Starting phenix.real_space_refine on Thu Sep 18 12:39:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnk_44728/09_2025/9bnk_44728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnk_44728/09_2025/9bnk_44728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bnk_44728/09_2025/9bnk_44728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnk_44728/09_2025/9bnk_44728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bnk_44728/09_2025/9bnk_44728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnk_44728/09_2025/9bnk_44728.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 118 5.16 5 C 10438 2.51 5 N 2790 2.21 5 O 3401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16747 Number of models: 1 Model: "" Number of chains: 33 Chain: "H" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1084 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 850 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "G" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3509 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "F" Number of atoms: 3578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3578 Classifications: {'peptide': 455} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 432} Chain breaks: 2 Chain: "C" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "A" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 977 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" 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: "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 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 3.96, per 1000 atoms: 0.24 Number of scatterers: 16747 At special positions: 0 Unit cell: (128.65, 124.5, 161.85, 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 118 16.00 O 3401 8.00 N 2790 7.00 C 10438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=1.81 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 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 E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=1.98 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=1.99 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=2.03 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 A 605 " distance=1.96 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA P 3 " - " MAN P 5 " " BMA V 3 " - " MAN V 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG D 1 " - " ASN F 133 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 295 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 332 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 355 " " NAG E 611 " - " ASN E 363 " " NAG E 612 " - " ASN E 386 " " NAG E 613 " - " ASN E 392 " " NAG E 614 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 197 " " NAG F 603 " - " ASN F 234 " " NAG F 604 " - " ASN F 301 " " NAG F 605 " - " ASN F 332 " " NAG F 606 " - " ASN F 339 " " NAG F 607 " - " ASN F 355 " " NAG F 608 " - " ASN F 363 " " NAG F 609 " - " ASN F 386 " " NAG F 610 " - " ASN F 392 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 276 " " NAG G 603 " - " ASN G 301 " " NAG G 604 " - " ASN G 332 " " NAG G 605 " - " ASN G 339 " " NAG G 606 " - " ASN G 355 " " NAG G 607 " - " ASN G 363 " " NAG G 608 " - " ASN G 392 " " NAG I 1 " - " ASN F 160 " " NAG J 1 " - " ASN G 88 " " NAG K 1 " - " ASN G 156 " " NAG M 1 " - " ASN G 160 " " NAG N 1 " - " ASN G 197 " " NAG O 1 " - " ASN G 234 " " NAG P 1 " - " ASN G 262 " " NAG Q 1 " - " ASN G 295 " " NAG R 1 " - " ASN G 386 " " NAG S 1 " - " ASN G 448 " " NAG T 1 " - " ASN E 156 " " NAG U 1 " - " ASN E 160 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN F 156 " " NAG X 1 " - " ASN F 262 " " NAG Y 1 " - " ASN F 276 " " NAG Z 1 " - " ASN F 295 " " NAG a 1 " - " ASN F 448 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 558.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3676 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 32 sheets defined 23.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.624A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.350A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.708A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.863A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 474 through 481 removed outlier: 4.641A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 569 through 595 removed outlier: 4.152A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.596A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.588A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.431A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.579A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.612A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 460 through 464 removed outlier: 4.067A pdb=" N SER E 463 " --> pdb=" O SER E 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 464 " --> pdb=" O THR E 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 460 through 464' Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.736A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.166A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.533A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 335 through 353 removed outlier: 4.184A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE F 353 " --> pdb=" O LEU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.609A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.957A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 543 Processing helix chain 'C' and resid 570 through 595 removed outlier: 3.504A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 616 removed outlier: 4.278A pdb=" N SER C 615 " --> pdb=" O ASN C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 