 (t80) cc_final: 0.5915 (t80) REVERT: B 542 ARG cc_start: 0.7664 (ttm170) cc_final: 0.6597 (ttm170) REVERT: F 374 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.8953 (t-170) REVERT: F 481 SER cc_start: 0.9389 (p) cc_final: 0.9135 (t) REVERT: I 305 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6171 (tp) REVERT: K 112 TRP cc_start: 0.7535 (t-100) cc_final: 0.6745 (t-100) REVERT: K 423 ILE cc_start: 0.9231 (mm) cc_final: 0.8908 (mm) REVERT: K 500 ARG cc_start: 0.7683 (ptp-170) cc_final: 0.7428 (ptp-170) REVERT: L 542 ARG cc_start: 0.8344 (ttm110) cc_final: 0.7536 (ttp-110) REVERT: M 45 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6464 (mp) outliers start: 73 outliers final: 52 residues processed: 307 average time/residue: 0.1329 time to fit residues: 64.4967 Evaluate side-chains 289 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 44 VAL 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 298 ARG Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 418 CYS 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 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 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 G residue 580 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 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 364 SER Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 45 LEU 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: 3.9990 chunk 184 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 GLN F 374 HIS G 616 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 HIS ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 616 ASN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.174384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158164 restraints weight = 30660.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156499 restraints weight = 48074.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.156318 restraints weight = 48763.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156099 restraints weight = 39748.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155916 restraints weight = 39173.400| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20752 Z= 0.143 Angle : 0.724 13.388 28376 Z= 0.362 Chirality : 0.046 0.218 3374 Planarity : 0.004 0.055 3469 Dihedral : 9.876 80.683 4119 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.99 % Favored : 94.80 % Rotamer: Outliers : 2.57 % Allowed : 15.16 % Favored : 82.28 % 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 aren not related in a simple way. whole: -0.87 (0.17), residues: 2463 helix: 0.82 (0.27), residues: 372 sheet: -0.32 (0.21), residues: 586 loop : -1.06 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 579 TYR 0.021 0.002 TYR N 319 PHE 0.018 0.001 PHE K 391 TRP 0.021 0.002 TRP G 571 HIS 0.015 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00317 (20633) covalent geometry : angle 0.69240 (28064) SS BOND : bond 0.00596 ( 45) SS BOND : angle 1.45951 ( 90) hydrogen bonds : bond 0.03820 ( 677) hydrogen bonds : angle 5.29509 ( 1920) link_ALPHA1-2 : bond 0.00887 ( 20) link_ALPHA1-2 : angle 2.39344 ( 60) link_ALPHA1-3 : bond 0.01064 ( 12) link_ALPHA1-3 : angle 1.47936 ( 36) link_ALPHA1-6 : bond 0.00372 ( 6) link_ALPHA1-6 : angle 1.81520 ( 18) link_BETA1-4 : bond 0.01123 ( 24) link_BETA1-4 : angle 2.92136 ( 72) link_NAG-ASN : bond 0.00525 ( 12) link_NAG-ASN : angle 1.89734 ( 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 324 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.668 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 417 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8350 (mm-40) REVERT: B 542 ARG cc_start: 0.7518 (ttm170) cc_final: 0.6872 (ttm170) REVERT: C 47 TRP cc_start: 0.8216 (t60) cc_final: 0.7886 (t60) REVERT: D 336 LYS cc_start: 0.7815 (tptp) cc_final: 0.7525 (ttmt) REVERT: F 374 HIS cc_start: 0.9041 (OUTLIER) cc_final: 0.8491 (t-170) REVERT: H 47 TRP cc_start: 0.7937 (t60) cc_final: 0.7437 (t60) REVERT: I 305 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6067 (tp) REVERT: K 112 TRP cc_start: 0.7356 (t-100) cc_final: 0.6640 (t-100) REVERT: K 374 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.7980 (t-90) REVERT: K 423 ILE cc_start: 0.9149 (mm) cc_final: 0.8912 (mm) REVERT: L 542 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7443 (ttp-110) REVERT: M 81 MET cc_start: 0.7353 (tmm) cc_final: 0.7135 (tmm) outliers start: 55 outliers final: 35 residues processed: 314 average time/residue: 0.1332 time to fit residues: 66.7798 Evaluate side-chains 285 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 398 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 424 ILE 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 284 ILE Chi-restraints excluded: chain F residue 347 ILE 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 50 TRP 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 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 347 ILE Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain M residue 70 MET Chi-restraints excluded: chain N residue 263 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 154 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** N 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.159165 restraints weight = 30919.