Starting phenix.real_space_refine on Sun May 18 09:28:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnk_44728/05_2025/9bnk_44728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnk_44728/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bnk_44728/05_2025/9bnk_44728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnk_44728/05_2025/9bnk_44728.map" model { file = "/net/cci-nas-00/data/ceres_data/9bnk_44728/05_2025/9bnk_44728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnk_44728/05_2025/9bnk_44728.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.77, per 1000 atoms: 0.64 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: 5.01 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.98 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: 6.42 Time building geometry restraints manager: 5.76 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 664 or resid 701 through 702)) selection = (chain 'B' and (resid 520 through 545 or resid 569 through 624 or resid 626 thro \ ugh 664 or resid 701 through 702)) selection = (chain 'C' and (resid 520 through 545 or resid 569 through 624 or resid 626 thro \ ugh 664 or resid 701 through 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 506 or resid 601 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 \ 506 or resid 601 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 40.650 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.200 ------------------------------------------------------------------------------- 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 : 4.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (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 TRP 0.016 0.002 TRP G 479 HIS 0.008 0.001 HIS F 216 PHE 0.017 0.002 PHE E 53 TYR 0.018 0.002 TYR E 484 ARG 0.021 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00808 ( 58) link_NAG-ASN : angle 3.43802 ( 174) 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_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) hydrogen bonds : bond 0.21059 ( 536) hydrogen bonds : angle 8.76169 ( 1509) SS BOND : bond 0.04077 ( 36) SS BOND : angle 3.00986 ( 72) covalent geometry : bond 0.00501 (17060) covalent geometry : angle 0.95880 (23167) *********************** 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 : 1.811 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: 0.2985 time to fit residues: 83.1109 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 : 1.873 ------------------------------------------------------------------------------- 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 162 optimal weight: 0.0370 chunk 146 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 175 optimal weight: 0.0770 overall best weight: 0.8018 ------------------------------------------------------------------------------- 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 B 543 ASN E 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.076197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061066 restraints weight = 47779.037| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.30 r_work: 0.3041 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17189 Z= 0.129 Angle : 0.639 15.388 23518 Z= 0.300 Chirality : 0.044 0.375 2892 Planarity : 0.004 0.051 2830 Dihedral : 8.145 79.210 4040 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.89 % Allowed : 15.54 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 1923 helix: -0.06 (0.26), residues: 398 sheet: -0.44 (0.25), residues: 482 loop : -1.22 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 631 HIS 0.004 0.001 HIS G 105 PHE 0.009 0.001 PHE G 361 TYR 0.020 0.001 TYR A 638 ARG 0.007 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 58) link_NAG-ASN : angle 3.18126 ( 174) link_ALPHA1-6 : bond 0.00496 ( 3) link_ALPHA1-6 : angle 1.56590 ( 9) link_BETA1-4 : bond 0.00561 ( 27) link_BETA1-4 : angle 1.97857 ( 81) link_ALPHA1-2 : bond 0.01309 ( 1) link_ALPHA1-2 : angle 1.62892 ( 3) link_ALPHA1-3 : bond 0.02277 ( 4) link_ALPHA1-3 : angle 3.12408 ( 12) hydrogen bonds : bond 0.04527 ( 536) hydrogen bonds : angle 5.94210 ( 1509) SS BOND : bond 0.00232 ( 36) SS BOND : angle 1.24747 ( 72) covalent geometry : bond 0.00274 (17060) covalent geometry : angle 0.55956 (23167) *********************** 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 187 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 79 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8128 (mm-30) REVERT: G 452 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9115 (mt) REVERT: B 542 ARG cc_start: 0.8724 (mtm110) cc_final: 0.8519 (mtm-85) REVERT: B 574 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8543 (ttmm) REVERT: B 588 ARG cc_start: 0.8352 (ttm170) cc_final: 0.8029 (ttp-170) REVERT: B 632 ASP cc_start: 0.9238 (t0) cc_final: 0.8802 (t0) REVERT: B 639 THR cc_start: 0.9000 (m) cc_final: 0.8740 (p) REVERT: F 80 ASN cc_start: 0.8736 (p0) cc_final: 0.8475 (p0) REVERT: F 271 MET cc_start: 0.8508 (mmt) cc_final: 0.8308 (mmm) REVERT: C 539 VAL cc_start: 0.8827 (m) cc_final: 0.8462 (m) REVERT: C 543 ASN cc_start: 0.8856 (m-40) cc_final: 0.8356 (m110) REVERT: C 620 SER cc_start: 0.9018 (p) cc_final: 0.8492 (p) REVERT: C 624 ASP cc_start: 0.8266 (m-30) cc_final: 0.7836 (m-30) REVERT: C 632 ASP cc_start: 0.9143 (t70) cc_final: 0.8535 (t0) REVERT: A 543 ASN cc_start: 0.8923 (t0) cc_final: 0.8622 (t0) REVERT: A 632 ASP cc_start: 0.8879 (t70) cc_final: 0.8663 (t0) REVERT: A 654 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8134 (mt-10) outliers start: 33 outliers final: 14 residues processed: 185 average time/residue: 0.2792 time to fit residues: 79.2848 Evaluate side-chains 159 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 58 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 F residue 120 VAL Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 595 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 111 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100LHIS L 6 GLN G 85 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS F 293 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.069991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053779 restraints weight = 47446.439| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.42 r_work: 0.2833 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 17189 Z= 0.297 Angle : 0.750 12.894 23518 Z= 0.357 Chirality : 0.049 0.466 2892 Planarity : 0.004 0.045 2830 Dihedral : 7.999 70.086 4028 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.21 % Allowed : 15.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 1923 helix: 0.38 (0.27), residues: 398 sheet: -0.49 (0.22), residues: 523 loop : -1.11 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 479 HIS 0.006 0.001 HIS G 216 PHE 0.015 0.002 PHE F 288 TYR 0.025 0.002 TYR A 638 ARG 0.010 0.001 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00877 ( 58) link_NAG-ASN : angle 3.02277 ( 174) link_ALPHA1-6 : bond 0.00250 ( 3) link_ALPHA1-6 : angle 1.69707 ( 9) link_BETA1-4 : bond 0.00429 ( 27) link_BETA1-4 : angle 1.98746 ( 81) link_ALPHA1-2 : bond 0.00680 ( 1) link_ALPHA1-2 : angle 1.29739 ( 3) link_ALPHA1-3 : bond 0.01898 ( 4) link_ALPHA1-3 : angle 2.47187 ( 12) hydrogen bonds : bond 0.04316 ( 536) hydrogen bonds : angle 5.39276 ( 1509) SS BOND : bond 0.00441 ( 36) SS BOND : angle 1.24112 ( 72) covalent geometry : bond 0.00695 (17060) covalent geometry : angle 0.69231 (23167) *********************** 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 194 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 105 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8875 (mm-40) REVERT: B 632 ASP cc_start: 0.9449 (t0) cc_final: 0.9075 (t0) REVERT: F 80 ASN cc_start: 0.9051 (p0) cc_final: 0.8752 (p0) REVERT: C 543 ASN cc_start: 0.8975 (m-40) cc_final: 0.8370 (m110) REVERT: C 620 SER cc_start: 0.9056 (p) cc_final: 0.8534 (p) REVERT: C 624 ASP cc_start: 0.8494 (m-30) cc_final: 0.8077 (m-30) REVERT: C 626 MET cc_start: 0.8418 (ttm) cc_final: 0.8210 (ttm) REVERT: C 632 ASP cc_start: 0.9376 (t70) cc_final: 0.8762 (t0) REVERT: A 543 ASN cc_start: 0.9163 (t0) cc_final: 0.8753 (t0) outliers start: 56 outliers final: 37 residues processed: 184 average time/residue: 0.2678 time to fit residues: 76.2009 Evaluate side-chains 163 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL 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 162 THR 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 B residue 539 VAL Chi-restraints excluded: chain B residue 591 GLN 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 125 LEU Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 202 THR 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 E residue 424 ILE Chi-restraints excluded: chain F residue 120 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 90 optimal weight: 0.8980 chunk 132 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.072650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056779 restraints weight = 47221.103| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.43 r_work: 0.2896 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17189 Z= 0.112 Angle : 0.611 12.717 23518 Z= 0.285 Chirality : 0.045 0.469 2892 Planarity : 0.003 0.052 2830 Dihedral : 7.354 61.489 4027 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.64 % Allowed : 15.60 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 1923 helix: 0.90 (0.28), residues: 398 sheet: -0.22 (0.24), residues: 505 loop : -0.98 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 479 HIS 0.002 0.001 HIS F 216 PHE 0.009 0.001 PHE E 391 TYR 0.031 0.001 TYR A 638 ARG 0.007 0.000 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 58) link_NAG-ASN : angle 2.87440 ( 174) link_ALPHA1-6 : bond 0.00480 ( 3) link_ALPHA1-6 : angle 1.65540 ( 9) link_BETA1-4 : bond 0.00428 ( 27) link_BETA1-4 : angle 1.74092 ( 81) link_ALPHA1-2 : bond 0.00702 ( 1) link_ALPHA1-2 : angle 1.28478 ( 3) link_ALPHA1-3 : bond 0.01949 ( 4) link_ALPHA1-3 : angle 2.25471 ( 12) hydrogen bonds : bond 0.03394 ( 536) hydrogen bonds : angle 5.02763 ( 1509) SS BOND : bond 0.00308 ( 36) SS BOND : angle 0.95201 ( 72) covalent geometry : bond 0.00239 (17060) covalent geometry : angle 0.54699 (23167) *********************** 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 189 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8345 (t0) cc_final: 0.8095 (t0) REVERT: L 24 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7907 (mtp-110) REVERT: G 39 TYR cc_start: 0.9353 (m-80) cc_final: 0.9075 (m-80) REVERT: B 574 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8516 (ttmm) REVERT: B 632 ASP cc_start: 0.9390 (t0) cc_final: 0.9013 (t0) REVERT: E 161 MET cc_start: 0.8858 (tpp) cc_final: 0.7941 (tpp) REVERT: F 80 ASN cc_start: 0.8982 (p0) cc_final: 0.8652 (p0) REVERT: C 539 VAL cc_start: 0.8959 (m) cc_final: 0.8641 (m) REVERT: C 543 ASN cc_start: 0.8926 (m-40) cc_final: 0.8365 (m110) REVERT: C 620 SER cc_start: 0.9069 (p) cc_final: 0.8511 (p) REVERT: C 624 ASP cc_start: 0.8425 (m-30) cc_final: 0.8021 (m-30) REVERT: C 632 ASP cc_start: 0.9303 (t70) cc_final: 0.8726 (t0) REVERT: C 647 GLU cc_start: 0.8691 (tt0) cc_final: 0.8421 (tt0) REVERT: A 542 ARG cc_start: 0.8758 (ptp90) cc_final: 0.8552 (ptp90) outliers start: 46 outliers final: 26 residues processed: 180 average time/residue: 0.2798 time to fit residues: 77.2882 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 : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL 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 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 199 SER 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 F residue 120 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 654 GLU Chi-restraints excluded: chain C residue 657 GLU 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 77 optimal weight: 0.3980 chunk 147 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** C 653 GLN A 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.071169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054908 restraints weight = 47503.815| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.50 r_work: 0.2868 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17189 Z= 0.157 Angle : 0.615 12.763 23518 Z= 0.286 Chirality : 0.045 0.354 2892 Planarity : 0.003 0.046 2830 Dihedral : 7.160 59.646 4027 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.10 % Allowed : 15.77 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1923 helix: 1.14 (0.28), residues: 391 sheet: -0.27 (0.23), residues: 537 loop : -0.83 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 479 HIS 0.003 0.001 HIS F 216 PHE 0.007 0.001 PHE G 382 TYR 0.029 0.001 TYR A 638 ARG 0.004 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 58) link_NAG-ASN : angle 2.80524 ( 174) link_ALPHA1-6 : bond 0.00377 ( 3) link_ALPHA1-6 : angle 1.72652 ( 9) link_BETA1-4 : bond 0.00397 ( 27) link_BETA1-4 : angle 1.73686 ( 81) link_ALPHA1-2 : bond 0.00513 ( 1) link_ALPHA1-2 : angle 1.32268 ( 3) link_ALPHA1-3 : bond 0.01920 ( 4) link_ALPHA1-3 : angle 2.38264 ( 12) hydrogen bonds : bond 0.03342 ( 536) hydrogen bonds : angle 4.88159 ( 1509) SS BOND : bond 0.00305 ( 36) SS BOND : angle 1.04319 ( 72) covalent geometry : bond 0.00358 (17060) covalent geometry : angle 0.55381 (23167) *********************** 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 186 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 50 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8281 (ptt90) REVERT: H 82 ASN cc_start: 0.8440 (t0) cc_final: 0.8125 (t0) REVERT: G 475 MET cc_start: 0.8181 (mmm) cc_final: 0.7557 (mmm) REVERT: B 574 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8513 (ttmm) REVERT: B 591 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8967 (tt0) REVERT: B 632 ASP cc_start: 0.9431 (t0) cc_final: 0.9065 (t0) REVERT: F 80 ASN cc_start: 0.9039 (p0) cc_final: 0.8725 (p0) REVERT: C 539 VAL cc_start: 0.8987 (m) cc_final: 0.8679 (m) REVERT: C 543 ASN cc_start: 0.8933 (m-40) cc_final: 0.8356 (m110) REVERT: C 620 SER cc_start: 0.9049 (p) cc_final: 0.8510 (p) REVERT: C 624 ASP cc_start: 0.8452 (m-30) cc_final: 0.8055 (m-30) REVERT: C 632 ASP cc_start: 0.9325 (t70) cc_final: 0.8758 (t0) REVERT: A 629 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8844 (mm) outliers start: 54 outliers final: 36 residues processed: 177 average time/residue: 0.2788 time to fit residues: 76.1497 Evaluate side-chains 168 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 85 VAL 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 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 292 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain B residue 591 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 663 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS 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 F residue 42 VAL Chi-restraints excluded: chain F residue 120 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 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 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 52 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 51 optimal weight: 0.4980 chunk 145 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 103 GLN A 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.072297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056389 restraints weight = 47449.720| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.44 r_work: 0.2890 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2533 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= 0.113 Angle : 0.583 12.708 23518 Z= 0.270 Chirality : 0.044 0.342 2892 Planarity : 0.003 0.049 2830 Dihedral : 6.948 57.054 4027 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.35 % Allowed : 16.34 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1923 helix: 1.27 (0.28), residues: 391 sheet: -0.17 (0.23), residues: 538 loop : -0.75 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 479 HIS 0.003 0.001 HIS F 216 PHE 0.006 0.001 PHE F 383 TYR 0.030 0.001 TYR A 638 ARG 0.006 0.000 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 58) link_NAG-ASN : angle 2.72779 ( 174) link_ALPHA1-6 : bond 0.00485 ( 3) link_ALPHA1-6 : angle 1.72541 ( 9) link_BETA1-4 : bond 0.00430 ( 27) link_BETA1-4 : angle 1.65988 ( 81) link_ALPHA1-2 : bond 0.00547 ( 1) link_ALPHA1-2 : angle 1.32960 ( 3) link_ALPHA1-3 : bond 0.01906 ( 4) link_ALPHA1-3 : angle 2.35302 ( 12) hydrogen bonds : bond 0.03050 ( 536) hydrogen bonds : angle 4.68495 ( 1509) SS BOND : bond 0.00276 ( 36) SS BOND : angle 0.93623 ( 72) covalent geometry : bond 0.00251 (17060) covalent geometry : angle 0.52231 (23167) *********************** 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 180 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8459 (t0) cc_final: 0.8154 (t0) REVERT: L 24 ARG cc_start: 0.8227 (mtp-110) cc_final: 0.7893 (mtp-110) REVERT: B 603 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8901 (mm) REVERT: B 632 ASP cc_start: 0.9400 (t0) cc_final: 0.9034 (t0) REVERT: E 161 MET cc_start: 0.8793 (tpp) cc_final: 0.7987 (tpp) REVERT: F 80 ASN cc_start: 0.9018 (p0) cc_final: 0.8709 (p0) REVERT: C 539 VAL cc_start: 0.8946 (m) cc_final: 0.8631 (m) REVERT: C 543 ASN cc_start: 0.8913 (m-40) cc_final: 0.8341 (m110) REVERT: C 620 SER cc_start: 0.9016 (p) cc_final: 0.8390 (p) REVERT: C 624 ASP cc_start: 0.8404 (m-30) cc_final: 0.7977 (m-30) REVERT: C 632 ASP cc_start: 0.9288 (t70) cc_final: 0.8745 (t0) REVERT: A 543 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8767 (t0) REVERT: A 629 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8831 (mm) outliers start: 41 outliers final: 29 residues processed: 173 average time/residue: 0.2833 time to fit residues: 75.3930 Evaluate side-chains 164 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 85 VAL 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 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 120 VAL 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 F residue 120 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 A residue 543 ASN 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 119 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 140 optimal weight: 0.3980 chunk 92 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 591 GLN A 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.069115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.053053 restraints weight = 47899.710| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.42 r_work: 0.2788 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 17189 Z= 0.338 Angle : 0.762 12.846 23518 Z= 0.359 Chirality : 0.049 0.354 2892 Planarity : 0.004 0.046 2830 Dihedral : 7.653 61.568 4025 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.84 % Allowed : 15.