Starting phenix.real_space_refine on Thu Mar 5 08:08:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6um5_20817/03_2026/6um5_20817_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6um5_20817/03_2026/6um5_20817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6um5_20817/03_2026/6um5_20817_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6um5_20817/03_2026/6um5_20817_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6um5_20817/03_2026/6um5_20817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6um5_20817/03_2026/6um5_20817.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 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 135 5.16 5 C 12822 2.51 5 N 3381 2.21 5 O 4224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20562 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 434} Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 434} Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 434} Chain: "J" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "M" 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: "N" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 2, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 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: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 2, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "V" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} 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: "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: 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: "Y" 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: "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: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 2, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} 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: "d" 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "g" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.84, per 1000 atoms: 0.24 Number of scatterers: 20562 At special positions: 0 Unit cell: (157.68, 160.92, 140.4, 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 135 16.00 O 4224 8.00 N 3381 7.00 C 12822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.12 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=1.98 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=1.86 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 155 " distance=2.09 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 433 " distance=2.05 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.15 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=1.99 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.00 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.15 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.25 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.12 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=1.98 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=1.86 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 155 " distance=2.09 Simple disulfide: pdb=" SG CYS E 200 " - pdb=" SG CYS E 433 " distance=2.05 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.01 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.15 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=1.99 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=2.00 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.15 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.25 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.12 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=1.98 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=1.86 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 155 " distance=2.09 Simple disulfide: pdb=" SG CYS I 200 " - pdb=" SG CYS I 433 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.01 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.15 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=1.99 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.00 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.15 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.25 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 Atom "HETATM20210 O5 NAG A 618 .*. O " rejected from bonding due to valence issues. Atom "HETATM20336 O5 NAG E 618 .*. O " rejected from bonding due to valence issues. Atom "HETATM20462 O5 NAG I 618 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN U 4 " - " MAN U 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA U 3 " - " MAN U 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA N 6 " - " MAN N 7 " " BMA U 6 " - " MAN U 7 " " BMA b 6 " - " MAN b 7 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " BMA O 3 " - " NAG O 4 " " 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 R 2 " - " BMA R 3 " " 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 " " BMA V 3 " - " NAG V 4 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " BMA c 3 " - " NAG c 4 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " BETA1-6 " BMA N 3 " - " BMA N 6 " " BMA U 3 " - " BMA U 6 " " BMA b 3 " - " BMA b 6 " NAG-ASN " NAG A 617 " - " ASN A 262 " " NAG A 618 " - " ASN A 386 " " NAG A 619 " - " ASN A 392 " " NAG A 622 " - " ASN A 158 " " NAG A 626 " - " ASN A 362 " " NAG A 627 " - " ASN A 276 " " NAG A 630 " - " ASN A 88 " " NAG A 631 " - " ASN A 241 " " NAG A 632 " - " ASN A 448 " " NAG E 617 " - " ASN E 262 " " NAG E 618 " - " ASN E 386 " " NAG E 619 " - " ASN E 392 " " NAG E 622 " - " ASN E 158 " " NAG E 626 " - " ASN E 362 " " NAG E 627 " - " ASN E 276 " " NAG E 630 " - " ASN E 88 " " NAG E 631 " - " ASN E 241 " " NAG E 632 " - " ASN E 448 " " NAG I 617 " - " ASN I 262 " " NAG I 618 " - " ASN I 386 " " NAG I 619 " - " ASN I 392 " " NAG I 622 " - " ASN I 158 " " NAG I 626 " - " ASN I 362 " " NAG I 627 " - " ASN I 276 " " NAG I 630 " - " ASN I 88 " " NAG I 631 " - " ASN I 241 " " NAG I 632 " - " ASN I 448 " " NAG M 1 " - " ASN A 154 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 300 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN A 339 " " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN E 154 " " NAG U 1 " - " ASN E 332 " " NAG V 1 " - " ASN E 300 " " NAG W 1 " - " ASN E 442 " " NAG X 1 " - " ASN E 197 " " NAG Y 1 " - " ASN E 339 " " NAG Z 1 " - " ASN E 234 " " NAG a 1 " - " ASN I 154 " " NAG b 1 " - " ASN I 332 " " NAG c 1 " - " ASN I 300 " " NAG d 1 " - " ASN I 442 " " NAG e 1 " - " ASN I 197 " " NAG f 1 " - " ASN I 339 " " NAG g 1 " - " ASN I 234 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 48 sheets defined 21.5% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 74 removed outlier: 4.168A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.346A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.511A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 483 removed outlier: 4.018A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.823A pdb=" N LEU B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.626A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.266A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.731A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.265A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 68 through 74 removed outlier: 4.168A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.347A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.512A pdb=" N GLY E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.019A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 525 removed outlier: 3.823A pdb=" N LEU F 523 " --> pdb=" O LEU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.625A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 4.266A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 626 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.730A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 