Starting phenix.real_space_refine on Fri Feb 16 17:40:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2024/7l8z_23242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2024/7l8z_23242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2024/7l8z_23242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2024/7l8z_23242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2024/7l8z_23242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2024/7l8z_23242_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 104 5.16 5 C 9951 2.51 5 N 2696 2.21 5 O 3238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 269": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15989 Number of models: 1 Model: "" Number of chains: 36 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 425 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'TRANS': 84} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'UNK:plan-1': 85} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3516 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 2 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1086 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "C" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3521 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 2 Chain: "E" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "D" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3443 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 4 Chain: "F" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1091 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 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: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" 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: "V" 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: "W" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "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: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.03, per 1000 atoms: 0.56 Number of scatterers: 15989 At special positions: 0 Unit cell: (125.66, 126.69, 155.53, 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 104 16.00 O 3238 8.00 N 2696 7.00 C 9951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.43 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS E 561 " distance=2.07 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.14 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.01 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.77 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA K 3 " - " MAN K 6 " " BMA T 3 " - " MAN T 5 " " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 241 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 133 " " NAG A 609 " - " ASN A 289 " " NAG A 610 " - " ASN A 137 " " NAG A 611 " - " ASN A 363 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 160 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 363 " " NAG D 601 " - " ASN D 241 " " NAG D 602 " - " ASN D 276 " " NAG D 603 " - " ASN D 392 " " NAG D 604 " - " ASN D 339 " " NAG D 605 " - " ASN D 332 " " NAG D 606 " - " ASN D 295 " " NAG D 607 " - " ASN D 301 " " NAG D 608 " - " ASN D 133 " " NAG D 609 " - " ASN D 355 " " NAG D 610 " - " ASN D 289 " " NAG D 611 " - " ASN D 137 " " NAG E 701 " - " ASN E 637 " " NAG E 702 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 332 " " NAG S 1 " - " ASN C 448 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN D 386 " " NAG Y 1 " - " ASN D 448 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 156 " " NAG b 1 " - " ASN D 160 " " NAG c 1 " - " ASN D 197 " " NAG d 1 " - " ASN D 363 " Time building additional restraints: 7.70 Conformation dependent library (CDL) restraints added in 2.6 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 32 sheets defined 28.0% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'H' and resid 38 through 40 No H-bonds generated for 'chain 'H' and resid 38 through 40' Processing helix chain 'A' and resid 59 through 62 No H-bonds generated for 'chain 'A' and resid 59 through 62' Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.547A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 352 removed outlier: 4.746A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.849A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 543 removed outlier: 3.875A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 551 removed outlier: 4.353A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 567 Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 629 through 661 removed outlier: 5.674A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 63 No H-bonds generated for 'chain 'C' and resid 60 through 63' Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 116 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.543A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 335 through 352 removed outlier: 4.203A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.533A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 527 removed outlier: 4.331A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 524 through 527' Processing helix chain 'E' and resid 532 through 549 removed outlier: 3.852A pdb=" N LEU E 537 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR E 538 " --> pdb=" O MET E 535 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 542 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU E 544 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 545 " --> pdb=" O ARG E 542 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 546 " --> pdb=" O ASN E 543 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY E 547 " --> pdb=" O LEU E 544 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE E 548 " --> pdb=" O LEU E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 567 Processing helix chain 'E' and resid 569 through 595 Processing helix chain 'E' and resid 619 through 621 No H-bonds generated for 'chain 'E' and resid 619 through 621' Processing helix chain 'E' and resid 628 through 634 Processing helix chain 'E' and resid 636 through 658 removed outlier: 5.095A pdb=" N GLN E 640 " --> pdb=" O ASN E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 662 No H-bonds generated for 'chain 'E' and resid 660 through 662' Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 335 through 352 removed outlier: 3.566A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 475 through 485 removed outlier: 3.533A pdb=" N ARG D 480 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER D 481 " --> pdb=" O ASN D 478 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR D 484 " --> pdb=" O SER D 481 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS D 485 " --> pdb=" O GLU D 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 removed outlier: 4.143A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 527' Processing helix chain 'F' and resid 533 through 544 removed outlier: 3.869A pdb=" N LEU F 537 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA F 541 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG F 542 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 567 No H-bonds generated for 'chain 'F' and resid 565 through 567' Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 628 through 662 removed outlier: 6.251A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 4 through 7 Processing sheet with id= B, first strand: chain 'H' and resid 54 through 56 removed outlier: 3.790A pdb=" N UNK H 54 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N UNK H 33 " --> pdb=" O UNK H 89 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N UNK H 89 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N UNK H 35 " --> pdb=" O UNK H 87 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N UNK H 87 " --> pdb=" O UNK H 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 31 through 34 Processing sheet with id= D, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= E, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= F, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= H, first strand: chain 'A' and resid 130 through 132 Processing sheet with id= I, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= J, first strand: chain 'A' and resid 200 through 203 Processing sheet with id= K, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.436A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.371A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.528A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= O, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.865A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= Q, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= R, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.613A pdb=" N THR C 132 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= T, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.578A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.354A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.311A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.583A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= Y, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= Z, first strand: chain 'D' and resid 91 through 94 Processing sheet with id= AA, first strand: chain 'D' and resid 130 through 132 Processing sheet with id= AB, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= AC, first strand: chain 'D' and resid 200 through 203 Processing sheet with id= AD, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.420A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA D 362 " --> pdb=" O PRO D 470 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 374 through 378 removed outlier: 4.291A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.736A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1320 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: 5.18 Time building geometry restraints manager: 8.