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1923 helix: 0.95 (0.27), residues: 393 sheet: -0.26 (0.23), residues: 540 loop : -0.96 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 479 HIS 0.005 0.001 HIS E 330 PHE 0.012 0.002 PHE F 383 TYR 0.027 0.002 TYR A 638 ARG 0.008 0.001 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 58) link_NAG-ASN : angle 2.91945 ( 174) link_ALPHA1-6 : bond 0.00215 ( 3) link_ALPHA1-6 : angle 1.83939 ( 9) link_BETA1-4 : bond 0.00397 ( 27) link_BETA1-4 : angle 1.85840 ( 81) link_ALPHA1-2 : bond 0.00344 ( 1) link_ALPHA1-2 : angle 1.26986 ( 3) link_ALPHA1-3 : bond 0.01865 ( 4) link_ALPHA1-3 : angle 2.53987 ( 12) hydrogen bonds : bond 0.03974 ( 536) hydrogen bonds : angle 5.11951 ( 1509) SS BOND : bond 0.00615 ( 36) SS BOND : angle 1.56713 ( 72) covalent geometry : bond 0.00793 (17060) covalent geometry : angle 0.70730 (23167) *********************** 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 188 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8666 (t0) cc_final: 0.8436 (t0) REVERT: G 162 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 603 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9193 (mm) REVERT: B 632 ASP cc_start: 0.9449 (t0) cc_final: 0.9085 (t0) REVERT: F 80 ASN cc_start: 0.9067 (p0) cc_final: 0.8743 (p0) REVERT: C 543 ASN cc_start: 0.8968 (m-40) cc_final: 0.8551 (m110) REVERT: C 601 LYS cc_start: 0.9127 (mtmm) cc_final: 0.8902 (mtpp) REVERT: C 620 SER cc_start: 0.9016 (p) cc_final: 0.8456 (p) REVERT: C 624 ASP cc_start: 0.8487 (m-30) cc_final: 0.8080 (m-30) REVERT: C 632 ASP cc_start: 0.9372 (t70) cc_final: 0.8857 (t0) REVERT: A 543 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8718 (t0) REVERT: A 629 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8849 (mm) outliers start: 67 outliers final: 43 residues processed: 176 average time/residue: 0.2625 time to fit residues: 71.7725 Evaluate side-chains 166 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 1.812 ------------------------------------------------------------------------------- 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 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 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 276 ASN Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 663 LEU 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 199 SER 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 F residue 120 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 270 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 159 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.070775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.054382 restraints weight = 47408.332| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.53 r_work: 0.2801 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17189 Z= 0.111 Angle : 0.615 12.763 23518 Z= 0.287 Chirality : 0.044 0.340 2892 Planarity : 0.003 0.048 2830 Dihedral : 7.051 56.302 4025 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.24 % Allowed : 17.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1923 helix: 1.21 (0.28), residues: 396 sheet: -0.20 (0.23), residues: 534 loop : -0.73 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 479 HIS 0.003 0.001 HIS F 216 PHE 0.010 0.001 PHE E 391 TYR 0.028 0.001 TYR A 638 ARG 0.008 0.000 ARG A 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 58) link_NAG-ASN : angle 2.76477 ( 174) link_ALPHA1-6 : bond 0.00578 ( 3) link_ALPHA1-6 : angle 1.75251 ( 9) link_BETA1-4 : bond 0.00415 ( 27) link_BETA1-4 : angle 1.62927 ( 81) link_ALPHA1-2 : bond 0.00673 ( 1) link_ALPHA1-2 : angle 1.27746 ( 3) link_ALPHA1-3 : bond 0.02022 ( 4) link_ALPHA1-3 : angle 2.40079 ( 12) hydrogen bonds : bond 0.03106 ( 536) hydrogen bonds : angle 4.74502 ( 1509) SS BOND : bond 0.00329 ( 36) SS BOND : angle 1.19650 ( 72) covalent geometry : bond 0.00241 (17060) covalent geometry : angle 0.55581 (23167) *********************** 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 171 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 2.044 Fit side-chains revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8604 (t0) cc_final: 0.8370 (t0) REVERT: L 24 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7847 (mtp-110) REVERT: G 162 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8664 (p) REVERT: B 632 ASP cc_start: 0.9447 (t0) cc_final: 0.9071 (t0) REVERT: E 161 MET cc_start: 0.8742 (tpp) cc_final: 0.7972 (tpp) REVERT: F 80 ASN cc_start: 0.9106 (p0) cc_final: 0.8808 (p0) REVERT: C 543 ASN cc_start: 0.8960 (m-40) cc_final: 0.8508 (m110) REVERT: C 620 SER cc_start: 0.8985 (p) cc_final: 0.8378 (p) REVERT: C 624 ASP cc_start: 0.8526 (m-30) cc_final: 0.8092 (m-30) REVERT: C 632 ASP cc_start: 0.9324 (t70) cc_final: 0.8775 (t0) REVERT: A 543 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8907 (t0) REVERT: A 629 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8789 (mm) REVERT: A 632 ASP cc_start: 0.9083 (t0) cc_final: 0.8851 (t0) outliers start: 39 outliers final: 32 residues processed: 168 average time/residue: 0.2984 time to fit residues: 77.4495 Evaluate side-chains 161 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL 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 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 342 LEU 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 126 CYS Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 500 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35BASN E 377 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 = 0.3355 r_free = 0.3355 target = 0.069552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.052783 restraints weight = 47383.585| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.55 r_work: 0.2779 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17189 Z= 0.157 Angle : 0.612 11.023 23518 Z= 0.286 Chirality : 0.045 0.342 2892 Planarity : 0.003 0.047 2830 Dihedral : 7.049 56.995 4025 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.75 % Allowed : 17.03 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1923 helix: 1.33 (0.28), residues: 390 sheet: -0.14 (0.23), residues: 542 loop : -0.72 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 479 HIS 0.002 0.001 HIS F 216 PHE 0.007 0.001 PHE F 383 TYR 0.026 0.001 TYR A 638 ARG 0.005 0.000 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 58) link_NAG-ASN : angle 2.47547 ( 174) link_ALPHA1-6 : bond 0.00394 ( 3) link_ALPHA1-6 : angle 1.74179 ( 9) link_BETA1-4 : bond 0.00385 ( 27) link_BETA1-4 : angle 1.64978 ( 81) link_ALPHA1-2 : bond 0.00475 ( 1) link_ALPHA1-2 : angle 1.31703 ( 3) link_ALPHA1-3 : bond 0.01805 ( 4) link_ALPHA1-3 : angle 2.39277 ( 12) hydrogen bonds : bond 0.03192 ( 536) hydrogen bonds : angle 4.71682 ( 1509) SS BOND : bond 0.00290 ( 36) SS BOND : angle 1.14258 ( 72) covalent geometry : bond 0.00361 (17060) covalent geometry : angle 0.56207 (23167) *********************** 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 172 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8627 (t0) cc_final: 0.8411 (t0) REVERT: L 24 ARG cc_start: 0.8223 (mtp-110) cc_final: 0.7911 (mtp-110) REVERT: G 162 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8759 (p) REVERT: B 603 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8928 (mm) REVERT: B 632 ASP cc_start: 0.9425 (t0) cc_final: 0.9061 (t0) REVERT: E 161 MET cc_start: 0.8777 (tpp) cc_final: 0.7867 (tpp) REVERT: F 80 ASN cc_start: 0.9072 (p0) cc_final: 0.8777 (p0) REVERT: C 543 ASN cc_start: 0.8943 (m-40) cc_final: 0.8524 (m110) REVERT: C 620 SER cc_start: 0.8999 (p) cc_final: 0.8382 (p) REVERT: C 624 ASP cc_start: 0.8497 (m-30) cc_final: 0.8076 (m-30) REVERT: C 632 ASP cc_start: 0.9303 (t70) cc_final: 0.8780 (t0) REVERT: A 629 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8854 (mm) outliers start: 48 outliers final: 35 residues processed: 167 average time/residue: 0.2796 time to fit residues: 72.1049 Evaluate side-chains 161 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL 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 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 284 ILE 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 126 CYS Chi-restraints excluded: chain E residue 199 SER 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 447 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 129 LEU 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 576 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 7 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 155 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35BASN G 85 HIS E 377 ASN F 478 ASN A 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.053655 restraints weight = 47492.361| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.47 