Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 00:09:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/04_2023/7l8x_23239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/04_2023/7l8x_23239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/04_2023/7l8x_23239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/04_2023/7l8x_23239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/04_2023/7l8x_23239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8x_23239/04_2023/7l8x_23239_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 10010 2.51 5 N 2703 2.21 5 O 3273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16090 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 3507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3507 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 20, 'TRANS': 423} Chain breaks: 2 Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1155 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "C" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3461 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "E" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3371 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 5 Chain: "F" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1101 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} 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 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 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 chiralities: 2 Chain: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 2, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 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 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 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 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 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 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 chiralities: 2 Chain: "T" 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 chiralities: 6 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 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 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 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 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 chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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 chiralities: 6 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 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 chiralities: 2 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 chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 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 chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "D" 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 chiralities: 1 Chain: "E" 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 chiralities: 11 Chain: "F" 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 chiralities: 2 Time building chain proxies: 8.24, per 1000 atoms: 0.51 Number of scatterers: 16090 At special positions: 0 Unit cell: (129.78, 128.75, 122.57, 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 3273 8.00 N 2703 7.00 C 10010 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=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 K 5 " - " MAN K 6 " " MAN T 4 " - " MAN T 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 9 " " BMA T 3 " - " MAN T 6 " " BMA b 3 " - " MAN b 6 " BETA1-3 " MAN K 7 " - " BMA K 8 " 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 295 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 160 " " NAG A 610 " - " ASN A 197 " " NAG A 611 " - " ASN A 133 " " NAG A 612 " - " ASN A 355 " " NAG A 613 " - " ASN A 289 " " NAG A 614 " - " ASN A 363 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 448 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 160 " " NAG C 608 " - " ASN C 197 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 289 " " NAG C 612 " - " ASN C 363 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 241 " " NAG E 603 " - " ASN E 276 " " NAG E 604 " - " ASN E 339 " " NAG E 605 " - " ASN E 448 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 156 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 133 " " NAG E 610 " - " ASN E 355 " " NAG E 611 " - " ASN E 289 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 392 " " NAG I 1 " - " ASN A 386 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN B 611 " " NAG O 1 " - " ASN C 88 " " NAG P 1 " - " ASN C 392 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 332 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN D 611 " " NAG W 1 " - " ASN E 88 " " NAG X 1 " - " ASN E 392 " " NAG Y 1 " - " ASN E 386 " " NAG Z 1 " - " ASN E 332 " " NAG a 1 " - " ASN E 295 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 197 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN F 611 " Time building additional restraints: 7.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 34 sheets defined 28.2% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' 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 117 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 194 through 197 removed outlier: 4.417A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 335 through 352 removed outlier: 4.211A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.579A 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 475 through 485 removed outlier: 5.042A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 removed outlier: 4.336A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 530 through 544 removed outlier: 4.033A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 557 removed outlier: 3.592A pdb=" N LEU B 556 " --> pdb=" O GLN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 removed outlier: 3.584A pdb=" N LEU B 566 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 663 removed outlier: 5.193A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) 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 117 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 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 353 removed