625 removed outlier: 3.524A pdb=" N TRP C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN C 625 " --> pdb=" O GLU C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 3.827A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 661 removed outlier: 3.596A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.696A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.167A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.755A pdb=" N ILE A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 624' Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.013A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.689A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.832A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.617A pdb=" N SER H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLN H 96 " --> pdb=" O LEU H 100R" (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU H 100R" --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 100A Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.843A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 495 through 499 removed outlier: 3.556A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.606A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.530A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AB2, first strand: chain 'G' and resid 154 through 162 Processing sheet with id=AB3, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.194A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 259 through 261 removed outlier: 5.779A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN G 302 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE G 443 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN G 300 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N CYS G 445 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ARG G 298 " --> pdb=" O CYS G 445 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER G 447 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N CYS G 296 " --> pdb=" O SER G 447 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE G 449 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE G 294 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N GLY G 451 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N VAL G 292 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 271 through 273 Processing sheet with id=AB6, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.853A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 393 through 395 removed outlier: 6.229A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 83 through 86 removed outlier: 4.510A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 245 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N VAL E 489 " --> pdb=" O TRP E 45 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TRP E 45 " --> pdb=" O VAL E 489 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ILE E 491 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL E 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.535A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.601A pdb=" N CYS E 131 " --> pdb=" O LYS E 189 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.400A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.707A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.144A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.305A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.621A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.305A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.144A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE E 359 " --> pdb=" O TRP E 395 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 302 through 307 removed outlier: 6.764A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 494 through 499 removed outlier: 4.924A pdb=" N VAL A 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL F 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR F 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS A 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.563A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.538A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 129 through 131 Processing sheet with id=AD1, first strand: chain 'F' and resid 154 through 162 Processing sheet with id=AD2, first strand: chain 'F' and resid 202 through 203 removed outlier: 7.390A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.509A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 11.459A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.941A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.459A pdb=" N CYS F 296 " --> pdb=" O VAL F 442 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N VAL F 442 " --> pdb=" O CYS F 296 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 304 through 307 553 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5095 1.34 - 1.46: 4020 1.46 - 1.58: 7786 1.58 - 1.70: 1 1.70 - 1.83: 158 Bond restraints: 17060 Sorted by residual: bond pdb=" C TYR C 638 " pdb=" O TYR C 638 " ideal model delta sigma weight residual 1.237 1.304 -0.067 1.38e-02 5.25e+03 2.38e+01 bond pdb=" C MET G 475 " pdb=" O MET G 475 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.32e-02 5.74e+03 2.26e+01 bond pdb=" C ASP G 477 " pdb=" O ASP G 477 " ideal model delta sigma weight residual 1.237 1.290 -0.054 1.19e-02 7.06e+03 2.04e+01 bond pdb=" N TYR C 638 " pdb=" CA TYR C 638 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.00e-02 1.00e+04 1.85e+01 bond pdb=" N VAL F 44 " pdb=" CA VAL F 44 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.14e-02 7.69e+03 1.20e+01 ... (remaining 