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 5200 1.35 - 1.51: 6379 1.51 - 1.67: 4541 1.67 - 1.82: 118 1.82 - 1.98: 19 Bond restraints: 16257 Sorted by residual: bond pdb=" NE ARG D 503 " pdb=" CZ ARG D 503 " ideal model delta sigma weight residual 1.326 1.412 -0.086 1.10e-02 8.26e+03 6.17e+01 bond pdb=" CB LEU E 663 " pdb=" CG LEU E 663 " ideal model delta sigma weight residual 1.530 1.674 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" CB HIS F 564 " pdb=" CG HIS F 564 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.27e+01 bond pdb=" CB ASN A 67 " pdb=" CG ASN A 67 " ideal model delta sigma weight residual 1.516 1.356 0.160 2.50e-02 1.60e+03 4.09e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.02e+01 ... (remaining 16252 not shown) Histogram of bond angle deviations from ideal: 94.69 - 102.63: 122 102.63 - 110.56: 5818 110.56 - 118.50: 7676 118.50 - 126.44: 8191 126.44 - 134.38: 291 Bond angle restraints: 22098 Sorted by residual: angle pdb=" N GLN C 428 " pdb=" CA GLN C 428 " pdb=" C GLN C 428 " ideal model delta sigma weight residual 114.04 95.97 18.07 1.24e+00 6.50e-01 2.12e+02 angle pdb=" N GLN D 428 " pdb=" CA GLN D 428 " pdb=" C GLN D 428 " ideal model delta sigma weight residual 114.04 97.50 16.54 1.24e+00 6.50e-01 1.78e+02 angle pdb=" N LEU F 629 " pdb=" CA LEU F 629 " pdb=" C LEU F 629 " ideal model delta sigma weight residual 110.55 94.69 15.86 1.35e+00 5.49e-01 1.38e+02 angle pdb=" N VAL D 242 " pdb=" CA VAL D 242 " pdb=" C VAL D 242 " ideal model delta sigma weight residual 109.34 127.10 -17.76 2.08e+00 2.31e-01 7.29e+01 angle pdb=" C GLU D 492 " pdb=" N PRO D 493 " pdb=" CA PRO D 493 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.94e+01 ... (remaining 22093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 10679 21.21 - 42.43: 207 42.43 - 63.64: 81 63.64 - 84.85: 40 84.85 - 106.07: 21 Dihedral angle restraints: 11028 sinusoidal: 5441 harmonic: 5587 Sorted by residual: dihedral pdb=" CB CYS D 228 " pdb=" SG CYS D 228 " pdb=" SG CYS D 239 " pdb=" CB CYS D 239 " ideal model delta sinusoidal sigma weight residual 93.00 176.67 -83.67 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.96 -65.96 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.73 -65.73 1 1.00e+01 1.00e-02 5.65e+01 ... (remaining 11025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 2550 0.278 - 0.557: 270 0.557 - 0.835: 1 0.835 - 1.114: 0 1.114 - 1.392: 2 Chirality restraints: 2823 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.63e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 2820 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 601 " 0.290 2.00e-02 2.50e+03 2.42e-01 7.29e+02 pdb=" C7 NAG D 601 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 601 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG D 601 " -0.406 2.00e-02 2.50e+03 pdb=" O7 NAG D 601 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " -0.155 2.00e-02 2.50e+03 1.93e-01 4.67e+02 pdb=" CG ASN D 234 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " 0.332 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 137 " -0.134 2.00e-02 2.50e+03 1.89e-01 4.47e+02 pdb=" CG ASN D 137 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN D 137 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN D 137 " 0.332 2.00e-02 2.50e+03 pdb=" C1 NAG D 611 " -0.215 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 161 2.62 - 3.19: 14224 3.19 - 3.76: 22617 3.76 - 4.33: 33434 4.33 - 4.90: 51984 Nonbonded interactions: 122420 Sorted by model distance: nonbonded pdb=" O3 NAG D 601 " pdb=" O7 NAG D 601 " model vdw 2.046 2.440 nonbonded pdb=" O3 NAG W 1 " pdb=" O7 NAG W 1 " model vdw 2.052 2.440 nonbonded pdb=" N LEU F 629 " pdb=" O LEU F 629 " model vdw 2.216 2.496 nonbonded pdb=" N GLN C 428 " pdb=" N ARG C 429 " model vdw 2.327 2.560 nonbonded pdb=" N UNK L 45 " pdb=" O UNK L 49 " model vdw 2.337 2.520 ... (remaining 122415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 56 or resid 63 through 140 or resid 151 through \ 503 or resid 601 through 611)) selection = (chain 'C' and (resid 33 