outlier: 4.023A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.413A 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 475 through 485 removed outlier: 4.494A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 527 removed outlier: 4.197A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 527' Processing helix chain 'D' and resid 532 through 543 removed outlier: 5.123A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 663 removed outlier: 5.394A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 657 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'E' and resid 101 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 140 through 150 No H-bonds generated for 'chain 'E' and resid 140 through 150' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 352 removed outlier: 4.161A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 378 through 380 No H-bonds generated for 'chain 'E' and resid 378 through 380' Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 475 through 482 removed outlier: 3.753A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 removed outlier: 4.405A 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 532 through 534 No H-bonds generated for 'chain 'F' and resid 532 through 534' Processing helix chain 'F' and resid 537 through 556 removed outlier: 4.161A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (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 570 through 595 Processing helix chain 'F' and resid 619 through 623 Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 636 through 656 removed outlier: 5.126A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.551A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 271 through 273 Processing sheet with id= I, first strand: chain 'A' and resid 443 through 449 removed outlier: 4.044A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 465 through 469 removed outlier: 6.485A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.421A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= M, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= N, first strand: chain 'C' and resid 52 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= P, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= R, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.326A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 443 through 448 removed outlier: 4.104A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 304 through 309 Processing sheet with id= U, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= V, first strand: chain 'H' and resid 113 through 115 removed outlier: 6.165A pdb=" N UNK H 33 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N UNK H 50 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= X, first strand: chain 'L' and resid 81 through 86 Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= Z, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.532A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AB, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= AC, first strand: chain 'E' and resid 130 through 132 Processing sheet with id= AD, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AE, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= AF, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.407A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 374 through 376 removed outlier: 4.288A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.754A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1299 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: 5.46 Time building geometry restraints manager: 8.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3151 1.32 - 1.45: 5158 1.45 - 1.59: 7855 1.59 - 1.73: 62 1.73 - 1.87: 133 Bond restraints: 16359 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.45e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.30e+01 bond pdb=" CB HIS E 105 " pdb=" CG HIS E 105 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.09e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.05e+01 ... (remaining 16354 not shown) Histogram of bond angle deviations from ideal: 94.53 - 102.62: 113 102.62 - 110.72: 6195 110.72 - 118.81: 7797 118.81 - 126.91: 7904 126.91 - 135.00: 240 Bond angle restraints: 22249 Sorted by residual: angle pdb=" N MET E 100 " pdb=" CA MET E 100 " pdb=" C MET E 100 " ideal model delta sigma weight residual 114.62 100.33 14.29 1.14e+00 7.69e-01 1.57e+02 angle pdb=" N THR C 464 " pdb=" CA THR C 464 " pdb=" C THR C 464 " ideal model delta sigma weight residual 114.56 102.88 11.68 1.27e+00 6.20e-01 8.46e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 127.87 -8.31 1.02e+00 9.61e-01 6.64e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.01e+00 9.80e-01 6.20e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.44 -7.88 1.01e+00 9.80e-01 6.09e+01 ... (remaining 22244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8735 17.98 - 35.97: 211 35.97 - 53.95: 73 53.95 - 71.94: 23 71.94 - 89.92: 14 Dihedral angle restraints: 9056 sinusoidal: 3440 harmonic: 5616 Sorted by residual: 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 93.00 160.43 -67.43 1 1.00e+01 1.00e-02 5.92e+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 93.00 153.41 -60.41 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS E 74 " pdb=" SG CYS E 74 " pdb=" SG CYS F 561 " pdb=" CB CYS F 561 " ideal model delta sinusoidal sigma weight residual 93.00 46.11 46.89 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 9053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 2748 0.329 - 0.657: 122 0.657 - 0.986: 0 0.986 - 1.314: 0 1.314 - 1.643: 1 Chirality restraints: 2871 Sorted by residual: chirality pdb=" C1 MAN K 7 " pdb=" O6 BMA K 3 " pdb=" C2 MAN K 7 " pdb=" O5 MAN K 7 " both_signs ideal model delta sigma weight residual False 2.40 0.76 1.64 2.00e-02 2.50e+03 6.75e+03 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.95e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.74e+02 ... (remaining 2868 not shown) Planarity restraints: 2773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG Z 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.113 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " -0.348 