4.265A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 81 through 85 Processing helix chain 'I' and resid 57 through 61 Processing helix chain 'I' and resid 68 through 74 removed outlier: 4.168A pdb=" N HIS I 72 " --> pdb=" O VAL I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 116 removed outlier: 4.346A pdb=" N ASP I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 350 removed outlier: 3.511A pdb=" N GLY I 346 " --> pdb=" O LEU I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 474 through 483 removed outlier: 4.019A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 525 removed outlier: 3.823A pdb=" N LEU J 523 " --> pdb=" O LEU J 520 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 543 removed outlier: 3.626A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 596 removed outlier: 4.266A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 626 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.731A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 4.265A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.690A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 217 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS A 249 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.850A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 136 removed outlier: 9.744A pdb=" N ILE A 130 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LYS A 153 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N SER A 132 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLU A 151 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 134 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 170 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 260 removed outlier: 4.086A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 4.086A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 358 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 361 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.770A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 309 Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.560A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 10 removed outlier: 6.246A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 10 removed outlier: 6.081A pdb=" N THR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.690A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR E 217 " --> pdb=" O HIS E 249 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS E 249 " --> pdb=" O TYR E 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.850A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 130 through 136 removed outlier: 9.744A pdb=" N ILE E 130 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LYS E 153 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N SER E 132 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLU E 151 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA E 134 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 170 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 179 through 180 Processing sheet with id=AC5, first strand: chain 'E' and resid 259 through 260 removed outlier: 4.086A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 260 removed outlier: 4.086A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR E 361 " --> pdb=" O GLY E 393 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.770A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 309 Processing sheet with id=AC9, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.561A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 9 through 10 removed outlier: 6.246A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 9 through 10 removed outlier: 6.081A pdb=" N THR H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD6, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'I' and resid 75 through 76 removed outlier: 6.689A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR I 217 " --> pdb=" O HIS I 249 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS I 249 " --> pdb=" O TYR I 217 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.851A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 130 through 136 removed outlier: 9.744A pdb=" N ILE I 130 " --> pdb=" O LYS I 153 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LYS I 153 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N SER I 132 " --> pdb=" O GLU I 151 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLU I 151 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA I 134 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 179 through 180 Processing sheet with id=AE3, first strand: chain 'I' and resid 259 through 260 removed outlier: 4.087A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 259 through 260 removed outlier: 4.087A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE I 358 " --> pdb=" O TYR I 395 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR I 361 " --> pdb=" O GLY I 393 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 374 through 378 removed outlier: 4.770A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 304 through 309 Processing sheet with id=AE7, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AE8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.560A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.246A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.081A pdb=" N THR L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 18 through 23 750 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3310 1.31 - 1.44: 5955 1.44 - 1.57: 11525 1.57 - 1.70: 0 1.70 - 1.83: 186 Bond restraints: 20976 Sorted by residual: bond pdb=" N PRO I 354 " pdb=" CA PRO I 354 " ideal model delta sigma weight residual 1.469 1.702 -0.234 1.28e-02 6.10e+03 3.33e+02 bond pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 1.469 1.702 -0.234 1.28e-02 6.10e+03 3.33e+02 bond pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 1.469 1.702 -0.233 1.28e-02 6.10e+03 3.31e+02 bond pdb=" N PRO I 220 " pdb=" CD PRO I 220 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.13e+01 bond pdb=" N PRO E 220 " pdb=" CD PRO E 220 " ideal model delta sigma weight residual 1.473 1.395 0.078 1.40e-02 5.10e+03 3.11e+01 ... (remaining 20971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 27826 4.69 - 9.39: 582 9.39 - 14.08: 80 14.08 - 18.77: 12 18.77 - 23.46: 9 Bond angle restraints: 28509 Sorted by residual: angle pdb=" C PHE I 353 " pdb=" N PRO I 354 " pdb=" CA PRO I 354 " ideal model delta sigma weight residual 119.84 139.04 -19.20 1.25e+00 6.40e-01 2.36e+02 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.84 139.03 -19.19 1.25e+00 6.40e-01 2.36e+02 angle pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.84 139.02 -19.18 1.25e+00 6.40e-01 2.35e+02 angle pdb=" C ASN E 197 " pdb=" CA ASN E 197 " pdb=" CB ASN E 197 " ideal model delta sigma weight residual 110.79 91.24 19.55 1.66e+00 3.63e-01 1.39e+02 angle pdb=" C ASN I 197 " pdb=" CA ASN I 197 " pdb=" CB ASN I 197 " ideal model delta sigma weight residual 110.79 91.26 19.53 1.66e+00 3.63e-01 1.38e+02 ... (remaining 28504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 12768 23.00 - 46.01: 663 46.01 - 69.01: 189 69.01 - 92.02: 87 92.02 - 115.02: 60 Dihedral angle restraints: 13767 sinusoidal: 6615 harmonic: 7152 Sorted by residual: dihedral pdb=" C HIS I 249 " pdb=" N HIS I 249 " pdb=" CA HIS I 249 " pdb=" CB HIS I 249 " ideal model delta harmonic sigma weight residual -122.60 -93.20 -29.40 0 2.50e+00 1.60e-01 1.38e+02 dihedral pdb=" C HIS E 249 " pdb=" N HIS E 249 " pdb=" CA HIS E 249 " pdb=" CB HIS E 249 " ideal model delta harmonic sigma weight residual -122.60 -93.23 -29.37 0 2.50e+00 1.60e-01 1.38e+02 dihedral pdb=" C HIS A 249 " pdb=" N HIS A 249 " pdb=" CA HIS A 249 " pdb=" CB HIS A 