17055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 22648 2.76 - 5.52: 468 5.52 - 8.28: 40 8.28 - 11.04: 8 11.04 - 13.80: 3 Bond angle restraints: 23167 Sorted by residual: angle pdb=" C ARG G 480 " pdb=" CA ARG G 480 " pdb=" CB ARG G 480 " ideal model delta sigma weight residual 110.31 96.51 13.80 2.09e+00 2.29e-01 4.36e+01 angle pdb=" C CYS F 54 " pdb=" CA CYS F 54 " pdb=" CB CYS F 54 " ideal model delta sigma weight residual 111.60 98.63 12.97 2.00e+00 2.50e-01 4.21e+01 angle pdb=" C ASN A 618 " pdb=" CA ASN A 618 " pdb=" CB ASN A 618 " ideal model delta sigma weight residual 109.64 120.06 -10.42 1.77e+00 3.19e-01 3.46e+01 angle pdb=" C ASN F 425 " pdb=" N MET F 426 " pdb=" CA MET F 426 " ideal model delta sigma weight residual 121.54 131.74 -10.20 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C ALA F 70 " pdb=" N THR F 71 " pdb=" CA THR F 71 " ideal model delta sigma weight residual 121.54 131.05 -9.51 1.91e+00 2.74e-01 2.48e+01 ... (remaining 23162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 10543 21.24 - 42.48: 718 42.48 - 63.72: 175 63.72 - 84.97: 30 84.97 - 106.21: 15 Dihedral angle restraints: 11481 sinusoidal: 5804 harmonic: 5677 Sorted by residual: 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 -149.04 63.04 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 155.77 -62.77 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -147.84 61.84 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 11478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 2888 0.330 - 0.660: 3 0.660 - 0.989: 0 0.989 - 1.319: 0 1.319 - 1.649: 1 Chirality restraints: 2892 Sorted by residual: chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 0.75 1.65 2.00e-02 2.50e+03 6.80e+03 chirality pdb=" C1 MAN I 5 " pdb=" O2 MAN I 4 " pdb=" C2 MAN I 5 " pdb=" O5 MAN I 5 " both_signs ideal model delta sigma weight residual False 2.40 2.12 0.28 2.00e-02 2.50e+03 1.92e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.05e+02 ... (remaining 2889 not shown) Planarity restraints: 2888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.088 2.00e-02 2.50e+03 7.42e-02 6.88e+01 pdb=" C7 NAG K 2 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.122 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.084 2.00e-02 2.50e+03 6.98e-02 6.10e+01 pdb=" C7 NAG I 1 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.113 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.060 2.00e-02 2.50e+03 4.95e-02 3.06e+01 pdb=" C7 NAG K 1 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.045 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.079 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.010 2.00e-02 2.50e+03 ... (remaining 2885 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3297 2.78 - 3.31: 14811 3.31 - 3.84: 27232 3.84 - 4.37: 30779 4.37 - 4.90: 54148 Nonbonded interactions: 130267 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 102 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP H 72 " pdb=" OG SER H 74 " model vdw 2.286 3.040 nonbonded pdb=" OE1 GLN E 258 " pdb=" OG1 THR E 387 " model vdw 2.291 3.040 nonbonded pdb=" O LEU G 369 " pdb=" OG1 THR G 373 " model vdw 2.293 3.040 nonbonded pdb=" OG SER E 256 " pdb=" O LEU E 259 " model vdw 2.309 3.040 ... (remaining 130262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 520 through 702) selection = (chain 'B' and (resid 520 through 545 or resid 569 through 624 or resid 626 thro \ ugh 702)) selection = (chain 'C' and (resid 520 through 545 or resid 569 through 624 or resid 626 thro \ ugh 702)) } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = (chain 'E' and (resid 32 through 58 or resid 66 through 185 or resid 189 through \ 398 or resid 412 through 608)) selection = (chain 'F' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 505 or (resid 506 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2)) or resid 601 through 608)) selection = (chain 'G' and (resid 32 through 58 or resid 66 through 398 or resid 412 through \ 608)) } ncs_group { reference = chain 'M' selection = chain 'U' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'P' selection = chain 'V' } 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=0.71 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 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 : 0.005 0.222 17189 Z= 0.334 Angle : 1.035 15.700 23518 Z= 0.572 Chirality : 0.067 1.649 2892 Planarity : 0.006 0.092 2830 Dihedral : 14.693 106.207 7697 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.97 % Allowed : 15.60 % Favored : 83.43 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.18), residues: 1923 helix: -1.43 (0.22), residues: 381 sheet: -0.76 (0.24), residues: 508 loop : -1.61 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 542 TYR 0.018 0.002 TYR E 484 PHE 0.017 0.002 PHE E 53 TRP 0.016 0.002 TRP G 479 HIS 0.008 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00501 (17060) covalent geometry : angle 0.95880 (23167) SS BOND : bond 0.04077 ( 36) SS BOND : angle 3.00986 ( 72) hydrogen bonds : bond 0.21059 ( 536) hydrogen bonds : angle 8.76169 ( 1509) link_ALPHA1-2 : bond 0.04490 ( 1) link_ALPHA1-2 : angle 6.46965 ( 3) link_ALPHA1-3 : bond 0.03340 ( 4) link_ALPHA1-3 : angle 5.69072 ( 12) link_ALPHA1-6 : bond 0.02270 ( 3) link_ALPHA1-6 : angle 2.57254 ( 9) link_BETA1-4 : bond 0.01907 ( 27) link_BETA1-4 : angle 2.78375 ( 81) link_NAG-ASN : bond 0.00808 ( 58) link_NAG-ASN : angle 3.43802 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: H 75 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8600 (pttp) REVERT: L 24 ARG cc_start: 0.8072 (mtp-110) cc_final: 0.7710 (mtp-110) REVERT: L 76 