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C 604 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.335 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG K 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.103 2.00e-02 2.50e+03 ... (remaining 2770 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3720 2.80 - 3.33: 15066 3.33 - 3.85: 25588 3.85 - 4.38: 30591 4.38 - 4.90: 48376 Nonbonded interactions: 123341 Sorted by model distance: nonbonded pdb=" O3 NAG A 605 " pdb=" O7 NAG A 605 " model vdw 2.275 2.440 nonbonded pdb=" O3 NAG C 602 " pdb=" O7 NAG C 602 " model vdw 2.324 2.440 nonbonded pdb=" N HIS A 72 " pdb=" O HIS A 72 " model vdw 2.345 2.496 nonbonded pdb=" N GLY D 597 " pdb=" O GLY D 597 " model vdw 2.393 2.496 nonbonded pdb=" N MET E 100 " pdb=" N VAL E 101 " model vdw 2.406 2.560 ... (remaining 123336 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 60 or resid 66 through 162 or resid 170 through \ 185 or resid 189 through 457 or resid 462 through 503 or resid 601 through 611) \ ) selection = (chain 'C' and (resid 33 through 162 or resid 170 through 185 or resid 189 throu \ gh 457 or resid 462 through 503 or resid 601 through 611)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 520 through 546 or resid 564 through 657 or resid 701)) selection = (chain 'D' and (resid 520 through 657 or resid 701)) selection = (chain 'F' and (resid 520 through 546 or resid 564 through 657 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 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = (chain 'H' and resid 19 through 117) selection = chain 'L' } ncs_group { reference = chain 'T' selection = chain 'b' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 12.350 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.200 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.022 0.144 16359 Z= 1.356 Angle : 1.697 14.290 22249 Z= 1.092 Chirality : 0.141 1.643 2871 Planarity : 0.018 0.300 2708 Dihedral : 10.323 89.922 5298 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.00 % 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: 0.95 (0.20), residues: 1687 helix: 0.58 (0.23), residues: 436 sheet: 0.78 (0.25), residues: 393 loop : 0.78 (0.21), residues: 858 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 492 average time/residue: 1.1546 time to fit residues: 631.6585 Evaluate side-chains 202 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 200 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.1888 time to fit residues: 2.6523 ------------------------------------------------------------------------------- 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: 7.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 575 GLN B 658 GLN C 33 ASN C 105 HIS C 114 GLN C 377 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 577 GLN D 651 ASN E 85 HIS E 99 ASN E 130 GLN E 195 ASN F 554 ASN F 591 GLN F 625 ASN F 630 GLN F 640 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 16359 Z= 0.240 Angle : 0.765 10.076 22249 Z= 0.381 Chirality : 0.048 0.457 2871 Planarity : 0.005 0.042 2708 Dihedral : 4.992 25.949 2036 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 5.62 % 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: 0.91 (0.20), residues: 1687 helix: 1.27 (0.24), residues: 418 sheet: 0.65 (0.22), residues: 468 loop : 0.37 (0.23), residues: 801 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 274 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 30 residues processed: 324 average time/residue: 1.0554 time to fit residues: 386.1155 Evaluate side-chains 221 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 8 average time/residue: 0.4474 time to fit residues: 6.9569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 98 ASN D 577 GLN E 99 ASN E 425 ASN F 554 ASN F 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 16359 Z= 0.333 Angle : 0.739 9.169 22249 Z= 0.367 Chirality : 0.048 0.331 2871 Planarity : 0.005 0.044 2708 Dihedral : 4.910 25.145 2036 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 5.88 % 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: 0.70 (0.20), residues: 1687 helix: 1.10 (0.26), residues: 406 sheet: 0.62 (0.22), residues: 469 loop : 0.17 (0.23), residues: 812 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 222 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 37 residues processed: 281 average time/residue: 1.0892 time to fit residues: 344.6400 Evaluate side-chains 221 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 1.789 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 27 residues processed: 10 average time/residue: 0.4943 time to fit residues: 8.5293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN D 591 GLN E 99 ASN E 425 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 16359 Z= 0.202 Angle : 0.649 9.038 22249 Z= 0.324 Chirality : 0.044 0.287 2871 Planarity : 0.004 0.045 2708 Dihedral : 4.665 22.960 2036 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.81 % Rotamer Outliers : 5.09 % 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: 0.50 (0.20), residues: 1687 helix: 0.98 (0.26), residues: 407 sheet: 0.58 (0.22), residues: 467 loop : -0.04 (0.22), residues: 813 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 216 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 42 residues processed: 270 average time/residue: 1.0505 time to fit residues: 321.7568 Evaluate side-chains 229 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 33 residues processed: 9 average time/residue: 0.3159 time to fit residues: 6.2475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN D 577 GLN D 640 GLN E 33 ASN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.065 16359 Z= 0.529 Angle : 0.871 9.820 22249 Z= 0.429 Chirality : 0.051 0.278 2871 Planarity : 0.005 0.044 2708 Dihedral : 5.241 25.210 2036 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer Outliers : 6.21 % 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: -0.18 (0.20), residues: 1687 helix: 0.49 (0.26), residues: 402 sheet: 0.16 (0.23), residues: 459 loop : -0.49 (0.22), residues: 826 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 186 