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157544 restraints weight = 47677.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156991 restraints weight = 48927.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156104 restraints weight = 44681.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156224 restraints weight = 42930.837| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20752 Z= 0.147 Angle : 0.719 13.019 28376 Z= 0.358 Chirality : 0.046 0.207 3374 Planarity : 0.004 0.052 3469 Dihedral : 9.508 77.728 4119 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.60 % Favored : 94.28 % Rotamer: Outliers : 2.52 % Allowed : 16.51 % 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 aren not related in a simple way. whole: -0.71 (0.17), residues: 2463 helix: 1.05 (0.27), residues: 369 sheet: -0.19 (0.21), residues: 586 loop : -1.00 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 579 TYR 0.036 0.002 TYR K 486 PHE 0.014 0.001 PHE K 391 TRP 0.020 0.002 TRP L 596 HIS 0.018 0.001 HIS K 374 Details of bonding type rmsd covalent geometry : bond 0.00332 (20633) covalent geometry : angle 0.68935 (28064) SS BOND : bond 0.00577 ( 45) SS BOND : angle 1.30666 ( 90) hydrogen bonds : bond 0.03703 ( 677) hydrogen bonds : angle 5.18940 ( 1920) link_ALPHA1-2 : bond 0.00848 ( 20) link_ALPHA1-2 : angle 2.32459 ( 60) link_ALPHA1-3 : bond 0.01063 ( 12) link_ALPHA1-3 : angle 1.44122 ( 36) link_ALPHA1-6 : bond 0.00392 ( 6) link_ALPHA1-6 : angle 1.76401 ( 18) link_BETA1-4 : bond 0.01114 ( 24) link_BETA1-4 : angle 2.91714 ( 72) link_NAG-ASN : bond 0.00582 ( 12) link_NAG-ASN : angle 1.86080 ( 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 315 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 0.779 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 298 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8478 (ttp-170) REVERT: A 417 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8219 (mm-40) REVERT: B 542 ARG cc_start: 0.7477 (ttm170) cc_final: 0.6667 (ttm170) REVERT: C 47 TRP cc_start: 0.8251 (t60) cc_final: 0.7987 (t60) REVERT: C 90 ASP cc_start: 0.5993 (m-30) cc_final: 0.5760 (m-30) REVERT: D 336 LYS cc_start: 0.7819 (tptp) cc_final: 0.7569 (ttmt) REVERT: H 47 TRP cc_start: 0.8062 (t60) cc_final: 0.7492 (t60) REVERT: I 305 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.5980 (tp) REVERT: K 112 TRP cc_start: 0.7341 (t-100) cc_final: 0.6655 (t-100) REVERT: K 423 ILE cc_start: 0.9177 (mm) cc_final: 0.8938 (mm) REVERT: K 500 ARG cc_start: 0.7560 (ptp-170) cc_final: 0.7306 (ptp-170) REVERT: L 542 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7390 (ttp-110) REVERT: M 47 TRP cc_start: 0.8151 (t60) cc_final: 0.7378 (t60) outliers start: 54 outliers final: 42 residues processed: 303 average time/residue: 0.1341 time to fit residues: 63.9116 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 : 0.506 ------------------------------------------------------------------------------- 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 244 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 481 SER 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 284 ILE Chi-restraints excluded: chain F residue 295 VAL 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 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 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 292 VAL 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 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: 5.9990 chunk 59 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 217 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 233 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 212 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS D 270 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.168086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157196 restraints weight = 28255.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156656 restraints weight = 45040.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156368 restraints weight = 44516.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156086 restraints weight = 41912.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.156008 restraints weight = 38957.028| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3244 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= 0.135 Angle : 0.694 12.520 28376 Z= 0.346 Chirality : 0.045 0.205 3374 Planarity : 0.004 0.052 3469 Dihedral : 8.859 73.174 4119 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 2.94 % Allowed : 16.18 % Favored : 80.88 % 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 aren not related in a simple way. whole: -0.57 (0.17), residues: 2463 helix: 1.28 (0.27), residues: 369 sheet: 0.01 (0.21), residues: 573 loop : -0.98 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 579 TYR 0.018 0.002 TYR D 268 PHE 0.012 0.001 PHE K 391 TRP 0.032 0.002 TRP G 596 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00298 (20633) covalent geometry : angle 0.66572 (28064) SS BOND : bond 0.00549 ( 45) SS BOND : angle 1.28805 ( 90) hydrogen bonds : bond 0.03528 ( 677) hydrogen bonds : angle 5.03054 ( 1920) link_ALPHA1-2 : bond 0.00828 ( 20) link_ALPHA1-2 : angle 2.20425 ( 60) link_ALPHA1-3 : bond 0.01020 ( 12) link_ALPHA1-3 : angle 1.36675 ( 36) link_ALPHA1-6 : bond 0.00446 ( 6) link_ALPHA1-6 : angle 1.69809 ( 18) link_BETA1-4 : bond 0.01067 ( 24) link_BETA1-4 : angle 2.77087 ( 72) link_NAG-ASN : bond 0.00465 ( 12) link_NAG-ASN : angle 1.69097 ( 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 329 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 266 time to evaluate : 0.897 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: symmetry clash REVERT: A 298 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8320 (ttp-170) REVERT: B 523 LEU cc_start: 0.8938 (mt) cc_final: 0.8734 (mp) REVERT: B 542 ARG cc_start: 0.7426 (ttm170) cc_final: 0.6578 (ttm170) REVERT: C 90 ASP cc_start: 0.5892 (m-30) cc_final: 0.5629 (m-30) REVERT: I 305 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5925 (tp) REVERT: K 112 TRP cc_start: 0.7318 (t-100) cc_final: 0.6639 (t-100) REVERT: K 423 ILE cc_start: 0.9141 (mm) cc_final: 0.8910 (mm) REVERT: L 542 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7646 (ttp-110) REVERT: M 47 TRP cc_start: 0.8172 (t60) cc_final: 0.7862 (t60) outliers start: 63 outliers final: 43 residues processed: 316 average time/residue: 0.1369 time to fit residues: 68.4256 Evaluate side-chains 296 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 298 ARG 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 A residue 481 SER Chi-restraints excluded: chain C residue 50 TRP 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 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 G residue 529 THR Chi-restraints excluded: chain G residue 604 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 10 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 HIS D 301 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 GLN ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.167459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 138)---------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148788 restraints weight = 27976.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147500 restraints weight = 34572.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147568 restraints weight = 40039.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147605 restraints weight = 39211.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147614 restraints weight = 37712.501| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3407 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= 0.147 Angle : 0.711 12.515 28376 Z= 0.355 Chirality : 0.045 0.210 3374 Planarity : 0.004 0.054 3469 Dihedral : 8.621 72.199 4119 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 2.57 % Allowed : 16.84 % Favored : 80.60 % 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 aren not related in a simple way. whole: -0.49 (0.17), residues: 2463 helix: 1.40 (0.27), residues: 369 sheet: 0.09 (0.21), residues: 575 loop : -0.95 (0.17), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.022 0.002 TYR K 486 PHE 0.011 0.001 PHE K 376 TRP 0.063 0.002 TRP H 36 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00333 (20633) covalent geometry : angle 0.68429 (28064) SS BOND : bond 0.00591 ( 45) SS BOND : angle 1.33793 ( 90) hydrogen bonds : bond 0.03540 ( 677) hydrogen bonds : angle 5.03910 ( 1920) link_ALPHA1-2 : bond 0.00823 ( 20) link_ALPHA1-2 : angle 2.15593 ( 60) link_ALPHA1-3 : bond 0.01011 ( 12) link_ALPHA1-3 : angle 1.35623 ( 36) link_ALPHA1-6 : bond 0.00468 ( 6) link_ALPHA1-6 : angle 1.66710 ( 18) link_BETA1-4 : bond 0.01030 ( 24) link_BETA1-4 : angle 2.74454 ( 72) link_NAG-ASN : bond 0.00525 ( 12) link_NAG-ASN : angle 1.75673 ( 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 313 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 0.786 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: 0.7031 (m-30) cc_final: 0.6408 (t0) REVERT: A 298 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8343 (ttp-170) REVERT: B 542 ARG cc_start: 0.7374 (ttm170) cc_final: 0.6444 (ttm170) REVERT: C 90 ASP cc_start: 0.5862 (m-30) cc_final: 0.5642 (m-30) REVERT: H 70 MET cc_start: 0.7232 (mtt) cc_final: 0.5975 (mmt) REVERT: I 305 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5808 (tp) REVERT: K 112 TRP cc_start: 0.7331 (t-100) cc_final: 0.6696 (t-100) REVERT: K 423 ILE cc_start: 0.9145 (mm) cc_final: 0.8915 (mm) REVERT: K 434 MET cc_start: 0.8599 (ttp) cc_final: 0.8398 (ttp) REVERT: L 542 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7617 (ttp-110) REVERT: L 645 LEU cc_start: 0.8289 (mt) cc_final: 0.7939 (tp) REVERT: M 47 TRP cc_start: 0.8166 (t60) cc_final: 0.7834 (t60) outliers start: 55 outliers final: 46 residues processed: 301 average time/residue: 0.1424 time to fit residues: 67.6946 Evaluate side-chains 294 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 298 ARG 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 A residue 481 SER 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 301 ASN 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 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 G residue 529 THR Chi-restraints excluded: chain G residue 604 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 239 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN C 116 HIS D 270 GLN G 540 GLN ** 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 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149828 restraints weight = 28190.