ASN cc_start: 0.8786 (m110) cc_final: 0.8427 (p0) REVERT: L 82 ASP cc_start: 0.8564 (m-30) cc_final: 0.8224 (m-30) REVERT: G 217 TYR cc_start: 0.8201 (m-80) cc_final: 0.7981 (m-80) REVERT: B 535 MET cc_start: 0.8824 (mmt) cc_final: 0.8440 (mpp) REVERT: B 542 ARG cc_start: 0.8833 (mtm110) cc_final: 0.8304 (mtm180) REVERT: B 574 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8624 (ttmm) REVERT: B 588 ARG cc_start: 0.8298 (ttm170) cc_final: 0.7969 (ttp-170) REVERT: B 632 ASP cc_start: 0.9319 (t0) cc_final: 0.8798 (t0) REVERT: B 657 GLU cc_start: 0.8844 (tt0) cc_final: 0.8498 (tm-30) REVERT: E 92 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8711 (tp30) REVERT: E 356 ASN cc_start: 0.8851 (m110) cc_final: 0.8551 (p0) REVERT: F 271 MET cc_start: 0.8362 (mmt) cc_final: 0.8153 (mmm) REVERT: F 484 TYR cc_start: 0.7723 (p90) cc_final: 0.7505 (p90) REVERT: C 539 VAL cc_start: 0.8707 (m) cc_final: 0.8237 (m) REVERT: C 543 ASN cc_start: 0.8888 (m-40) cc_final: 0.8305 (m110) REVERT: C 587 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8947 (mt) REVERT: C 601 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8366 (mtpp) REVERT: C 632 ASP cc_start: 0.9030 (t70) cc_final: 0.8321 (t0) REVERT: C 647 GLU cc_start: 0.8646 (tt0) cc_final: 0.8202 (tt0) REVERT: A 543 ASN cc_start: 0.9066 (t0) cc_final: 0.8664 (t0) REVERT: A 632 ASP cc_start: 0.9088 (t70) cc_final: 0.8880 (t0) outliers start: 17 outliers final: 12 residues processed: 187 average time/residue: 0.1369 time to fit residues: 37.9955 Evaluate side-chains 162 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain A residue 570 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 543 ASN E 478 ASN F 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.071886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.055729 restraints weight = 47789.263| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.51 r_work: 0.2888 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17189 Z= 0.259 Angle : 0.728 13.024 23518 Z= 0.345 Chirality : 0.047 0.368 2892 Planarity : 0.004 0.048 2830 Dihedral : 8.325 77.220 4040 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.10 % Allowed : 14.91 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.19), residues: 1923 helix: -0.10 (0.26), residues: 398 sheet: -0.48 (0.24), residues: 490 loop : -1.24 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 77 TYR 0.022 0.002 TYR A 638 PHE 0.014 0.002 PHE G 383 TRP 0.021 0.002 TRP A 631 HIS 0.006 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00599 (17060) covalent geometry : angle 0.66203 (23167) SS BOND : bond 0.00439 ( 36) SS BOND : angle 1.33212 ( 72) hydrogen bonds : bond 0.04463 ( 536) hydrogen bonds : angle 5.67989 ( 1509) link_ALPHA1-2 : bond 0.01208 ( 1) link_ALPHA1-2 : angle 1.29483 ( 3) link_ALPHA1-3 : bond 0.01756 ( 4) link_ALPHA1-3 : angle 3.14641 ( 12) link_ALPHA1-6 : bond 0.00308 ( 3) link_ALPHA1-6 : angle 1.72536 ( 9) link_BETA1-4 : bond 0.00461 ( 27) link_BETA1-4 : angle 2.06501 ( 81) link_NAG-ASN : bond 0.00513 ( 58) link_NAG-ASN : angle 3.10924 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 6 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: L 76 ASN cc_start: 0.8778 (m110) cc_final: 0.8442 (p0) REVERT: L 79 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7911 (mm-30) REVERT: L 82 ASP cc_start: 0.8563 (m-30) cc_final: 0.8274 (m-30) REVERT: G 452 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9186 (mt) REVERT: B 574 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8603 (ttmm) REVERT: B 588 ARG cc_start: 0.8433 (ttm170) cc_final: 0.8134 (ttp-170) REVERT: B 632 ASP cc_start: 0.9420 (t0) cc_final: 0.8977 (t0) REVERT: B 657 GLU cc_start: 0.8694 (tt0) cc_final: 0.8468 (tm-30) REVERT: F 80 ASN cc_start: 0.8987 (p0) cc_final: 0.8701 (p0) REVERT: C 543 ASN cc_start: 0.8956 (m-40) cc_final: 0.8388 (m110) REVERT: C 620 SER cc_start: 0.9060 (p) cc_final: 0.8543 (p) REVERT: C 624 ASP cc_start: 0.8464 (m-30) cc_final: 0.8043 (m-30) REVERT: C 632 ASP cc_start: 0.9327 (t70) cc_final: 0.8725 (t0) REVERT: A 543 ASN cc_start: 0.9084 (t0) cc_final: 0.8762 (t0) REVERT: A 629 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8814 (mm) REVERT: A 632 ASP cc_start: 0.9041 (t70) cc_final: 0.8826 (t0) outliers start: 54 outliers final: 27 residues processed: 193 average time/residue: 0.1159 time to fit residues: 34.6270 Evaluate side-chains 162 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 638 TYR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 629 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.072845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.056769 restraints weight = 47976.153| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.53 r_work: 0.2917 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17189 Z= 0.127 Angle : 0.616 12.757 23518 Z= 0.287 Chirality : 0.045 0.403 2892 Planarity : 0.003 0.043 2830 Dihedral : 7.656 69.212 4029 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.29 % Allowed : 16.17 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.19), residues: 1923 helix: 0.66 (0.28), residues: 392 sheet: -0.32 (0.23), residues: 510 loop : -1.06 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.026 0.001 TYR A 638 PHE 0.009 0.001 PHE F 382 TRP 0.021 0.001 TRP G 479 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00281 (17060) covalent geometry : angle 0.54667 (23167) SS BOND : bond 0.00379 ( 36) SS BOND : angle 1.10997 ( 72) hydrogen bonds : bond 0.03748 ( 536) hydrogen bonds : angle 5.27475 ( 1509) link_ALPHA1-2 : bond 0.00679 ( 1) link_ALPHA1-2 : angle 1.45031 ( 3) link_ALPHA1-3 : bond 0.01983 ( 