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 55 residues processed: 256 average time/residue: 1.0910 time to fit residues: 315.6740 Evaluate side-chains 220 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 165 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 47 residues processed: 9 average time/residue: 0.4203 time to fit residues: 7.1805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 181 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16359 Z= 0.181 Angle : 0.649 11.226 22249 Z= 0.324 Chirality : 0.044 0.318 2871 Planarity : 0.004 0.042 2708 Dihedral : 4.729 25.184 2036 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.81 % Rotamer Outliers : 5.36 % 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: -0.07 (0.20), residues: 1687 helix: 0.68 (0.27), residues: 407 sheet: 0.17 (0.23), residues: 451 loop : -0.44 (0.22), residues: 829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 206 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 49 residues processed: 268 average time/residue: 1.0069 time to fit residues: 307.4782 Evaluate side-chains 237 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 188 time to evaluate : 1.796 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 42 residues processed: 8 average time/residue: 0.5873 time to fit residues: 8.0992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN E 99 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 16359 Z= 0.365 Angle : 0.743 11.279 22249 Z= 0.365 Chirality : 0.047 0.312 2871 Planarity : 0.005 0.065 2708 Dihedral : 4.880 25.543 2036 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.50 % Rotamer Outliers : 5.09 % 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: -0.29 (0.20), residues: 1687 helix: 0.54 (0.27), residues: 408 sheet: 0.02 (0.23), residues: 459 loop : -0.60 (0.22), residues: 820 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 193 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 59 residues processed: 253 average time/residue: 1.0310 time to fit residues: 295.5571 Evaluate side-chains 240 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 181 time to evaluate : 1.741 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 52 residues processed: 8 average time/residue: 0.1886 time to fit residues: 4.8387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 164 optimal weight: 0.3980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 328 GLN D 577 GLN E 33 ASN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16359 Z= 0.176 Angle : 0.639 11.568 22249 Z= 0.319 Chirality : 0.043 0.334 2871 Planarity : 0.004 0.040 2708 Dihedral : 4.565 25.494 2036 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Rotamer Outliers : 5.03 % 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: -0.22 (0.20), residues: 1687 helix: 0.65 (0.26), residues: 407 sheet: 0.03 (0.23), residues: 456 loop : -0.57 (0.22), residues: 824 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 213 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 51 residues processed: 276 average time/residue: 1.0564 time to fit residues: 331.4349 Evaluate side-chains 241 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 190 time to evaluate : 1.817 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 44 residues processed: 8 average time/residue: 0.2024 time to fit residues: 5.0971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 178 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN D 577 GLN D 590 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16359 Z= 0.182 Angle : 0.641 12.903 22249 Z= 0.316 Chirality : 0.043 0.334 2871 Planarity : 0.004 0.042 2708 Dihedral : 4.447 23.297 2036 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer Outliers : 3.98 % 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: -0.19 (0.21), residues: 1687 helix: 0.67 (0.27), residues: 407 sheet: 0.02 (0.23), residues: 446 loop : -0.53 (0.22), residues: 834 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 208 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 49 residues processed: 259 average time/residue: 1.0110 time to fit residues: 298.8678 Evaluate side-chains 243 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 44 residues processed: 8 average time/residue: 0.3815 time to fit residues: 6.3465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 187 optimal weight: 0.4980 chunk 172 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 16359 Z= 0.251 Angle : 0.682 13.381 22249 Z= 0.338 Chirality : 0.044 0.331 2871 Planarity : 0.004 0.041 2708 Dihedral : 4.529 23.024 2036 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.10 % Rotamer Outliers : 3.66 % 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: -0.29 (0.21), residues: 1687 helix: 0.52 (0.27), residues: 414 sheet: -0.04 (0.23), residues: 455 loop : -0.56 (0.23), residues: 818 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 197 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 46 residues processed: 245 average time/residue: 1.0101 time to fit residues: 281.3134 Evaluate side-chains 236 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 1.786 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 42 residues processed: 5 average time/residue: 0.3788 time to fit residues: 4.8808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN D 590 GLN E 33 ASN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.106920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.087896 restraints weight = 35992.053| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 4.27 r_work: 0.3211 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 16359 Z= 0.350 Angle : 0.759 13.794 22249 Z= 0.372 Chirality : 0.047 0.321 2871 Planarity : 0.004 0.041 2708 Dihedral : 4.824 23.768 2036 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer Outliers : 3.53 % 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: -0.40 (0.21), residues: 1687 helix: 0.50 (0.27), residues: 407 sheet: -0.10 (0.23), residues: 457 loop : -0.67 (0.22), residues: 823 =============================================================================== Job complete usr+sys time: 5524.27 seconds wall clock time: 99 minutes 18.62 seconds (5958.62 seconds total)