r_work: 0.2804 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17189 Z= 0.118 Angle : 0.598 11.138 23518 Z= 0.281 Chirality : 0.044 0.339 2892 Planarity : 0.003 0.047 2830 Dihedral : 6.920 56.966 4025 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.47 % Allowed : 17.26 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1923 helix: 1.42 (0.28), residues: 390 sheet: -0.03 (0.23), residues: 523 loop : -0.71 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 631 HIS 0.002 0.001 HIS F 216 PHE 0.008 0.001 PHE E 376 TYR 0.026 0.001 TYR A 638 ARG 0.005 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 58) link_NAG-ASN : angle 2.44316 ( 174) link_ALPHA1-6 : bond 0.00478 ( 3) link_ALPHA1-6 : angle 1.69196 ( 9) link_BETA1-4 : bond 0.00397 ( 27) link_BETA1-4 : angle 1.61629 ( 81) link_ALPHA1-2 : bond 0.00512 ( 1) link_ALPHA1-2 : angle 1.36358 ( 3) link_ALPHA1-3 : bond 0.01882 ( 4) link_ALPHA1-3 : angle 2.38082 ( 12) hydrogen bonds : bond 0.03040 ( 536) hydrogen bonds : angle 4.62558 ( 1509) SS BOND : bond 0.00260 ( 36) SS BOND : angle 1.04732 ( 72) covalent geometry : bond 0.00266 (17060) covalent geometry : angle 0.54920 (23167) ********************** 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 170 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8636 (t0) cc_final: 0.8421 (t0) REVERT: L 24 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7866 (mtp-110) REVERT: G 162 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8719 (p) REVERT: B 603 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8833 (mm) REVERT: B 632 ASP cc_start: 0.9431 (t0) cc_final: 0.9052 (t0) REVERT: E 161 MET cc_start: 0.8767 (tpp) cc_final: 0.7941 (tpp) REVERT: E 475 MET cc_start: 0.8028 (pmm) cc_final: 0.7664 (ptp) REVERT: F 80 ASN cc_start: 0.9072 (p0) cc_final: 0.8782 (p0) REVERT: C 543 ASN cc_start: 0.8942 (m-40) cc_final: 0.8519 (m110) REVERT: C 620 SER cc_start: 0.8988 (p) cc_final: 0.8374 (p) REVERT: C 624 ASP cc_start: 0.8496 (m-30) cc_final: 0.8072 (m-30) REVERT: C 632 ASP cc_start: 0.9311 (t70) cc_final: 0.8778 (t0) REVERT: A 629 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8827 (mm) outliers start: 43 outliers final: 36 residues processed: 165 average time/residue: 0.2908 time to fit residues: 74.6948 Evaluate side-chains 165 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL 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 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 284 ILE 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 126 CYS Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 258 GLN Chi-restraints excluded: chain E residue 292 VAL 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 129 LEU Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 500 ARG Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 638 TYR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain A residue 543 ASN 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 167 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 59 optimal weight: 0.0870 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6562 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.070558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.054060 restraints weight = 47232.425| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.47 r_work: 0.2817 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17189 Z= 0.111 Angle : 0.580 10.806 23518 Z= 0.271 Chirality : 0.044 0.337 2892 Planarity : 0.003 0.046 2830 Dihedral : 6.817 56.932 4025 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.24 % Allowed : 17.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1923 helix: 1.46 (0.28), residues: 390 sheet: -0.01 (0.23), residues: 533 loop : -0.61 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 479 HIS 0.002 0.001 HIS F 216 PHE 0.006 0.001 PHE E 391 TYR 0.026 0.001 TYR A 638 ARG 0.005 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 58) link_NAG-ASN : angle 2.39188 ( 174) link_ALPHA1-6 : bond 0.00488 ( 3) link_ALPHA1-6 : angle 1.69136 ( 9) link_BETA1-4 : bond 0.00413 ( 27) link_BETA1-4 : angle 1.59858 ( 81) link_ALPHA1-2 : bond 0.00505 ( 1) link_ALPHA1-2 : angle 1.39404 ( 3) link_ALPHA1-3 : bond 0.01911 ( 4) link_ALPHA1-3 : angle 2.32024 ( 12) hydrogen bonds : bond 0.02987 ( 536) hydrogen bonds : angle 4.58417 ( 1509) SS BOND : bond 0.00254 ( 36) SS BOND : angle 1.00102 ( 72) covalent geometry : bond 0.00244 (17060) covalent geometry : angle 0.53115 (23167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7384.77 seconds wall clock time: 129 minutes 21.71 seconds (7761.71 seconds total)