4) link_ALPHA1-3 : angle 2.45574 ( 12) link_ALPHA1-6 : bond 0.00440 ( 3) link_ALPHA1-6 : angle 1.63745 ( 9) link_BETA1-4 : bond 0.00447 ( 27) link_BETA1-4 : angle 1.81709 ( 81) link_NAG-ASN : bond 0.00493 ( 58) link_NAG-ASN : angle 2.96652 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8359 (t0) cc_final: 0.8121 (t0) REVERT: H 105 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8829 (mm-40) REVERT: L 6 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8690 (tt0) REVERT: L 24 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7936 (mtp-110) REVERT: L 76 ASN cc_start: 0.8748 (m110) cc_final: 0.8485 (p0) REVERT: L 79 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7977 (mm-30) REVERT: L 82 ASP cc_start: 0.8626 (m-30) cc_final: 0.8329 (m-30) REVERT: G 452 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9145 (mt) REVERT: B 574 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8562 (ttmm) REVERT: B 632 ASP cc_start: 0.9410 (t0) cc_final: 0.8980 (t0) REVERT: F 80 ASN cc_start: 0.9003 (p0) cc_final: 0.8704 (p0) REVERT: C 539 VAL cc_start: 0.8883 (m) cc_final: 0.8571 (m) REVERT: C 543 ASN cc_start: 0.8946 (m-40) cc_final: 0.8389 (m110) REVERT: C 620 SER cc_start: 0.9058 (p) cc_final: 0.8417 (p) REVERT: C 624 ASP cc_start: 0.8396 (m-30) cc_final: 0.7970 (m-30) REVERT: C 632 ASP cc_start: 0.9290 (t70) cc_final: 0.8675 (t0) REVERT: A 543 ASN cc_start: 0.9092 (t0) cc_final: 0.8778 (t0) outliers start: 40 outliers final: 24 residues processed: 176 average time/residue: 0.1290 time to fit residues: 34.7863 Evaluate side-chains 161 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 638 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 641 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 29 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100LHIS H 100PASN G 203 GLN B 540 GLN C 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.070035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053670 restraints weight = 47641.620| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.51 r_work: 0.2831 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17189 Z= 0.232 Angle : 0.676 12.843 23518 Z= 0.318 Chirality : 0.046 0.360 2892 Planarity : 0.003 0.048 2830 Dihedral : 7.603 64.263 4027 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.44 % Allowed : 15.60 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.19), residues: 1923 helix: 0.77 (0.27), residues: 391 sheet: -0.40 (0.23), residues: 531 loop : -0.90 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 77 TYR 0.031 0.002 TYR A 638 PHE 0.010 0.002 PHE G 361 TRP 0.034 0.002 TRP G 479 HIS 0.005 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00538 (17060) covalent geometry : angle 0.61666 (23167) SS BOND : bond 0.00416 ( 36) SS BOND : angle 1.08553 ( 72) hydrogen bonds : bond 0.03775 ( 536) hydrogen bonds : angle 5.11352 ( 1509) link_ALPHA1-2 : bond 0.00514 ( 1) link_ALPHA1-2 : angle 1.21332 ( 3) link_ALPHA1-3 : bond 0.01827 ( 4) link_ALPHA1-3 : angle 2.33379 ( 12) link_ALPHA1-6 : bond 0.00285 ( 3) link_ALPHA1-6 : angle 1.78835 ( 9) link_BETA1-4 : bond 0.00368 ( 27) link_BETA1-4 : angle 1.85297 ( 81) link_NAG-ASN : bond 0.00500 ( 58) link_NAG-ASN : angle 2.91186 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 133 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 50 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8365 (ptt90) REVERT: H 82 ASN cc_start: 0.8526 (t0) cc_final: 0.8313 (t0) REVERT: L 6 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8631 (tt0) REVERT: L 24 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7953 (mtp-110) REVERT: L 82 ASP cc_start: 0.8672 (m-30) cc_final: 0.8315 (m-30) REVERT: B 574 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8537 (ttmm) REVERT: B 584 GLU cc_start: 0.8433 (tt0) cc_final: 0.8095 (tt0) REVERT: B 632 ASP cc_start: 0.9442 (t0) cc_final: 0.9085 (t0) REVERT: E 161 MET cc_start: 0.8906 (tpp) cc_final: 0.7883 (tpp) REVERT: F 80 ASN cc_start: 0.9059 (p0) cc_final: 0.8739 (p0) REVERT: C 543 ASN cc_start: 0.8962 (m-40) cc_final: 0.8369 (m110) REVERT: C 620 SER cc_start: 0.9053 (p) cc_final: 0.8532 (p) REVERT: C 624 ASP cc_start: 0.8459 (m-30) cc_final: 0.8056 (m-30) REVERT: C 632 ASP cc_start: 0.9358 (t70) cc_final: 0.8802 (t0) REVERT: A 543 ASN cc_start: 0.9170 (t0) cc_final: 0.8850 (t0) outliers start: 60 outliers final: 39 residues processed: 184 average time/residue: 0.1204 time to fit residues: 34.4525 Evaluate side-chains 165 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 638 TYR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 641 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 46 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 57 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 0.0170 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100PASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.071994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055953 restraints weight = 46972.981| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.46 r_work: 0.2894 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17189 Z= 0.105 Angle : 0.586 12.706 23518 Z= 0.272 Chirality : 0.044 0.347 2892 Planarity : 0.003 0.047 2830 Dihedral : 7.092 57.017 4027 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.10 % Allowed : 15.83 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.20), residues: 1923 helix: 1.17 (0.28), residues: 390 sheet: -0.26 (0.23), residues: 526 loop : -0.77 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 77 TYR 0.030 0.001 TYR A 638 PHE 0.009 0.001 PHE E 391 TRP 0.017 0.001 TRP G 479 