249 " ideal model delta harmonic sigma weight residual -122.60 -93.24 -29.36 0 2.50e+00 1.60e-01 1.38e+02 ... (remaining 13764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 3360 0.271 - 0.541: 96 0.541 - 0.812: 15 0.812 - 1.082: 3 1.082 - 1.353: 6 Chirality restraints: 3480 Sorted by residual: chirality pdb=" C1 MAN U 7 " pdb=" O6 BMA U 6 " pdb=" C2 MAN U 7 " pdb=" O5 MAN U 7 " both_signs ideal model delta sigma weight residual False 2.40 1.05 1.35 2.00e-02 2.50e+03 4.57e+03 chirality pdb=" C1 MAN N 7 " pdb=" O6 BMA N 6 " pdb=" C2 MAN N 7 " pdb=" O5 MAN N 7 " both_signs ideal model delta sigma weight residual False 2.40 1.05 1.35 2.00e-02 2.50e+03 4.56e+03 chirality pdb=" C1 MAN b 7 " pdb=" O6 BMA b 6 " pdb=" C2 MAN b 7 " pdb=" O5 MAN b 7 " both_signs ideal model delta sigma weight residual False 2.40 1.05 1.35 2.00e-02 2.50e+03 4.56e+03 ... (remaining 3477 not shown) Planarity restraints: 3549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 622 " -0.317 2.00e-02 2.50e+03 2.63e-01 8.65e+02 pdb=" C7 NAG I 622 " 0.100 2.00e-02 2.50e+03 pdb=" C8 NAG I 622 " -0.207 2.00e-02 2.50e+03 pdb=" N2 NAG I 622 " 0.439 2.00e-02 2.50e+03 pdb=" O7 NAG I 622 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 622 " 0.316 2.00e-02 2.50e+03 2.63e-01 8.64e+02 pdb=" C7 NAG A 622 " -0.100 2.00e-02 2.50e+03 pdb=" C8 NAG A 622 " 0.207 2.00e-02 2.50e+03 pdb=" N2 NAG A 622 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG A 622 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 622 " -0.316 2.00e-02 2.50e+03 2.63e-01 8.64e+02 pdb=" C7 NAG E 622 " 0.101 2.00e-02 2.50e+03 pdb=" C8 NAG E 622 " -0.207 2.00e-02 2.50e+03 pdb=" N2 NAG E 622 " 0.438 2.00e-02 2.50e+03 pdb=" O7 NAG E 622 " -0.015 2.00e-02 2.50e+03 ... (remaining 3546 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 330 2.60 - 3.17: 17866 3.17 - 3.75: 29267 3.75 - 4.32: 40517 4.32 - 4.90: 65542 Nonbonded interactions: 153522 Sorted by model distance: nonbonded pdb=" O3 NAG A 630 " pdb=" O7 NAG A 630 " model vdw 2.022 3.040 nonbonded pdb=" O3 NAG E 630 " pdb=" O7 NAG E 630 " model vdw 2.022 3.040 nonbonded pdb=" O3 NAG I 630 " pdb=" O7 NAG I 630 " model vdw 2.022 3.040 nonbonded pdb=" O4 NAG I 626 " pdb=" O6 NAG I 626 " model vdw 2.029 3.040 nonbonded pdb=" O4 NAG A 626 " pdb=" O6 NAG A 626 " model vdw 2.029 3.040 ... (remaining 153517 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'b' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'c' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'W' selection = chain 'Y' selection = chain 'd' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.140 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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 : 0.012 0.234 21114 Z= 0.643 Angle : 1.938 28.767 28881 Z= 0.913 Chirality : 0.118 1.353 3480 Planarity : 0.022 0.263 3501 Dihedral : 17.842 115.020 9069 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 1.22 % Allowed : 5.98 % Favored : 92.80 % Rotamer: Outliers : 4.06 % Allowed : 6.57 % Favored : 89.37 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.16), residues: 2457 helix: -0.81 (0.24), residues: 393 sheet: -0.30 (0.18), residues: 717 loop : -1.98 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 98 TYR 0.013 0.002 TYR G 95 PHE 0.025 0.003 PHE I 353 TRP 0.019 0.002 TRP J 596 HIS 0.005 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.01042 (20976) covalent geometry : angle 1.57455 (28509) SS BOND : bond 0.09325 ( 42) SS BOND : angle 9.91417 ( 84) hydrogen bonds : bond 0.24977 ( 738) hydrogen bonds : angle 8.28831 ( 1872) link_ALPHA1-2 : bond 0.06497 ( 3) link_ALPHA1-2 : angle 21.12874 ( 9) link_ALPHA1-3 : bond 0.06725 ( 3) link_ALPHA1-3 : angle 11.42671 ( 9) link_ALPHA1-6 : bond 0.06431 ( 3) link_ALPHA1-6 : angle 19.69646 ( 9) link_BETA1-4 : bond 0.03764 ( 36) link_BETA1-4 : angle 7.37358 ( 108) link_BETA1-6 : bond 0.06430 ( 3) link_BETA1-6 : angle 17.75689 ( 9) link_NAG-ASN : bond 0.04235 ( 48) link_NAG-ASN : angle 9.20062 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 438 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 SER cc_start: 0.6814 (t) cc_final: 0.6561 (p) REVERT: B 584 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7453 (tm-30) REVERT: F 584 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7339 (tm-30) REVERT: I 99 ASP cc_start: 0.5812 (p0) cc_final: 0.5528 (p0) REVERT: J 584 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7511 (tm-30) outliers start: 87 outliers final: 34 residues processed: 510 average time/residue: 0.1495 time to fit residues: 115.6158 Evaluate side-chains 236 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN A 249 HIS A 289 HIS A 404 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 203 GLN E 249 HIS E 289 HIS E 404 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN G 1 GLN G 39 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 203 GLN I 249 HIS I 289 HIS I 404 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.050250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039239 restraints weight = 136702.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.040567 restraints weight = 82700.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.041482 restraints weight = 59096.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.042136 restraints weight = 46834.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.042589 restraints weight = 39721.723| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 21114 Z= 0.362 Angle : 1.176 17.882 28881 Z= 0.541 Chirality : 0.064 0.660 3480 Planarity : 0.006 0.075 3501 Dihedral : 15.177 88.309 4641 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.86 % Favored : 91.66 % Rotamer: Outliers : 0.37 % Allowed : 4.38 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.51 % Twisted Proline : 3.03 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.16), residues: 2457 helix: -0.43 (0.24), residues: 408 sheet: -0.54 (0.19), residues: 723 loop : -2.06 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 85 TYR 0.017 0.002 TYR G 94 PHE 0.024 0.004 PHE E 157 TRP 0.027 0.003 TRP B 596 HIS 0.005 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00778 (20976) covalent geometry : angle 1.08912 (28509) SS BOND : bond 0.01099 ( 42) SS BOND : angle 1.71903 ( 84) hydrogen bonds : bond 0.06539 ( 738) hydrogen bonds : angle 6.69452 ( 1872) link_ALPHA1-2 : bond 0.00218 ( 3) link_ALPHA1-2 : angle 3.28287 ( 9) link_ALPHA1-3 : bond 0.01012 ( 3) link_ALPHA1-3 : angle 1.04554 ( 9) link_ALPHA1-6 : bond 0.01494 ( 3) link_ALPHA1-6 : angle 1.46815 ( 9) link_BETA1-4 : bond 0.00888 ( 36) link_BETA1-4 : angle 3.48409 ( 108) link_BETA1-6 : bond 0.01006 ( 3) link_BETA1-6 : angle 3.10110 ( 9) link_NAG-ASN : bond 0.01022 ( 48) link_NAG-ASN : angle 5.49157 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 263 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9056 (ttp) cc_final: 0.8708 (ttm) REVERT: A 249 HIS cc_start: 0.8644 (t70) cc_final: 0.8288 (t-90) REVERT: A 369 MET cc_start: 0.9015 (mtp) cc_final: 0.8065 (ttm) REVERT: A 426 MET cc_start: 0.8645 (ptt) cc_final: 0.8093 (ptt) REVERT: A 434 MET cc_start: 0.8326 (mtm) cc_final: 0.7768 (mtm) REVERT: B 574 LYS cc_start: 0.9337 (mptt) cc_final: 0.8926 (mppt) REVERT: B 584 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8215 (tm-30) REVERT: B 589 ASP cc_start: 0.9028 (m-30) cc_final: 0.8506 (t0) REVERT: B 621 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: B 626 MET cc_start: 0.7967 (tpp) cc_final: 0.7696 (tpp) REVERT: C 48 MET cc_start: 0.8799 (mpp) cc_final: 0.8530 (mpp) REVERT: C 83 LEU cc_start: 0.8747 (mm) cc_final: 0.8153 (mm) REVERT: C 90 ASP cc_start: 0.8610 (m-30) cc_final: 0.8338 (m-30) REVERT: D 22 CYS cc_start: 0.5906 (p) cc_final: 0.5523 (p) REVERT: E 95 MET cc_start: 0.8863 (ttp) cc_final: 0.8570 (ttm) REVERT: E 104 MET cc_start: 0.9603 (ttt) cc_final: 0.9360 (ttt) REVERT: E 107 ASP cc_start: 0.8908 (t0) cc_final: 0.8166 (t0) REVERT: E 249 HIS cc_start: 0.8686 (t70) cc_final: 0.8391 (t-90) REVERT: E 369 MET cc_start: 0.9036 (mtp) cc_final: 0.7873 (ttm) REVERT: F 522 PHE cc_start: 0.7854 (m-10) cc_final: 0.7462 (m-10) REVERT: F 584 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8276 (tm-30) REVERT: F 621 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: G 48 MET cc_start: 0.8807 (mpp) cc_final: 0.8297 (mpp) REVERT: G 90 ASP cc_start: 0.8683 (m-30) cc_final: 0.8450 (m-30) REVERT: H 22 CYS cc_start: 0.5763 (p) cc_final: 0.5505 (p) REVERT: I 95 MET cc_start: 0.8940 (ttp) cc_final: 0.8553 (ttm) REVERT: I 249 HIS cc_start: 0.8770 (t70) cc_final: 0.8545 (t-170) REVERT: J 584 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8203 (tm-30) REVERT: J 589 ASP cc_start: 0.9051 (m-30) cc_final: 0.8642 (p0) REVERT: J 621 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: K 48 MET cc_start: 0.8909 (mpp) cc_final: 0.8605 (mpp) REVERT: K 81 MET cc_start: 0.8771 (mtp) cc_final: 0.8519 (ppp) REVERT: K 90 ASP cc_start: 0.8711 (m-30) cc_final: 0.8499 (m-30) REVERT: L 22 CYS cc_start: 0.6171 (p) cc_final: 0.5859 (p) REVERT: L 80 LEU cc_start: 0.9491 (tt) cc_final: 0.9080 (tt) outliers start: 8 outliers final: 0 residues processed: 271 average time/residue: 0.1337 time to fit residues: 57.8009 Evaluate side-chains 182 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 231 optimal weight: 0.8980 chunk 180 optimal weight: 0.0770 chunk 149 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS A 279 ASN A 302 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 279 ASN F 540 GLN H 6 GLN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 HIS I 279 ASN J 540 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.053191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.042019 restraints weight = 131303.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043465 restraints weight = 78272.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.044473 restraints weight = 55262.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.045176 restraints weight = 43269.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.045675 restraints weight = 36410.427| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21114 Z= 0.154 Angle : 0.885 13.127 28881 Z= 0.414 Chirality : 0.056 0.535 3480 Planarity : 0.005 0.070 3501 Dihedral : 13.041 79.349 4641 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.63 % Favored : 93.00 % Rotamer: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.51 % Twisted Proline : 3.03 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.16), residues: 2457 helix: -0.23 (0.25), residues: 399 sheet: -0.04 (0.19), residues: 666 loop : -1.83 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 85 TYR 0.017 0.001 TYR F 638 PHE 0.031 0.002 PHE I 157 TRP 0.023 0.002 TRP D 37 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00308 (20976) covalent geometry : angle 0.79917 (28509) SS BOND : bond 0.00386 ( 42) SS BOND : angle 1.34423 ( 84) hydrogen bonds : bond 0.05336 ( 738) hydrogen bonds : angle 5.83976 ( 1872) link_ALPHA1-2 : bond 0.00974 ( 3) link_ALPHA1-2 : angle 1.80304 ( 9) link_ALPHA1-3 : bond 0.01045 ( 3) link_ALPHA1-3 : angle 1.64902 ( 9) link_ALPHA1-6 : bond 0.01755 ( 3) link_ALPHA1-6 : angle 1.41697 ( 9) link_BETA1-4 : bond 0.00939 ( 36) link_BETA1-4 : angle 3.04732 ( 108) link_BETA1-6 : bond 0.00982 ( 3) link_BETA1-6 : angle 1.99457 ( 9) link_NAG-ASN : bond 0.00931 ( 48) link_NAG-ASN : angle 4.67480 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 274 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 HIS cc_start: 0.8499 (t-90) cc_final: 0.8244 (t70) REVERT: A 288 LEU cc_start: 0.9474 (mp) cc_final: 0.9160 (mp) REVERT: A 303 THR cc_start: 0.7958 (t) cc_final: 0.7655 (t) REVERT: A 426 MET cc_start: 0.8413 (ptt) cc_final: 0.7494 (ptt) REVERT: A 434 MET cc_start: 0.8114 (mtm) cc_final: 0.7376 (mtm) REVERT: B 584 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 589 ASP cc_start: 0.8998 (m-30) cc_final: 0.8400 (t0) REVERT: C 48 MET cc_start: 0.8852 (mpp) cc_final: 0.8587 (mpp) REVERT: C 70 MET cc_start: 0.8401 (mmp) cc_final: 0.7719 (mmm) REVERT: C 90 ASP cc_start: 0.8659 (m-30) cc_final: 0.8245 (m-30) REVERT: D 22 CYS cc_start: 0.5965 (p) cc_final: 0.5602 (p) REVERT: E 95 MET cc_start: 0.8687 (ttp) cc_final: 0.8454 (ttm) REVERT: E 107 ASP cc_start: 0.8836 (t0) cc_final: 0.8582 (t0) REVERT: E 249 HIS cc_start: 0.8525 (t-90) cc_final: 0.8277 (t70) REVERT: F 522 PHE cc_start: 0.7962 (m-10) cc_final: 0.7462 (m-10) REVERT: F 584 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8230 (tm-30) REVERT: G 48 MET cc_start: 0.8835 (mpp) cc_final: 0.8532 (mpp) REVERT: G 70 MET cc_start: 0.8145 (mmp) cc_final: 0.7895 (mmm) REVERT: G 81 MET cc_start: 0.8746 (mtt) cc_final: 0.8278 (tmm) REVERT: G 90 ASP cc_start: 0.8773 (m-30) cc_final: 0.8422 (m-30) REVERT: H 22 CYS cc_start: 0.6199 (p) cc_final: 0.5884 (p) REVERT: I 95 MET cc_start: 0.8867 (ttp) cc_final: 0.8553 (ttm) REVERT: I 157 PHE cc_start: 0.8044 (t80) cc_final: 0.7690 (t80) REVERT: I 249 HIS cc_start: 0.8620 (t-90) cc_final: 0.8369 (t70) REVERT: I 288 LEU cc_start: 0.9513 (mp) cc_final: 0.9195 (mp) REVERT: J 574 LYS cc_start: 0.9332 (mptt) cc_final: 0.9063 (mppt) REVERT: J 584 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8093 (tm-30) REVERT: J 589 ASP cc_start: 0.8940 (m-30) cc_final: 0.8461 (t0) REVERT: J 626 MET cc_start: 0.7662 (tpp) cc_final: 0.7445 (tpp) REVERT: K 48 MET cc_start: 0.8884 (mpp) cc_final: 0.8544 (mpp) REVERT: K 86 LEU cc_start: 0.9388 (mp) cc_final: 0.9180 (mt) REVERT: K 90 ASP cc_start: 0.8783 (m-30) cc_final: 0.8481 (m-30) REVERT: L 22 CYS cc_start: 0.6168 (p) cc_final: 0.5842 (p) outliers start: 4 outliers final: 1 residues processed: 277 average time/residue: 0.1247 time to fit residues: 56.4458 Evaluate side-chains 183 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 111 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 147 optimal weight: 0.0010 chunk 149 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 126 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 overall best weight: 2.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.051019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040164 restraints weight = 133950.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.041521 restraints weight = 80436.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.042478 restraints weight = 57101.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.043149 restraints weight = 44836.