through 56 or resid 63 through 140 or resid 151 through \ 503 or resid 601 through 611)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 521 through 550 or resid 561 through 663 or resid 701)) selection = (chain 'E' and (resid 521 through 550 or resid 561 through 663 or resid 701)) selection = (chain 'F' and (resid 521 through 550 or resid 561 through 663 or resid 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'K' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.780 Check model and map are aligned: 0.240 Set scattering table: 0.180 Process input model: 46.240 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.023 0.175 16257 Z= 1.473 Angle : 1.754 18.072 22098 Z= 1.117 Chirality : 0.153 1.392 2823 Planarity : 0.010 0.242 2699 Dihedral : 11.795 106.065 7292 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1700 helix: -0.10 (0.24), residues: 420 sheet: 0.85 (0.22), residues: 464 loop : 0.86 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.009 TRP E 610 HIS 0.015 0.003 HIS A 374 PHE 0.030 0.006 PHE D 383 TYR 0.051 0.008 TYR D 40 ARG 0.010 0.001 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8667 (mttm) cc_final: 0.7928 (mtpt) REVERT: A 80 ASN cc_start: 0.8414 (m-40) cc_final: 0.8057 (m-40) REVERT: A 115 SER cc_start: 0.9169 (m) cc_final: 0.8780 (t) REVERT: A 163 THR cc_start: 0.9297 (p) cc_final: 0.9038 (t) REVERT: B 607 ASN cc_start: 0.8278 (m-40) cc_final: 0.8007 (m-40) REVERT: B 613 THR cc_start: 0.9177 (p) cc_final: 0.8735 (t) REVERT: B 639 THR cc_start: 0.8895 (m) cc_final: 0.8542 (p) REVERT: C 80 ASN cc_start: 0.8489 (m-40) cc_final: 0.8278 (m-40) REVERT: C 125 LEU cc_start: 0.8987 (mt) cc_final: 0.8738 (tt) REVERT: C 217 TYR cc_start: 0.9206 (m-80) cc_final: 0.8997 (m-80) REVERT: C 264 SER cc_start: 0.8465 (m) cc_final: 0.8257 (m) REVERT: C 426 MET cc_start: 0.8227 (tpp) cc_final: 0.7984 (tpp) REVERT: C 427 TRP cc_start: 0.8339 (t-100) cc_final: 0.7910 (t-100) REVERT: E 585 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.8277 (mtm180) REVERT: D 128 THR cc_start: 0.9236 (m) cc_final: 0.8995 (p) REVERT: F 545 LEU cc_start: 0.8840 (tp) cc_final: 0.8608 (tp) REVERT: F 637 ASN cc_start: 0.7671 (p0) cc_final: 0.6932 (t0) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.3075 time to fit residues: 185.0542 Evaluate side-chains 207 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 422 GLN A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 72 HIS E 564 HIS E 577 GLN D 440 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16257 Z= 0.249 Angle : 0.728 8.838 22098 Z= 0.376 Chirality : 0.049 0.273 2823 Planarity : 0.004 0.028 2699 Dihedral : 9.020 83.528 3999 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.92 % Allowed : 9.07 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1700 helix: 0.80 (0.26), residues: 412 sheet: 0.83 (0.23), residues: 456 loop : 0.46 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 427 HIS 0.005 0.001 HIS A 374 PHE 0.019 0.003 PHE D 353 TYR 0.019 0.002 TYR F 643 ARG 0.007 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 255 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 SER cc_start: 0.8976 (m) cc_final: 0.8621 (t) REVERT: A 163 THR cc_start: 0.9272 (p) cc_final: 0.9038 (t) REVERT: A 199 SER cc_start: 0.9210 (p) cc_final: 0.8985 (t) REVERT: A 231 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8097 (ptmt) REVERT: B 543 ASN cc_start: 0.8454 (t0) cc_final: 0.8249 (t0) REVERT: B 586 TYR cc_start: 0.9242 (t80) cc_final: 0.9030 (t80) REVERT: B 591 GLN cc_start: 0.9139 (tt0) cc_final: 0.8923 (tt0) REVERT: B 613 THR cc_start: 0.9125 (p) cc_final: 0.8716 (t) REVERT: B 639 THR cc_start: 0.8838 (m) cc_final: 0.8567 (p) REVERT: B 654 GLU cc_start: 0.7815 (tp30) cc_final: 0.7595 (tp30) REVERT: C 103 GLN cc_start: 0.8443 (tp40) cc_final: 0.7937 (tp-100) REVERT: C 215 ILE cc_start: 0.9247 (mm) cc_final: 0.8885 (tt) REVERT: C 426 MET cc_start: 0.8057 (tpp) cc_final: 0.7513 (tpt) REVERT: F 637 ASN cc_start: 0.7487 (p0) cc_final: 0.6963 (t0) outliers start: 45 outliers final: 28 residues processed: 280 average time/residue: 0.2729 time to fit residues: 114.5560 Evaluate side-chains 226 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 646 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 658 GLN C 348 GLN C 422 GLN F 658 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16257 Z= 0.279 Angle : 0.648 8.562 22098 Z= 0.335 Chirality : 0.046 0.345 2823 Planarity : 0.004 0.051 2699 Dihedral : 7.974 75.836 3999 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.69 % Allowed : 10.82 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1700 helix: 0.99 (0.27), residues: 