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00225 (17060) covalent geometry : angle 0.52168 (23167) SS BOND : bond 0.00405 ( 36) SS BOND : angle 0.99630 ( 72) hydrogen bonds : bond 0.03137 ( 536) hydrogen bonds : angle 4.80868 ( 1509) link_ALPHA1-2 : bond 0.00633 ( 1) link_ALPHA1-2 : angle 1.30469 ( 3) link_ALPHA1-3 : bond 0.01960 ( 4) link_ALPHA1-3 : angle 2.37733 ( 12) link_ALPHA1-6 : bond 0.00504 ( 3) link_ALPHA1-6 : angle 1.70960 ( 9) link_BETA1-4 : bond 0.00433 ( 27) link_BETA1-4 : angle 1.66810 ( 81) link_NAG-ASN : bond 0.00393 ( 58) link_NAG-ASN : angle 2.79906 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.9085 (ttt) cc_final: 0.8792 (ttt) REVERT: H 82 ASN cc_start: 0.8440 (t0) cc_final: 0.8199 (t0) REVERT: L 6 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8645 (tt0) REVERT: L 24 ARG cc_start: 0.8206 (mtp-110) cc_final: 0.7939 (mtp-110) REVERT: L 54 ARG cc_start: 0.8985 (ttm-80) cc_final: 0.8728 (tpp80) REVERT: B 574 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8482 (ttmm) REVERT: B 584 GLU cc_start: 0.8398 (tt0) cc_final: 0.8050 (tt0) REVERT: B 632 ASP cc_start: 0.9406 (t0) cc_final: 0.9034 (t0) REVERT: E 161 MET cc_start: 0.8906 (tpp) cc_final: 0.7967 (tpp) REVERT: F 80 ASN cc_start: 0.9030 (p0) cc_final: 0.8701 (p0) REVERT: C 539 VAL cc_start: 0.9011 (m) cc_final: 0.8712 (m) REVERT: C 543 ASN cc_start: 0.8941 (m-40) cc_final: 0.8381 (m110) REVERT: C 620 SER cc_start: 0.9046 (p) cc_final: 0.8474 (p) REVERT: C 624 ASP cc_start: 0.8410 (m-30) cc_final: 0.7995 (m-30) REVERT: C 632 ASP cc_start: 0.9295 (t70) cc_final: 0.8742 (t0) REVERT: A 543 ASN cc_start: 0.9126 (t0) cc_final: 0.8794 (t0) REVERT: A 629 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8817 (mm) outliers start: 54 outliers final: 29 residues processed: 189 average time/residue: 0.1238 time to fit residues: 35.8842 Evaluate side-chains 158 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 638 TYR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 109 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.069466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053155 restraints weight = 47445.314| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.48 r_work: 0.2816 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17189 Z= 0.257 Angle : 0.683 12.805 23518 Z= 0.319 Chirality : 0.047 0.378 2892 Planarity : 0.003 0.049 2830 Dihedral : 7.442 60.265 4025 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.56 % Allowed : 15.65 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.20), residues: 1923 helix: 1.06 (0.28), residues: 391 sheet: -0.36 (0.23), residues: 548 loop : -0.82 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 444 TYR 0.029 0.002 TYR A 638 PHE 0.011 0.001 PHE G 382 TRP 0.015 0.001 TRP G 479 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00600 (17060) covalent geometry : angle 0.62597 (23167) SS BOND : bond 0.00397 ( 36) SS BOND : angle 1.33119 ( 72) hydrogen bonds : bond 0.03660 ( 536) hydrogen bonds : angle 5.02160 ( 1509) link_ALPHA1-2 : bond 0.00434 ( 1) link_ALPHA1-2 : angle 1.25413 ( 3) link_ALPHA1-3 : bond 0.01904 ( 4) link_ALPHA1-3 : angle 2.47766 ( 12) link_ALPHA1-6 : bond 0.00268 ( 3) link_ALPHA1-6 : angle 1.80507 ( 9) link_BETA1-4 : bond 0.00389 ( 27) link_BETA1-4 : angle 1.78288 ( 81) link_NAG-ASN : bond 0.00552 ( 58) link_NAG-ASN : angle 2.83411 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 127 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 50 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8230 (ptt90) REVERT: H 82 ASN cc_start: 0.8607 (t0) cc_final: 0.8363 (t0) REVERT: L 6 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: B 574 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8502 (ttmm) REVERT: B 584 GLU cc_start: 0.8462 (tt0) cc_final: 0.8128 (tt0) REVERT: B 603 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9002 (mm) REVERT: B 632 ASP cc_start: 0.9448 (t0) cc_final: 0.9082 (t0) REVERT: E 161 MET cc_start: 0.8960 (tpp) cc_final: 0.7862 (tpp) REVERT: F 80 ASN cc_start: 0.9072 (p0) cc_final: 0.8742 (p0) REVERT: C 539 VAL cc_start: 0.9097 (m) cc_final: 0.8791 (m) REVERT: C 543 ASN cc_start: 0.8953 (m-40) cc_final: 0.8373 (m110) REVERT: C 620 SER cc_start: 0.9023 (p) cc_final: 0.8418 (p) REVERT: C 624 ASP cc_start: 0.8484 (m-30) cc_final: 0.8060 (m-30) REVERT: C 632 ASP cc_start: 0.9378 (t70) cc_final: 0.8841 (t0) REVERT: A 543 ASN cc_start: 0.9115 (t0) cc_final: 0.8795 (t0) REVERT: A 629 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8812 (mm) outliers start: 62 outliers final: 43 residues processed: 180 average time/residue: 0.1256 time to fit residues: 34.6089 Evaluate side-chains 171 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.052923 restraints weight = 47248.864| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.48 r_work: 0.2789 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17189 Z= 0.139 Angle : 0.611 12.756 23518 Z= 0.285 Chirality : 0.044 0.347 2892 Planarity : 0.003 0.049 2830 Dihedral : 7.127 56.660 4025 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.64 % Allowed : 16.86 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.20), residues: 1923 helix: 1.28 (0.28), residues: 391 sheet: -0.23 (0.23), residues: 528 loop : -0.78 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 77 TYR 0.026 0.001 TYR A 638 PHE 0.009 0.001 PHE E 391 TRP 0.014 0.001 TRP G 479 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00315 (17060) covalent geometry : angle 0.55107 (23167) SS BOND : bond 0.00289 ( 36) SS BOND : angle 1.20506 ( 72) hydrogen bonds : bond 0.03208 ( 536) hydrogen bonds : angle 4.81140 ( 1509) link_ALPHA1-2 : bond 