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043619 restraints weight = 37813.073| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 21114 Z= 0.203 Angle : 0.864 12.976 28881 Z= 0.411 Chirality : 0.054 0.498 3480 Planarity : 0.005 0.074 3501 Dihedral : 12.031 70.185 4641 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.34 % Favored : 91.29 % Rotamer: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.51 % Twisted Proline : 3.03 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2457 helix: -0.37 (0.24), residues: 405 sheet: -0.32 (0.20), residues: 636 loop : -1.78 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 85 TYR 0.016 0.002 TYR E 217 PHE 0.024 0.002 PHE E 157 TRP 0.015 0.002 TRP E 479 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00438 (20976) covalent geometry : angle 0.78946 (28509) SS BOND : bond 0.00317 ( 42) SS BOND : angle 1.09136 ( 84) hydrogen bonds : bond 0.04622 ( 738) hydrogen bonds : angle 5.72473 ( 1872) link_ALPHA1-2 : bond 0.00350 ( 3) link_ALPHA1-2 : angle 2.24090 ( 9) link_ALPHA1-3 : bond 0.01028 ( 3) link_ALPHA1-3 : angle 1.58459 ( 9) link_ALPHA1-6 : bond 0.01459 ( 3) link_ALPHA1-6 : angle 1.26691 ( 9) link_BETA1-4 : bond 0.00870 ( 36) link_BETA1-4 : angle 2.95809 ( 108) link_BETA1-6 : bond 0.00569 ( 3) link_BETA1-6 : angle 1.52275 ( 9) link_NAG-ASN : bond 0.00860 ( 48) link_NAG-ASN : angle 4.28983 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8945 (ttm) cc_final: 0.8598 (ttm) REVERT: A 195 ASN cc_start: 0.8900 (t0) cc_final: 0.8548 (t0) REVERT: A 288 LEU cc_start: 0.9437 (mp) cc_final: 0.9152 (mp) REVERT: A 369 MET cc_start: 0.8994 (mtp) cc_final: 0.8164 (ttm) REVERT: A 426 MET cc_start: 0.8352 (ptt) cc_final: 0.7489 (ptt) REVERT: A 434 MET cc_start: 0.8468 (mtm) cc_final: 0.7532 (mtm) REVERT: B 522 PHE cc_start: 0.7998 (m-10) cc_final: 0.7331 (m-10) REVERT: B 530 MET cc_start: 0.7902 (mtm) cc_final: 0.7668 (mtm) REVERT: B 584 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8214 (tm-30) REVERT: B 589 ASP cc_start: 0.9018 (m-30) cc_final: 0.8403 (t0) REVERT: B 626 MET cc_start: 0.8142 (tpp) cc_final: 0.7897 (tpp) REVERT: B 648 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8687 (pm20) REVERT: C 48 MET cc_start: 0.8855 (mpp) cc_final: 0.8580 (mpp) REVERT: C 70 MET cc_start: 0.8507 (mmp) cc_final: 0.7621 (mmm) REVERT: C 90 ASP cc_start: 0.8626 (m-30) cc_final: 0.8219 (m-30) REVERT: D 22 CYS cc_start: 0.5935 (p) cc_final: 0.5585 (p) REVERT: D 81 GLN cc_start: 0.6973 (mp10) cc_final: 0.6613 (mp10) REVERT: E 104 MET cc_start: 0.9291 (tmm) cc_final: 0.9079 (tmm) REVERT: E 249 HIS cc_start: 0.8632 (t-90) cc_final: 0.8429 (t70) REVERT: E 288 LEU cc_start: 0.9511 (mp) cc_final: 0.9245 (mp) REVERT: E 369 MET cc_start: 0.9031 (mtp) cc_final: 0.8076 (ttm) REVERT: F 522 PHE cc_start: 0.8067 (m-10) cc_final: 0.7654 (m-80) REVERT: F 584 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8189 (tm-30) REVERT: F 589 ASP cc_start: 0.9130 (t70) cc_final: 0.8675 (t70) REVERT: G 48 MET cc_start: 0.8911 (mpp) cc_final: 0.8382 (mpp) REVERT: G 70 MET cc_start: 0.8329 (mmp) cc_final: 0.8008 (mmm) REVERT: G 81 MET cc_start: 0.8711 (mtt) cc_final: 0.8468 (tmm) REVERT: G 90 ASP cc_start: 0.8815 (m-30) cc_final: 0.8475 (m-30) REVERT: H 22 CYS cc_start: 0.5842 (p) cc_final: 0.5544 (p) REVERT: I 95 MET cc_start: 0.8911 (ttp) cc_final: 0.8586 (ttm) REVERT: I 104 MET cc_start: 0.9657 (ttt) cc_final: 0.9436 (ttt) REVERT: I 157 PHE cc_start: 0.8237 (t80) cc_final: 0.7988 (t80) REVERT: I 195 ASN cc_start: 0.8787 (t0) cc_final: 0.8400 (t0) REVERT: I 288 LEU cc_start: 0.9499 (mp) cc_final: 0.9298 (mp) REVERT: J 584 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8186 (tm-30) REVERT: J 589 ASP cc_start: 0.9043 (m-30) cc_final: 0.8574 (t0) REVERT: K 48 MET cc_start: 0.8860 (mpp) cc_final: 0.8560 (mpp) REVERT: K 52 ASN cc_start: 0.9773 (t0) cc_final: 0.9569 (t0) REVERT: K 90 ASP cc_start: 0.8771 (m-30) cc_final: 0.8496 (m-30) outliers start: 3 outliers final: 1 residues processed: 246 average time/residue: 0.1297 time to fit residues: 51.8761 Evaluate side-chains 167 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 82 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 168 optimal weight: 0.0670 chunk 164 optimal weight: 9.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 287 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.050855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.040007 restraints weight = 133125.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041357 restraints weight = 80250.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.042310 restraints weight = 56975.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.042978 restraints weight = 44802.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.043449 restraints weight = 37780.803| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21114 Z= 0.179 Angle : 0.843 14.989 28881 Z= 0.401 Chirality : 0.054 0.468 3480 Planarity : 0.004 0.070 3501 Dihedral : 11.434 68.349 4641 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.06 % Favored : 91.70 % Rotamer: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.51 % Twisted Proline : 3.03 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.16), residues: 2457 helix: -0.34 (0.24), residues: 408 sheet: -0.42 (0.20), residues: 618 loop : -1.67 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 85 TYR 0.016 0.001 TYR C 94 PHE 0.016 0.002 PHE L 101 TRP 0.017 0.002 TRP A 479 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00385 (20976) covalent geometry : angle 0.76637 (28509) SS BOND : bond 0.00430 ( 42) SS BOND : angle 1.37125 ( 84) hydrogen bonds : bond 0.04252 ( 738) hydrogen bonds : angle 5.52645 ( 1872) link_ALPHA1-2 : bond 0.00498 ( 3) link_ALPHA1-2 : angle 1.98301 ( 9) link_ALPHA1-3 : bond 0.01125 ( 3) link_ALPHA1-3 : angle 1.68781 ( 9) link_ALPHA1-6 : bond 0.01319 ( 3) link_ALPHA1-6 : angle 1.32812 ( 9) link_BETA1-4 : bond 0.00865 ( 36) link_BETA1-4 : angle 2.87615 ( 108) link_BETA1-6 : bond 0.00724 ( 3) link_BETA1-6 : angle 1.46791 ( 9) link_NAG-ASN : bond 0.00831 ( 48) link_NAG-ASN : angle 4.28821 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8985 (ttm) cc_final: 0.8671 (ttm) REVERT: A 104 MET cc_start: 0.9250 (ppp) cc_final: 0.8864 (ppp) REVERT: A 195 ASN cc_start: 0.8798 (t0) cc_final: 0.8529 (t0) REVERT: A 288 LEU cc_start: 0.9484 (mp) cc_final: 0.9201 (mp) REVERT: A 369 MET cc_start: 0.9077 (mtp) cc_final: 0.8265 (ttm) REVERT: A 426 MET cc_start: 0.8380 (ptt) cc_final: 0.6936 (ptt) REVERT: A 434 MET cc_start: 0.8651 (mtm) cc_final: 0.7455 (mtm) REVERT: B 522 PHE cc_start: 0.8081 (m-10) cc_final: 0.7453 (m-10) REVERT: B 584 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8136 (tm-30) REVERT: B 626 MET cc_start: 0.7739 (tpp) cc_final: 0.7202 (mmm) REVERT: B 648 GLU cc_start: 0.8959 (pm20) cc_final: 0.8737 (pm20) REVERT: C 48 MET cc_start: 0.8798 (mpp) cc_final: 0.8492 (mpp) REVERT: C 52 ASN cc_start: 0.9731 (t0) cc_final: 0.9512 (t0) REVERT: C 70 MET cc_start: 0.8596 (mmp) cc_final: 0.8020 (mmm) REVERT: D 22 CYS cc_start: 0.5978 (p) cc_final: 0.5667 (p) REVERT: E 95 MET cc_start: 0.9002 (ttm) cc_final: 0.8637 (ttm) REVERT: E 104 MET cc_start: 0.9267 (tmm) cc_final: 0.8994 (tmm) REVERT: E 288 LEU cc_start: 0.9516 (mp) cc_final: 0.9272 (mp) REVERT: E 369 MET cc_start: 0.9026 (mtp) cc_final: 0.8040 (ttm) REVERT: F 522 PHE cc_start: 0.8042 (m-10) cc_final: 0.7706 (m-80) REVERT: F 584 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8228 (tm-30) REVERT: F 589 ASP cc_start: 0.9164 (t70) cc_final: 0.8688 (t70) REVERT: G 48 MET cc_start: 0.8932 (mpp) cc_final: 0.8421 (mpp) REVERT: G 70 MET cc_start: 0.8189 (mmp) cc_final: 0.7946 (mmm) REVERT: H 22 CYS cc_start: 0.5999 (p) cc_final: 0.5732 (p) REVERT: I 95 MET cc_start: 0.8917 (ttp) cc_final: 0.8639 (ttm) REVERT: I 195 ASN cc_start: 0.8664 (t0) cc_final: 0.8376 (t0) REVERT: I 288 LEU cc_start: 0.9511 (mp) cc_final: 0.9185 (mp) REVERT: I 369 MET cc_start: 0.8768 (mtt) cc_final: 0.8397 (ttm) REVERT: I 434 MET cc_start: 0.8324 (ttm) cc_final: 0.7823 (ttm) REVERT: J 584 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8265 (tm-30) REVERT: J 589 ASP cc_start: 0.9009 (m-30) cc_final: 0.8562 (t0) REVERT: K 48 MET cc_start: 0.8859 (mpp) cc_final: 0.8468 (mpp) REVERT: K 52 ASN cc_start: 0.9757 (t0) cc_final: 0.9498 (t0) REVERT: K 70 MET cc_start: 0.8397 (mmp) cc_final: 0.8050 (mmm) REVERT: L 22 CYS cc_start: 0.5916 (p) cc_final: 0.5602 (p) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.1284 time to fit residues: 49.1167 Evaluate side-chains 168 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 21 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 46 optimal weight: 0.0050 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 173 optimal weight: 0.0170 chunk 101 optimal weight: 0.3980 chunk 191 optimal weight: 7.9990 overall best weight: 0.6434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 374 HIS A 478 ASN B 591 GLN C 6 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN G 6 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 HIS ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041451 restraints weight = 131576.