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.149016 restraints weight = 28838.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148696 restraints weight = 31531.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148693 restraints weight = 31906.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148691 restraints weight = 30413.498| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20752 Z= 0.150 Angle : 0.712 12.501 28376 Z= 0.356 Chirality : 0.046 0.214 3374 Planarity : 0.004 0.053 3469 Dihedral : 8.406 70.972 4119 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.20 % Favored : 94.64 % Rotamer: Outliers : 2.52 % Allowed : 16.74 % Favored : 80.74 % 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 aren not related in a simple way. whole: -0.46 (0.17), residues: 2463 helix: 1.44 (0.27), residues: 369 sheet: 0.14 (0.22), residues: 575 loop : -0.95 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 542 TYR 0.022 0.002 TYR I 319 PHE 0.013 0.001 PHE F 210 TRP 0.047 0.002 TRP H 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00339 (20633) covalent geometry : angle 0.68742 (28064) SS BOND : bond 0.00578 ( 45) SS BOND : angle 1.19816 ( 90) hydrogen bonds : bond 0.03563 ( 677) hydrogen bonds : angle 5.01287 ( 1920) link_ALPHA1-2 : bond 0.00814 ( 20) link_ALPHA1-2 : angle 2.11185 ( 60) link_ALPHA1-3 : bond 0.01007 ( 12) link_ALPHA1-3 : angle 1.34761 ( 36) link_ALPHA1-6 : bond 0.00492 ( 6) link_ALPHA1-6 : angle 1.63795 ( 18) link_BETA1-4 : bond 0.01028 ( 24) link_BETA1-4 : angle 2.68227 ( 72) link_NAG-ASN : bond 0.00519 ( 12) link_NAG-ASN : angle 1.74566 ( 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 316 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 262 time to evaluate : 0.759 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: 0.7032 (m-30) cc_final: 0.6474 (t0) REVERT: A 298 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8321 (ttp-170) REVERT: B 542 ARG cc_start: 0.7342 (ttm170) cc_final: 0.6375 (ttm170) REVERT: I 305 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5737 (tp) REVERT: K 112 TRP cc_start: 0.7292 (t-100) cc_final: 0.6668 (t-100) REVERT: K 423 ILE cc_start: 0.9134 (mm) cc_final: 0.8911 (mm) REVERT: K 434 MET cc_start: 0.8604 (ttp) cc_final: 0.8381 (ttp) REVERT: L 542 ARG cc_start: 0.7938 (ttm110) cc_final: 0.7634 (ttp-110) REVERT: M 47 TRP cc_start: 0.8160 (t60) cc_final: 0.7809 (t60) outliers start: 54 outliers final: 46 residues processed: 301 average time/residue: 0.1475 time to fit residues: 69.6570 Evaluate side-chains 302 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 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 298 ARG 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 A residue 481 SER 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 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 G residue 529 THR Chi-restraints excluded: chain G residue 604 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 126 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 HIS D 301 ASN 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 105 HIS ** L 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 301 ASN N 311 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.154045 restraints weight = 28245.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153536 restraints weight = 40635.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.153248 restraints weight = 40869.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.152775 restraints weight = 39771.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.152467 restraints weight = 39490.693| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20752 Z= 0.184 Angle : 0.740 12.713 28376 Z= 0.369 Chirality : 0.047 0.216 3374 Planarity : 0.004 0.054 3469 Dihedral : 8.412 71.791 4119 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.97 % Favored : 93.87 % Rotamer: Outliers : 2.47 % Allowed : 16.70 % 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 aren not related in a simple way. whole: -0.51 (0.17), residues: 2463 helix: 1.41 (0.27), residues: 369 sheet: 0.06 (0.22), residues: 571 loop : -0.97 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 542 TYR 0.020 0.002 TYR A 361 PHE 0.012 0.002 PHE K 376 TRP 0.045 0.002 TRP H 36 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00427 (20633) covalent geometry : angle 0.71577 (28064) SS BOND : bond 0.00615 ( 45) SS BOND : angle 1.24143 ( 90) hydrogen bonds : bond 0.03699 ( 677) hydrogen bonds : angle 5.11976 ( 1920) link_ALPHA1-2 : bond 0.00831 ( 20) link_ALPHA1-2 : angle 2.08343 ( 60) link_ALPHA1-3 : bond 0.00963 ( 12) link_ALPHA1-3 : angle 1.37292 ( 36) link_ALPHA1-6 : bond 0.00520 ( 6) link_ALPHA1-6 : angle 1.63386 ( 18) link_BETA1-4 : bond 0.01027 ( 24) link_BETA1-4 : angle 2.69767 ( 72) link_NAG-ASN : bond 0.00697 ( 12) link_NAG-ASN : angle 1.95947 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.70 seconds wall clock time: 53 minutes 27.27 seconds (3207.27 seconds total)