0.00568 ( 1) link_ALPHA1-2 : angle 1.25703 ( 3) link_ALPHA1-3 : bond 0.01886 ( 4) link_ALPHA1-3 : angle 2.37798 ( 12) link_ALPHA1-6 : bond 0.00438 ( 3) link_ALPHA1-6 : angle 1.75888 ( 9) link_BETA1-4 : bond 0.00383 ( 27) link_BETA1-4 : angle 1.65397 ( 81) link_NAG-ASN : bond 0.00429 ( 58) link_NAG-ASN : angle 2.76078 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8590 (t0) cc_final: 0.8360 (t0) REVERT: L 6 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8659 (tt0) REVERT: L 24 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.7973 (mtp-110) REVERT: B 584 GLU cc_start: 0.8475 (tt0) cc_final: 0.8137 (tt0) REVERT: B 603 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8879 (mm) REVERT: B 632 ASP cc_start: 0.9427 (t0) cc_final: 0.9059 (t0) REVERT: E 161 MET cc_start: 0.8936 (tpp) cc_final: 0.7992 (tpp) REVERT: F 80 ASN cc_start: 0.9046 (p0) cc_final: 0.8715 (p0) REVERT: C 539 VAL cc_start: 0.9043 (m) cc_final: 0.8753 (m) REVERT: C 543 ASN cc_start: 0.8965 (m-40) cc_final: 0.8409 (m110) REVERT: C 620 SER cc_start: 0.9003 (p) cc_final: 0.8411 (p) REVERT: C 624 ASP cc_start: 0.8484 (m-30) cc_final: 0.8073 (m-30) REVERT: C 632 ASP cc_start: 0.9324 (t70) cc_final: 0.8781 (t0) REVERT: A 629 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8818 (mm) outliers start: 46 outliers final: 38 residues processed: 169 average time/residue: 0.1240 time to fit residues: 32.5052 Evaluate side-chains 167 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 638 TYR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 6 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 246 GLN F 478 ASN A 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.053178 restraints weight = 47718.340| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.48 r_work: 0.2793 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17189 Z= 0.136 Angle : 0.592 11.014 23518 Z= 0.277 Chirality : 0.044 0.341 2892 Planarity : 0.003 0.048 2830 Dihedral : 6.979 56.997 4025 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.92 % Allowed : 16.63 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.20), residues: 1923 helix: 1.40 (0.28), residues: 390 sheet: -0.07 (0.23), residues: 511 loop : -0.71 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 77 TYR 0.027 0.001 TYR A 638 PHE 0.007 0.001 PHE F 383 TRP 0.013 0.001 TRP G 479 HIS 0.002 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00311 (17060) covalent geometry : angle 0.54178 (23167) SS BOND : bond 0.00286 ( 36) SS BOND : angle 1.05977 ( 72) hydrogen bonds : bond 0.03079 ( 536) hydrogen bonds : angle 4.69419 ( 1509) link_ALPHA1-2 : bond 0.00485 ( 1) link_ALPHA1-2 : angle 1.33667 ( 3) link_ALPHA1-3 : bond 0.01862 ( 4) link_ALPHA1-3 : angle 2.38025 ( 12) link_ALPHA1-6 : bond 0.00427 ( 3) link_ALPHA1-6 : angle 1.73631 ( 9) link_BETA1-4 : bond 0.00399 ( 27) link_BETA1-4 : angle 1.63985 ( 81) link_NAG-ASN : bond 0.00374 ( 58) link_NAG-ASN : angle 2.46341 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8620 (t0) cc_final: 0.8365 (t0) REVERT: L 6 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: L 24 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.7961 (mtp-110) REVERT: B 584 GLU cc_start: 0.8494 (tt0) cc_final: 0.8131 (tt0) REVERT: B 603 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8868 (mm) REVERT: B 632 ASP cc_start: 0.9443 (t0) cc_final: 0.9068 (t0) REVERT: E 161 MET cc_start: 0.8945 (tpp) cc_final: 0.8028 (tpp) REVERT: F 80 ASN cc_start: 0.9069 (p0) cc_final: 0.8753 (p0) REVERT: F 478 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8911 (t0) REVERT: C 539 VAL cc_start: 0.9026 (m) cc_final: 0.8743 (m) REVERT: C 543 ASN cc_start: 0.8978 (m-40) cc_final: 0.8454 (m110) REVERT: C 620 SER cc_start: 0.8984 (p) cc_final: 0.8347 (p) REVERT: C 624 ASP cc_start: 0.8486 (m-30) cc_final: 0.8055 (m-30) REVERT: C 632 ASP cc_start: 0.9348 (t70) cc_final: 0.8809 (t0) REVERT: A 543 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8825 (t0) REVERT: A 629 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8803 (mm) REVERT: A 633 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8551 (mmtm) outliers start: 51 outliers final: 41 residues processed: 172 average time/residue: 0.1226 time to fit residues: 33.1063 Evaluate side-chains 173 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 478 ASN Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 638 TYR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 377 ASN F 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.051993 restraints weight = 47359.689| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.51 r_work: 0.2760 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17189 Z= 0.204 Angle : 0.630 11.430 23518 Z= 0.296 Chirality : 0.045 0.340 2892 Planarity : 0.003 0.046 2830 Dihedral : 7.082 56.997 4025 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.33 % Allowed : 16.23 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.20), residues: 1923 helix: 1.35 (0.28), residues: 390 sheet: -0.11 (0.23), residues: 529 loop : -0.72 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 77 TYR 0.025 0.001 TYR A 638 PHE 0.009 0.001 PHE F 383 TRP 0.018 0.001 TRP F 479 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00475 (17060) covalent geometry : angle 0.58217 (23167) SS BOND : bond 0.00332 ( 36) SS BOND : angle 1.08341 ( 72) hydrogen bonds : bond 0.03248 ( 536) hydrogen bonds : angle 4.75982 ( 1509) link_ALPHA1-2 : bond 0.00440 ( 1) link_ALPHA1-2 : angle 1.28768 ( 3) link_ALPHA1-3 : bond 0.01815 ( 4) link_ALPHA1-3 : angle 2.39269 ( 12) link_ALPHA1-6 : bond 0.00341 ( 3) link_ALPHA1-6 : angle 1.80612 ( 9) link_BETA1-4 : bond 0.00377 ( 27) link_BETA1-4 : angle 1.65849 ( 81) link_NAG-ASN : bond 0.00430 ( 58) link_NAG-ASN : angle 2.49581 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 127 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8654 (t0) cc_final: 0.8396 (t0) REVERT: L 6 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: B 584 GLU cc_start: 0.8513 (tt0) cc_final: 0.8165 (tt0) REVERT: B 603 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8950 (mm) REVERT: B 632 ASP cc_start: 0.9443 (t0) cc_final: 0.9065 (t0) REVERT: E 161 MET cc_start: 0.8957 (tpp) cc_final: 0.7983 (tpp) REVERT: F 80 ASN cc_start: 0.9078 (p0) cc_final: 0.8727 (p0) REVERT: F 478 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8690 (m-40) REVERT: C 539 VAL cc_start: 0.9063 (m) cc_final: 0.8785 (m) REVERT: C 543 ASN cc_start: 0.8966 (m-40) cc_final: 0.8449 (m110) REVERT: C 620 SER cc_start: 0.8993 (p) cc_final: 0.8401 (p) REVERT: C 624 ASP cc_start: 0.8496 (m-30) cc_final: 0.8080 (m-30) REVERT: C 632 ASP cc_start: 0.9361 (t70) cc_final: 0.8831 (t0) REVERT: A 629 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8797 (mm) REVERT: A 633 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8567 (mmtm) outliers start: 58 outliers final: 44 residues processed: 176 average time/residue: 0.1163 time to fit residues: 32.2683 Evaluate side-chains 174 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 478 ASN Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 68 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.052415 restraints weight = 47388.239| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.57 r_work: 0.2770 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17189 Z= 0.167 Angle : 0.618 11.283 23518 Z= 0.290 Chirality : 0.044 0.339 2892 Planarity : 0.003 0.046 2830 Dihedral : 7.046 56.816 4025 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.87 % Allowed : 16.46 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.20), residues: 1923 helix: 1.40 (0.28), residues: 389 sheet: -0.10 (0.23), residues: 525 loop : -0.70 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 77 TYR 0.025 0.001 TYR A 638 PHE 0.008 0.001 PHE F 383 TRP 0.013 0.001 TRP G 479 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00387 (17060) covalent geometry : angle 0.56924 (23167) SS BOND : bond 0.00320 ( 36) SS BOND : angle 1.05440 ( 72) hydrogen bonds : bond 0.03193 ( 536) hydrogen bonds : angle 4.74022 ( 1509) link_ALPHA1-2 : bond 0.00477 ( 1) link_ALPHA1-2 : angle 1.31591 ( 3) link_ALPHA1-3 : bond 0.01797 ( 4) link_ALPHA1-3 : angle 2.36460 ( 12) link_ALPHA1-6 : bond 0.00387 ( 3) link_ALPHA1-6 : angle 1.74508 ( 9) link_BETA1-4 : bond 0.00362 ( 27) link_BETA1-4 : angle 1.63636 ( 81) link_NAG-ASN : bond 0.00401 ( 58) link_NAG-ASN : angle 2.48301 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8662 (t0) cc_final: 0.8404 (t0) REVERT: L 6 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: G 475 MET cc_start: 0.8282 (mmm) cc_final: 0.7632 (mmm) REVERT: B 584 GLU cc_start: 0.8511 (tt0) cc_final: 0.8159 (tt0) REVERT: B 603 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8941 (mm) REVERT: B 632 ASP cc_start: 0.9436 (t0) cc_final: 0.9055 (t0) REVERT: E 161 MET cc_start: 0.8938 (tpp) cc_final: 0.7990 (tpp) REVERT: E 444 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7574 (tmm160) REVERT: F 80 ASN cc_start: 0.9078 (p0) cc_final: 0.8736 (p0) REVERT: C 539 VAL cc_start: 0.9051 (m) cc_final: 0.8768 (m) REVERT: C 543 ASN cc_start: 0.8970 (m-40) cc_final: 0.8457 (m110) REVERT: C 624 ASP cc_start: 0.8507 (m-30) cc_final: 0.8121 (m-30) REVERT: C 632 ASP cc_start: 0.9352 (t70) cc_final: 0.8821 (t0) REVERT: A 543 ASN cc_start: 0.8915 (m-40) cc_final: 0.8607 (m110) REVERT: A 629 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8794 (mm) REVERT: A 633 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8541 (mmtm) outliers start: 50 outliers final: 42 residues processed: 170 average time/residue: 0.1235 time to fit residues: 32.5980 Evaluate side-chains 172 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 122 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 chunk 86 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS E 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051235 restraints weight = 47341.894| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.53 r_work: 0.2738 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17189 Z= 0.243 Angle : 0.671 11.433 23518 Z= 0.316 Chirality : 0.046 0.340 2892 Planarity : 0.003 0.047 2830 Dihedral : 7.300 57.095 4025 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.87 % Allowed : 16.51 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.20), residues: 1923 helix: 1.39 (0.28), residues: 387 sheet: -0.18 (0.23), residues: 538 loop : -0.73 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 77 TYR 0.025 0.001 TYR A 638 PHE 0.010 0.001 PHE F 383 TRP 0.013 0.001 TRP G 479 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00569 (17060) covalent geometry : angle 0.62320 (23167) SS BOND : bond 0.00423 ( 36) SS BOND : angle 1.21894 ( 72) hydrogen bonds : bond 0.03503 ( 536) hydrogen bonds : angle 4.92060 ( 1509) link_ALPHA1-2 : bond 0.00418 ( 1) link_ALPHA1-2 : angle 1.29343 ( 3) link_ALPHA1-3 : bond 0.01795 ( 4) link_ALPHA1-3 : angle 2.44906 ( 12) link_ALPHA1-6 : bond 0.00298 ( 3) link_ALPHA1-6 : angle 1.78423 ( 9) link_BETA1-4 : bond 0.00363 ( 27) link_BETA1-4 : angle 1.67172 ( 81) link_NAG-ASN : bond 0.00505 ( 58) link_NAG-ASN : angle 2.56097 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3385.36 seconds wall clock time: 59 minutes 6.21 seconds (3546.21 seconds total)