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.042837 restraints weight = 78745.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.043814 restraints weight = 55571.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.044497 restraints weight = 43392.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.044976 restraints weight = 36420.007| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21114 Z= 0.129 Angle : 0.796 14.111 28881 Z= 0.378 Chirality : 0.053 0.500 3480 Planarity : 0.004 0.070 3501 Dihedral : 10.577 65.342 4641 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.20 % Favored : 92.47 % Rotamer: Outliers : 0.14 % Allowed : 1.86 % Favored : 98.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.05 % Cis-general : 0.51 % Twisted Proline : 1.01 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.16), residues: 2457 helix: -0.00 (0.25), residues: 381 sheet: -0.40 (0.19), residues: 660 loop : -1.67 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 85 TYR 0.017 0.001 TYR K 95 PHE 0.032 0.002 PHE I 157 TRP 0.039 0.001 TRP J 596 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00263 (20976) covalent geometry : angle 0.72234 (28509) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.30415 ( 84) hydrogen bonds : bond 0.03906 ( 738) hydrogen bonds : angle 5.30881 ( 1872) link_ALPHA1-2 : bond 0.00715 ( 3) link_ALPHA1-2 : angle 1.58354 ( 9) link_ALPHA1-3 : bond 0.01126 ( 3) link_ALPHA1-3 : angle 2.02268 ( 9) link_ALPHA1-6 : bond 0.01311 ( 3) link_ALPHA1-6 : angle 1.42542 ( 9) link_BETA1-4 : bond 0.00906 ( 36) link_BETA1-4 : angle 2.85415 ( 108) link_BETA1-6 : bond 0.00897 ( 3) link_BETA1-6 : angle 1.49442 ( 9) link_NAG-ASN : bond 0.00620 ( 48) link_NAG-ASN : angle 3.98604 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 252 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8989 (ttm) cc_final: 0.8672 (ttm) REVERT: A 195 ASN cc_start: 0.8771 (t0) cc_final: 0.8457 (t0) REVERT: A 249 HIS cc_start: 0.8710 (t-90) cc_final: 0.8448 (t70) REVERT: A 288 LEU cc_start: 0.9454 (mp) cc_final: 0.9236 (mp) REVERT: A 369 MET cc_start: 0.9056 (mtp) cc_final: 0.8258 (ttm) REVERT: A 426 MET cc_start: 0.8281 (ptt) cc_final: 0.6987 (ptt) REVERT: A 434 MET cc_start: 0.8467 (mtm) cc_final: 0.7274 (mtm) REVERT: B 584 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 648 GLU cc_start: 0.8966 (pm20) cc_final: 0.8709 (pm20) REVERT: C 48 MET cc_start: 0.8888 (mpp) cc_final: 0.8626 (mpp) REVERT: C 70 MET cc_start: 0.8472 (mmp) cc_final: 0.7650 (mmm) REVERT: D 22 CYS cc_start: 0.5968 (p) cc_final: 0.5576 (p) REVERT: D 100 ILE cc_start: 0.9664 (mm) cc_final: 0.9329 (tp) REVERT: E 95 MET cc_start: 0.8971 (ttm) cc_final: 0.8563 (ttm) REVERT: E 104 MET cc_start: 0.9362 (tmm) cc_final: 0.8973 (tmm) REVERT: E 290 THR cc_start: 0.8229 (p) cc_final: 0.7753 (p) REVERT: E 369 MET cc_start: 0.9003 (mtp) cc_final: 0.8050 (ttm) REVERT: F 584 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8076 (tm-30) REVERT: F 585 ARG cc_start: 0.9213 (ttm110) cc_final: 0.8779 (mtp-110) REVERT: F 589 ASP cc_start: 0.9115 (t70) cc_final: 0.8631 (t70) REVERT: G 48 MET cc_start: 0.8902 (mpp) cc_final: 0.8352 (mpp) REVERT: G 70 MET cc_start: 0.8343 (mmp) cc_final: 0.7745 (mmm) REVERT: I 95 MET cc_start: 0.8867 (ttp) cc_final: 0.8629 (ttm) REVERT: I 195 ASN cc_start: 0.8688 (t0) cc_final: 0.8360 (t0) REVERT: I 249 HIS cc_start: 0.8764 (t-90) cc_final: 0.8464 (t70) REVERT: I 288 LEU cc_start: 0.9443 (mp) cc_final: 0.9209 (mp) REVERT: I 369 MET cc_start: 0.8811 (mtt) cc_final: 0.8345 (ttm) REVERT: I 389 ASN cc_start: 0.9444 (m-40) cc_final: 0.8806 (t0) REVERT: I 434 MET cc_start: 0.7969 (ttm) cc_final: 0.7762 (ttm) REVERT: J 581 LEU cc_start: 0.9482 (tp) cc_final: 0.9157 (pp) REVERT: J 584 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8102 (tm-30) REVERT: J 589 ASP cc_start: 0.9027 (m-30) cc_final: 0.8614 (t0) REVERT: K 34 MET cc_start: 0.9291 (tpt) cc_final: 0.8932 (mmm) REVERT: K 48 MET cc_start: 0.8809 (mpp) cc_final: 0.8437 (mpp) REVERT: K 52 ASN cc_start: 0.9747 (t0) cc_final: 0.9532 (t0) REVERT: L 22 CYS cc_start: 0.5969 (p) cc_final: 0.5698 (p) outliers start: 3 outliers final: 0 residues processed: 255 average time/residue: 0.1342 time to fit residues: 54.1817 Evaluate side-chains 172 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 103 optimal weight: 0.9990 chunk 187 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 0.0370 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 177 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.050381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.039691 restraints weight = 134257.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041026 restraints weight = 80542.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.041961 restraints weight = 57144.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.042610 restraints weight = 44891.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.043078 restraints weight = 37890.794| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21114 Z= 0.198 Angle : 0.836 13.039 28881 Z= 0.406 Chirality : 0.054 0.506 3480 Planarity : 0.004 0.069 3501 Dihedral : 10.382 64.173 4641 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.63 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.16), residues: 2457 helix: -0.30 (0.25), residues: 390 sheet: -0.54 (0.19), residues: 699 loop : -1.66 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 164 TYR 0.018 0.001 TYR C 95 PHE 0.042 0.002 PHE F 522 TRP 0.021 0.002 TRP D 37 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00432 (20976) covalent geometry : angle 0.76366 (28509) SS BOND : bond 0.00413 ( 42) SS BOND : angle 1.17940 ( 84) hydrogen bonds : bond 0.04163 ( 738) hydrogen bonds : angle 5.47649 ( 1872) link_ALPHA1-2 : bond 0.00327 ( 3) link_ALPHA1-2 : angle 2.27073 ( 9) link_ALPHA1-3 : bond 0.01190 ( 3) link_ALPHA1-3 : angle 1.73048 ( 9) link_ALPHA1-6 : bond 0.01184 ( 3) link_ALPHA1-6 : angle 1.18791 ( 9) link_BETA1-4 : bond 0.00853 ( 36) link_BETA1-4 : angle 2.84113 ( 108) link_BETA1-6 : bond 0.00643 ( 3) link_BETA1-6 : angle 1.26889 ( 9) link_NAG-ASN : bond 0.00718 ( 48) link_NAG-ASN : angle 4.12869 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9007 (ttm) cc_final: 0.8689 (ttm) REVERT: A 195 ASN cc_start: 0.8770 (t0) cc_final: 0.8512 (t0) REVERT: A 249 HIS cc_start: 0.8701 (t-90) cc_final: 0.8412 (t-90) REVERT: A 369 MET cc_start: 0.9117 (mtp) cc_final: 0.8334 (ttm) REVERT: A 426 MET cc_start: 0.8392 (ptt) cc_final: 0.7038 (ptt) REVERT: A 434 MET cc_start: 0.8581 (mtm) cc_final: 0.7230 (mtm) REVERT: B 584 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8164 (tm-30) REVERT: C 48 MET cc_start: 0.8813 (mpp) cc_final: 0.8397 (mpp) REVERT: C 52 ASN cc_start: 0.9680 (t0) cc_final: 0.9442 (t0) REVERT: D 22 CYS cc_start: 0.5882 (p) cc_final: 0.5635 (p) REVERT: E 52 LEU cc_start: 0.9692 (mt) cc_final: 0.9254 (mp) REVERT: E 95 MET cc_start: 0.9055 (ttm) cc_final: 0.8677 (ttm) REVERT: E 104 MET cc_start: 0.9385 (tmm) cc_final: 0.9008 (tmm) REVERT: E 249 HIS cc_start: 0.8832 (t70) cc_final: 0.8632 (t-90) REVERT: E 369 MET cc_start: 0.9027 (mtp) cc_final: 0.8102 (ttm) REVERT: F 522 PHE cc_start: 0.8257 (m-80) cc_final: 0.7865 (m-80) REVERT: F 584 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8186 (tm-30) REVERT: F 589 ASP cc_start: 0.9155 (t70) cc_final: 0.8882 (t70) REVERT: G 34 MET cc_start: 0.8919 (mmm) cc_final: 0.8688 (mmm) REVERT: G 48 MET cc_start: 0.8936 (mpp) cc_final: 0.8378 (mpp) REVERT: H 22 CYS cc_start: 