401 sheet: 0.53 (0.23), residues: 467 loop : 0.36 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 427 HIS 0.005 0.001 HIS A 374 PHE 0.016 0.002 PHE D 383 TYR 0.013 0.002 TYR A 484 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 214 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9237 (p) cc_final: 0.9004 (t) REVERT: A 231 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8156 (ptmt) REVERT: B 613 THR cc_start: 0.9243 (p) cc_final: 0.9003 (t) REVERT: B 647 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 648 GLU cc_start: 0.8282 (pt0) cc_final: 0.8075 (pt0) REVERT: C 51 THR cc_start: 0.9427 (m) cc_final: 0.9164 (p) REVERT: C 103 GLN cc_start: 0.8444 (tp40) cc_final: 0.7817 (tp-100) REVERT: C 215 ILE cc_start: 0.9306 (mm) cc_final: 0.9053 (tt) REVERT: C 217 TYR cc_start: 0.9149 (m-80) cc_final: 0.8941 (m-80) REVERT: F 637 ASN cc_start: 0.7443 (p0) cc_final: 0.6902 (t0) outliers start: 57 outliers final: 42 residues processed: 252 average time/residue: 0.2694 time to fit residues: 102.3248 Evaluate side-chains 231 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 181 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 658 GLN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN D 99 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16257 Z= 0.350 Angle : 0.688 7.056 22098 Z= 0.349 Chirality : 0.048 0.337 2823 Planarity : 0.004 0.057 2699 Dihedral : 7.483 67.128 3999 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.18 % Allowed : 11.34 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1700 helix: 0.92 (0.27), residues: 404 sheet: 0.25 (0.23), residues: 465 loop : 0.03 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 427 HIS 0.006 0.002 HIS A 374 PHE 0.016 0.002 PHE D 383 TYR 0.017 0.002 TYR D 217 ARG 0.003 0.001 ARG C 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 206 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6404 (pt0) REVERT: A 199 SER cc_start: 0.9382 (p) cc_final: 0.9115 (t) REVERT: A 231 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8185 (ptmt) REVERT: B 551 GLN cc_start: 0.6190 (OUTLIER) cc_final: 0.5305 (pm20) REVERT: B 586 TYR cc_start: 0.9375 (t80) cc_final: 0.9083 (t80) REVERT: B 613 THR cc_start: 0.9339 (p) cc_final: 0.9116 (t) REVERT: B 653 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: C 51 THR cc_start: 0.9483 (m) cc_final: 0.9235 (p) REVERT: C 103 GLN cc_start: 0.8390 (tp40) cc_final: 0.8184 (tm-30) REVERT: C 114 GLN cc_start: 0.8767 (tp40) cc_final: 0.8444 (tp40) REVERT: C 125 LEU cc_start: 0.9234 (tp) cc_final: 0.8982 (tt) REVERT: C 217 TYR cc_start: 0.9264 (m-80) cc_final: 0.8921 (m-80) REVERT: E 621 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8619 (tp30) REVERT: D 125 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9175 (tt) REVERT: D 199 SER cc_start: 0.9422 (p) cc_final: 0.9069 (t) REVERT: D 282 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8766 (mttm) REVERT: F 647 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7451 (tt0) outliers start: 80 outliers final: 56 residues processed: 257 average time/residue: 0.2698 time to fit residues: 103.3353 Evaluate side-chains 237 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 176 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 72 HIS C 428 GLN E 577 GLN D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16257 Z= 0.321 Angle : 0.647 7.519 22098 Z= 0.328 Chirality : 0.050 0.752 2823 Planarity : 0.004 0.043 2699 Dihedral : 7.361 61.530 3999 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 4.93 % Allowed : 12.05 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1700 helix: 0.96 (0.27), residues: 403 sheet: 0.33 (0.24), residues: 444 loop : -0.16 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 479 HIS 0.012 0.002 HIS A 66 PHE 0.015 0.002 PHE E 522 TYR 0.014 0.002 TYR D 217 ARG 0.003 0.000 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 198 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9442 (p) cc_final: 0.9116 (t) REVERT: A 208 VAL cc_start: 0.9399 (t) cc_final: 0.9150 (p) REVERT: A 231 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8206 (ptmt) REVERT: B 653 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: C 51 THR cc_start: 0.9471 (m) cc_final: 0.9262 (p) REVERT: C 103 GLN cc_start: 0.8395 (tp40) cc_final: 0.8082 (tp40) REVERT: C 125 LEU cc_start: 0.9324 (tp) cc_final: 0.8994 (tt) REVERT: D 199 SER cc_start: 0.9411 (p) cc_final: 0.9106 (t) REVERT: D 282 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8843 (mttm) REVERT: F 647 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7403 (tt0) outliers start: 76 outliers final: 55 residues