0.6039 (p) cc_final: 0.5820 (p) REVERT: I 104 MET cc_start: 0.9199 (ppp) cc_final: 0.8951 (ppp) REVERT: I 195 ASN cc_start: 0.8690 (t0) cc_final: 0.8342 (t0) REVERT: I 249 HIS cc_start: 0.8754 (t-90) cc_final: 0.8442 (t-90) REVERT: I 288 LEU cc_start: 0.9452 (mp) cc_final: 0.9202 (mp) REVERT: I 369 MET cc_start: 0.8859 (mtt) cc_final: 0.8393 (ttm) REVERT: J 581 LEU cc_start: 0.9518 (tp) cc_final: 0.9193 (pp) REVERT: J 584 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8256 (tm-30) REVERT: J 589 ASP cc_start: 0.9080 (m-30) cc_final: 0.8683 (t0) REVERT: K 34 MET cc_start: 0.9003 (tpt) cc_final: 0.8748 (mmm) REVERT: K 48 MET cc_start: 0.8889 (mpp) cc_final: 0.8406 (mpp) REVERT: K 52 ASN cc_start: 0.9704 (t0) cc_final: 0.9393 (t0) REVERT: K 70 MET cc_start: 0.8372 (mmp) cc_final: 0.8135 (mmm) REVERT: L 22 CYS cc_start: 0.5935 (p) cc_final: 0.5648 (p) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1272 time to fit residues: 46.4680 Evaluate side-chains 166 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 235 optimal weight: 0.1980 chunk 223 optimal weight: 10.0000 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.051211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.040496 restraints weight = 132982.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.041854 restraints weight = 79678.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.042807 restraints weight = 56437.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.043471 restraints weight = 44264.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.043947 restraints weight = 37266.162| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21114 Z= 0.143 Angle : 0.793 12.917 28881 Z= 0.383 Chirality : 0.052 0.465 3480 Planarity : 0.004 0.070 3501 Dihedral : 10.128 62.087 4641 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.81 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.16), residues: 2457 helix: -0.26 (0.25), residues: 390 sheet: -0.55 (0.19), residues: 669 loop : -1.65 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 585 TYR 0.021 0.001 TYR E 217 PHE 0.026 0.001 PHE I 157 TRP 0.019 0.001 TRP D 37 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00301 (20976) covalent geometry : angle 0.72271 (28509) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.02665 ( 84) hydrogen bonds : bond 0.03962 ( 738) hydrogen bonds : angle 5.36063 ( 1872) link_ALPHA1-2 : bond 0.00628 ( 3) link_ALPHA1-2 : angle 1.95543 ( 9) link_ALPHA1-3 : bond 0.01221 ( 3) link_ALPHA1-3 : angle 1.97171 ( 9) link_ALPHA1-6 : bond 0.01124 ( 3) link_ALPHA1-6 : angle 1.29972 ( 9) link_BETA1-4 : bond 0.00868 ( 36) link_BETA1-4 : angle 2.82305 ( 108) link_BETA1-6 : bond 0.00932 ( 3) link_BETA1-6 : angle 1.26882 ( 9) link_NAG-ASN : bond 0.00742 ( 48) link_NAG-ASN : angle 3.93345 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9026 (ttm) cc_final: 0.8698 (ttm) REVERT: A 195 ASN cc_start: 0.8783 (t0) cc_final: 0.8529 (t0) REVERT: A 249 HIS cc_start: 0.8727 (t-90) cc_final: 0.8452 (t70) REVERT: A 369 MET cc_start: 0.9092 (mtp) cc_final: 0.8310 (ttm) REVERT: A 426 MET cc_start: 0.8366 (ptt) cc_final: 0.6885 (ptt) REVERT: A 434 MET cc_start: 0.8524 (mtm) cc_final: 0.7265 (mtm) REVERT: B 584 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8142 (tm-30) REVERT: C 48 MET cc_start: 0.8848 (mpp) cc_final: 0.8445 (mpp) REVERT: C 52 ASN cc_start: 0.9674 (t0) cc_final: 0.9457 (t0) REVERT: C 70 MET cc_start: 0.8343 (mmp) cc_final: 0.7547 (mmm) REVERT: D 22 CYS cc_start: 0.5965 (p) cc_final: 0.5668 (p) REVERT: E 40 TYR cc_start: 0.8888 (t80) cc_final: 0.8408 (t80) REVERT: E 95 MET cc_start: 0.9001 (ttm) cc_final: 0.8589 (ttm) REVERT: E 369 MET cc_start: 0.9016 (mtp) cc_final: 0.8091 (ttm) REVERT: F 584 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8252 (tm-30) REVERT: F 585 ARG cc_start: 0.9236 (ttm110) cc_final: 0.8946 (ttm110) REVERT: F 589 ASP cc_start: 0.9117 (t70) cc_final: 0.8825 (t70) REVERT: G 34 MET cc_start: 0.8910 (mmm) cc_final: 0.8616 (mmm) REVERT: G 48 MET cc_start: 0.8971 (mpp) cc_final: 0.8449 (mpp) REVERT: H 22 CYS cc_start: 0.6082 (p) cc_final: 0.5867 (p) REVERT: I 95 MET cc_start: 0.9133 (ttm) cc_final: 0.8673 (ttm) REVERT: I 195 ASN cc_start: 0.8795 (t0) cc_final: 0.8511 (t0) REVERT: I 249 HIS cc_start: 0.8728 (t-90) cc_final: 0.8501 (t70) REVERT: I 288 LEU cc_start: 0.9395 (mp) cc_final: 0.9182 (mp) REVERT: I 369 MET cc_start: 0.8938 (mtt) cc_final: 0.8595 (ttm) REVERT: J 581 LEU cc_start: 0.9507 (tp) cc_final: 0.9184 (pp) REVERT: J 584 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8243 (tm-30) REVERT: K 48 MET cc_start: 0.8902 (mpp) cc_final: 0.8432 (mpp) REVERT: K 52 ASN cc_start: 0.9726 (t0) cc_final: 0.9458 (t0) REVERT: K 70 MET cc_start: 0.8398 (mmp) cc_final: 0.8129 (mmm) REVERT: L 22 CYS cc_start: 0.5940 (p) cc_final: 0.5673 (p) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1273 time to fit residues: 47.7542 Evaluate side-chains 164 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 43 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 227 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 16 optimal weight: 0.0370 chunk 156 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 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 = 0.3261 r_free = 0.3261 target = 0.051794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.040952 restraints weight = 130409.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.042333 restraints weight = 78657.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043293 restraints weight = 55844.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.043969 restraints weight = 43880.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.044434 restraints weight = 36948.527| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21114 Z= 0.130 Angle : 0.786 13.004 28881 Z= 0.381 Chirality : 0.052 0.444 3480 Planarity : 0.004 0.071 3501 Dihedral : 9.888 60.308 4641 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.57 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.16), residues: 2457 helix: -0.32 (0.25), residues: 390 sheet: -0.48 (0.19), residues: 693 loop : -1.59 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 585 TYR 0.013 0.001 TYR K 95 PHE 0.026 0.002 PHE I 157 TRP 0.021 0.001 TRP E 45 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00266 (20976) covalent geometry : angle 0.71930 (28509) SS BOND : bond 0.00313 ( 42) SS BOND : angle 1.03259 ( 84) hydrogen bonds : bond 0.03935 ( 738) hydrogen bonds : angle 5.38044 ( 1872) link_ALPHA1-2 : bond 0.00652 ( 3) link_ALPHA1-2 : angle 1.84614 ( 9) link_ALPHA1-3 : bond 0.01154 ( 3) link_ALPHA1-3 : angle 2.03602 ( 9) link_ALPHA1-6 : bond 0.01017 ( 3) link_ALPHA1-6 : angle 1.31957 ( 9) link_BETA1-4 : bond 0.00865 ( 36) link_BETA1-4 : angle 2.82112 ( 108) link_BETA1-6 : bond 0.00805 ( 3) link_BETA1-6 : angle 1.23258 ( 9) link_NAG-ASN : bond 0.00688 ( 48) link_NAG-ASN : angle 3.78417 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9018 (ttm) cc_final: 0.8696 (ttm) REVERT: A 195 ASN cc_start: 0.8796 (t0) cc_final: 0.8544 (t0) REVERT: A 249 HIS cc_start: 0.8768 (t-90) cc_final: 0.8451 (t70) REVERT: A 369 MET cc_start: 0.9077 (mtp) cc_final: 0.8319 (ttm) REVERT: A 426 MET cc_start: 0.8350 (ptt) cc_final: 0.6850 (ptt) REVERT: A 434 MET cc_start: 0.8506 (mtm) cc_final: 0.7240 (mtm) REVERT: B 584 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 648 GLU cc_start: 0.8949 (pm20) cc_final: 0.8559 (pm20) REVERT: C 48 MET cc_start: 0.8847 (mpp) cc_final: 0.8391 (mpp) REVERT: C 70 MET cc_start: 0.8316 (mmp) cc_final: 0.7575 (mmm) REVERT: D 4 LEU cc_start: 0.8136 (mm) cc_final: 0.7919 (mt) REVERT: D 22 CYS cc_start: 0.6004 (p) cc_final: 0.5630 (p) REVERT: D 100 ILE cc_start: 0.9654 (mm) cc_final: 0.9317 (tp) REVERT: E 95 MET cc_start: 0.8978 (ttm) cc_final: 0.8586 (ttm) REVERT: E 369 MET cc_start: 0.9004 (mtp) cc_final: 0.8092 (ttm) REVERT: E 389 ASN cc_start: 0.9376 (m-40) cc_final: 0.8840 (t0) REVERT: F 584 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8253 (tm-30) REVERT: F 589 ASP cc_start: 0.9151 (t70) cc_final: 0.8861 (t70) REVERT: F 647 GLU cc_start: 0.9242 (pm20) cc_final: 0.8990 (pm20) REVERT: F 648 GLU cc_start: 0.9111 (pm20) cc_final: 0.8601 (pm20) REVERT: G 34 MET cc_start: 0.8924 (mmm) cc_final: 0.8603 (mmm) REVERT: G 48 MET cc_start: 0.8993 (mpp) cc_final: 0.8497 (mpp) REVERT: G 82 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8639 (mm-30) REVERT: I 40 TYR cc_start: 0.9142 (t80) cc_final: 0.7365 (t80) REVERT: I 95 MET cc_start: 0.9140 (ttm) cc_final: 0.8690 (ttm) REVERT: I 195 ASN cc_start: 0.8807 (t0) cc_final: 0.8576 (t0) REVERT: I 369 MET cc_start: 0.8913 (mtt) cc_final: 0.8593 (ttm) REVERT: I 389 ASN cc_start: 0.9413 (m-40) cc_final: 0.8892 (t0) REVERT: J 581 LEU cc_start: 0.9503 (tp) cc_final: 0.9141 (pp) REVERT: J 584 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8262 (tm-30) REVERT: J 589 ASP cc_start: 0.8972 (m-30) cc_final: 0.8628 (t70) REVERT: J 626 MET cc_start: 0.7078 (tpp) cc_final: 0.6561 (tpp) REVERT: J 648 GLU cc_start: 0.9091 (pm20) cc_final: 0.8617 (pm20) REVERT: K 34 MET cc_start: 0.9010 (tpt) cc_final: 0.8763 (tmm) REVERT: K 48 MET cc_start: 0.8892 (mpp) cc_final: 0.8440 (mpp) REVERT: K 52 ASN cc_start: 0.9723 (t0) cc_final: 0.9457 (t0) REVERT: K 70 MET cc_start: 0.8300 (mmp) cc_final: 0.8091 (mmm) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1319 time to fit residues: 50.5188 Evaluate side-chains 171 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 171 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 182 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN C 39 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 350 GLN ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.049512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.038862 restraints weight = 135780.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.040158 restraints weight = 82312.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.041066 restraints weight = 58887.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.041695 restraints weight = 46562.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.042136 restraints weight = 39553.738| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21114 Z= 0.229 Angle : 0.849 12.517 28881 Z= 0.415 Chirality : 0.053 0.478 3480 Planarity : 0.004 0.068 3501 Dihedral : 10.197 59.985 4641 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.89 % Favored : 89.95 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.16), residues: 2457 helix: -0.49 (0.24), residues: 390 sheet: -0.66 (0.18), residues: 714 loop : -1.68 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 164 TYR 0.015 0.002 TYR C 80 PHE 0.022 0.002 PHE A 157 TRP 0.023 0.002 TRP A 112 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00500 (20976) covalent geometry : angle 0.78267 (28509) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.27433 ( 84) hydrogen bonds : bond 0.04261 ( 738) hydrogen bonds : angle 5.55104 ( 1872) link_ALPHA1-2 : bond 0.00088 ( 3) link_ALPHA1-2 : angle 2.54189 ( 9) link_ALPHA1-3 : bond 0.01104 ( 3) link_ALPHA1-3 : angle 1.67055 ( 9) link_ALPHA1-6 : bond 0.00804 ( 3) link_ALPHA1-6 : angle 1.29101 ( 9) link_BETA1-4 : bond 0.00842 ( 36) link_BETA1-4 : angle 2.83012 ( 108) link_BETA1-6 : bond 0.00640 ( 3) link_BETA1-6 : angle 1.02919 ( 9) link_NAG-ASN : bond 0.00814 ( 48) link_NAG-ASN : angle 3.94113 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8608 (t80) cc_final: 0.8363 (t80) REVERT: A 95 MET cc_start: 0.9067 (ttm) cc_final: 0.8651 (ttm) REVERT: A 152 MET cc_start: 0.9241 (mmt) cc_final: 0.8980 (mmm) REVERT: A 195 ASN cc_start: 0.8776 (t0) cc_final: 0.8505 (t0) REVERT: A 249 HIS cc_start: 0.8725 (t-90) cc_final: 0.8418 (t-90) REVERT: A 369 MET cc_start: 0.9111 (mtp) cc_final: 0.8245 (ttm) REVERT: B 584 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8175 (tm-30) REVERT: B 589 ASP cc_start: 0.9066 (m-30) cc_final: 0.8697 (t70) REVERT: C 48 MET cc_start: 0.8822 (mpp) cc_final: 0.8379 (mpp) REVERT: C 52 ASN cc_start: 0.9644 (t0) cc_final: 0.9405 (t0) REVERT: C 70 MET cc_start: 0.8447 (mmp) cc_final: 0.7689 (mmm) REVERT: D 22 CYS cc_start: 0.5959 (p) cc_final: 0.5660 (p) REVERT: E 95 MET cc_start: 0.9026 (ttm) cc_final: 0.8524 (ttm) REVERT: E 369 MET cc_start: 0.9056 (mtp) cc_final: 0.8155 (ttm) REVERT: F 584 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8273 (tm-30) REVERT: F 589 ASP cc_start: 0.9092 (t70) cc_final: 0.8826 (t70) REVERT: G 34 MET cc_start: 0.8743 (mmm) cc_final: 0.8537 (mmm) REVERT: G 48 MET cc_start: 0.8980 (mpp) cc_final: 0.8502 (mpp) REVERT: G 52 ASN cc_start: 0.9699 (t0) cc_final: 0.9448 (t0) REVERT: G 82 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8738 (mm-30) REVERT: H 22 CYS cc_start: 0.6170 (p) cc_final: 0.5963 (p) REVERT: I 95 MET cc_start: 0.9184 (ttm) cc_final: 0.8747 (ttm) REVERT: I 195 ASN cc_start: 0.8761 (t0) cc_final: 0.8502 (t0) REVERT: I 369 MET cc_start: 0.9008 (mtt) cc_final: 0.8614 (ttm) REVERT: J 522 PHE cc_start: 0.8119 (m-80) cc_final: 0.7651 (m-80) REVERT: J 581 LEU cc_start: 0.9518 (tp) cc_final: 0.9222 (pp) REVERT: J 584 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8227 (tm-30) REVERT: J 589 ASP cc_start: 0.9079 (m-30) cc_final: 0.8674 (t70) REVERT: J 626 MET cc_start: 0.7191 (tpp) cc_final: 0.6771 (tpp) REVERT: K 48 MET cc_start: 0.8997 (mpp) cc_final: 0.8545 (mpp) REVERT: K 52 ASN cc_start: 0.9660 (t0) cc_final: 0.9364 (t0) REVERT: K 70 MET cc_start: 0.8484 (mmp) cc_final: 0.8215 (mmm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1316 time to fit residues: 45.2047 Evaluate side-chains 153 residues out of total 2145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 140 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 157 optimal weight: 0.0020 chunk 171 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.051275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.040495 restraints weight = 131977.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.041865 restraints weight = 78749.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.042824 restraints weight = 55701.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.043491 restraints weight = 43632.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.043966 restraints weight = 36769.709| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21114 Z= 0.131 Angle : 0.789 12.715 28881 Z= 0.385 Chirality : 0.052 0.425 3480 Planarity : 0.004 0.071 3501 Dihedral : 9.964 59.731 4641 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.16), residues: 2457 helix: -0.30 (0.25), residues: 390 sheet: -0.52 (0.19), residues: 666 loop : -1.60 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 585 TYR 0.017 0.001 TYR C 95 PHE 0.027 0.002 PHE E 157 TRP 0.019 0.002 TRP A 112 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00268 (20976) covalent geometry : angle 0.72330 (28509) SS BOND : bond 0.00320 ( 42) SS BOND : angle 1.49262 ( 84) hydrogen bonds : bond 0.03974 ( 738) hydrogen bonds : angle 5.35825 ( 1872) link_ALPHA1-2 : bond 0.00854 ( 3) link_ALPHA1-2 : angle 1.72874 ( 9) link_ALPHA1-3 : bond 0.01167 ( 3) link_ALPHA1-3 : angle 2.03428 ( 9) link_ALPHA1-6 : bond 0.00886 ( 3) link_ALPHA1-6 : angle 1.30383 ( 9) link_BETA1-4 : bond 0.00874 ( 36) link_BETA1-4 : angle 2.80473 ( 108) link_BETA1-6 : bond 0.00862 ( 3) link_BETA1-6 : angle 1.22356 ( 9) link_NAG-ASN : bond 0.00678 ( 48) link_NAG-ASN : angle 3.67000 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2948.55 seconds wall clock time: 52 minutes 15.15 seconds (3135.15 seconds total)