processed: 246 average time/residue: 0.2964 time to fit residues: 107.4147 Evaluate side-chains 243 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 186 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN E 577 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 16257 Z= 0.381 Angle : 0.700 10.507 22098 Z= 0.352 Chirality : 0.049 0.643 2823 Planarity : 0.004 0.042 2699 Dihedral : 7.477 59.940 3999 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 5.64 % Allowed : 11.86 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1700 helix: 0.82 (0.27), residues: 406 sheet: 0.20 (0.23), residues: 440 loop : -0.34 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 631 HIS 0.006 0.002 HIS A 374 PHE 0.016 0.002 PHE E 522 TYR 0.016 0.002 TYR D 217 ARG 0.003 0.001 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 193 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8326 (p0) REVERT: A 199 SER cc_start: 0.9432 (p) cc_final: 0.9070 (t) REVERT: A 231 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8211 (ptmt) REVERT: B 586 TYR cc_start: 0.9358 (t80) cc_final: 0.9076 (t80) REVERT: B 653 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: C 51 THR cc_start: 0.9473 (m) cc_final: 0.9263 (p) REVERT: C 125 LEU cc_start: 0.9336 (tp) cc_final: 0.9023 (tt) REVERT: C 348 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 125 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9250 (tt) REVERT: D 199 SER cc_start: 0.9383 (p) cc_final: 0.9062 (t) REVERT: F 567 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8137 (mmtt) outliers start: 87 outliers final: 63 residues processed: 250 average time/residue: 0.2873 time to fit residues: 106.6215 Evaluate side-chains 238 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 171 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN D 88 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 562 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16257 Z= 0.195 Angle : 0.601 11.381 22098 Z= 0.304 Chirality : 0.047 0.543 2823 Planarity : 0.004 0.039 2699 Dihedral : 6.911 58.181 3999 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.35 % Favored : 95.53 % Rotamer: Outliers : 4.34 % Allowed : 13.93 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1700 helix: 1.15 (0.28), residues: 402 sheet: 0.19 (0.23), residues: 448 loop : -0.21 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 623 HIS 0.004 0.001 HIS A 66 PHE 0.013 0.002 PHE B 522 TYR 0.013 0.001 TYR B 586 ARG 0.008 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 198 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6088 (pt0) REVERT: A 199 SER cc_start: 0.9433 (p) cc_final: 0.9100 (t) REVERT: A 231 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8296 (ptmt) REVERT: B 548 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7570 (pt) REVERT: B 551 GLN cc_start: 0.6063 (OUTLIER) cc_final: 0.5156 (pm20) REVERT: B 586 TYR cc_start: 0.9308 (t80) cc_final: 0.9020 (t80) REVERT: C 51 THR cc_start: 0.9439 (m) cc_final: 0.9202 (p) REVERT: C 125 LEU cc_start: 0.9360 (tp) cc_final: 0.9014 (tt) REVERT: C 498 PRO cc_start: 0.8927 (Cg_exo) cc_final: 0.8589 (Cg_endo) REVERT: E 562 GLN cc_start: 0.5347 (mt0) cc_final: 0.5142 (tt0) REVERT: D 199 SER cc_start: 0.9373 (p) cc_final: 0.9023 (t) REVERT: F 647 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7162 (tt0) outliers start: 67 outliers final: 48 residues processed: 239 average time/residue: 0.2829 time to fit residues: 101.3090 Evaluate side-chains 227 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 175 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN E 577 GLN D 88 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 16257 Z= 0.241 Angle : 0.607 10.463 22098 Z= 0.305 Chirality : 0.047 0.495 2823 Planarity : 0.004 0.039 2699 Dihedral : 6.729 59.245 3999 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.71 % Favored : 95.18 % Rotamer: Outliers : 4.08 % Allowed : 15.04 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1700 helix: 1.24 (0.28), residues: 401 sheet: 0.19 (0.23), residues: 444 loop : -0.21 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 631 HIS 0.007 0.001 HIS A 66 PHE 0.014 0.002 PHE B 522 TYR 0.014 0.001 TYR B 586 ARG 0.006 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 183 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6066 (pt0) REVERT: A 199 SER cc_start: 0.9405 (p) cc_final: 0.9072 (t) REVERT: A 208 VAL cc_start: 0.9353 (t) cc_final: 0.9133 (p) REVERT: A 231 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8299 (ptmt) REVERT: B 551 GLN cc_start: 0.6008 (OUTLIER) cc_final: 0.5193 (pm20) REVERT: B 586 TYR cc_start: 0.9357 (t80) cc_final: 0.9046 (t80) REVERT: C 103 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8608 (tm-30) REVERT: C 125 LEU cc_start: 0.9351 (tp) cc_final: 0.8966 (tt) REVERT: D 199 SER cc_start: 0.9362 (p) cc_final: 0.9090 (t) REVERT: F 647 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7357 (tt0) outliers start: 63 outliers final: 50 residues processed: 223 average time/residue: 0.2693 time to fit residues: 89.8868 Evaluate side-chains 231 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 178 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 159 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 178 optimal weight: 0.0970 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN E 563 GLN E 577 GLN D 88 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16257 Z= 0.158 Angle : 0.567 10.638 22098 Z= 0.288 Chirality : 0.045 0.467 2823 Planarity : 0.004 0.040 2699 Dihedral : 6.302 59.969 3999 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.00 % Favored : 95.88 % Rotamer: Outliers : 3.43 % Allowed : 15.36 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1700 helix: 1.36 (0.28), residues: 401 sheet: 0.19 (0.23), residues: 453 loop : -0.14 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 623 HIS 0.003 0.001 HIS C 374 PHE 0.012 0.001 PHE A 383 TYR 0.014 0.001 TYR B 586 ARG 0.006 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5972 (pt0) REVERT: A 199 SER cc_start: 0.9391 (p) cc_final: 0.9029 (t) REVERT: A 208 VAL cc_start: 0.9333 (t) cc_final: 0.9130 (p) REVERT: A 231 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8279 (ptmt) REVERT: B 551 GLN cc_start: 0.5571 (OUTLIER) cc_final: 0.4815 (pm20) REVERT: B 586 TYR cc_start: 0.9322 (t80) cc_final: 0.9018 (t80) REVERT: C 498 PRO cc_start: 0.8878 (Cg_exo) cc_final: 0.8504 (Cg_endo) REVERT: E 621 GLU cc_start: 0.8723 (tp30) cc_final: 0.8480 (tp30) REVERT: D 199 SER cc_start: 0.9344 (p) cc_final: 0.9026 (t) outliers start: 53 outliers final: 42 residues processed: 232 average time/residue: 0.2842 time to fit residues: 98.7195 Evaluate side-chains 232 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 187 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 124 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN E 577 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16257 Z= 0.171 Angle : 0.573 10.807 22098 Z= 0.289 Chirality : 0.045 0.457 2823 Planarity : 0.004 0.037 2699 Dihedral : 5.921 56.538 3999 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 2.92 % Allowed : 16.14 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1700 helix: 1.34 (0.28), residues: 407 sheet: 0.22 (0.23), residues: 447 loop : -0.11 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 628 HIS 0.004 0.001 HIS A 66 PHE 0.013 0.001 PHE A 383 TYR 0.015 0.001 TYR B 586 ARG 0.006 0.000 ARG C 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 195 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.5919 (pt0) REVERT: A 199 SER cc_start: 0.9368 (p) cc_final: 0.9012 (t) REVERT: A 231 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8217 (ptmt) REVERT: B 551 GLN cc_start: 0.5571 (OUTLIER) cc_final: 0.4867 (pm20) REVERT: B 586 TYR cc_start: 0.9333 (t80) cc_final: 0.8991 (t80) REVERT: C 498 PRO cc_start: 0.8867 (Cg_exo) cc_final: 0.8540 (Cg_endo) REVERT: E 621 GLU cc_start: 0.8713 (tp30) cc_final: 0.8479 (tp30) REVERT: D 199 SER cc_start: 0.9330 (p) cc_final: 0.9009 (t) outliers start: 45 outliers final: 39 residues processed: 225 average time/residue: 0.2708 time to fit residues: 91.1907 Evaluate side-chains 226 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.0030 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN E 577 GLN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099634 restraints weight = 28704.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102454 restraints weight = 16815.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104330 restraints weight = 11985.066| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16257 Z= 0.248 Angle : 0.610 11.499 22098 Z= 0.306 Chirality : 0.046 0.459 2823 Planarity : 0.004 0.039 2699 Dihedral : 6.072 56.359 3999 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.24 % Rotamer: Outliers : 2.85 % Allowed : 16.20 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1700 helix: 1.18 (0.28), residues: 405 sheet: 0.20 (0.23), residues: 439 loop : -0.13 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 628 HIS 0.005 0.001 HIS A 66 PHE 0.013 0.002 PHE A 383 TYR 0.012 0.001 TYR B 586 ARG 0.005 0.000 ARG C 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.69 seconds wall clock time: 59 minutes 6.59 seconds (3546.59 seconds total)