Starting phenix.real_space_refine (version: dev) on Tue Feb 21 23:52:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2023/7l8z_23242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2023/7l8z_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_2023/7l8z_23242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2023/7l8z_23242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2023/7l8z_23242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8z_23242/02_2023/7l8z_23242_updated.pdb" } resolution = 3.8 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 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-4877/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 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: 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: 4 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 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: 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: 3 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 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: 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: 4 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: 1 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 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 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: "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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 9.36, per 1000 atoms: 0.59 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: 7.63 Conformation dependent library (CDL) restraints added in 2.1 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: 1.94 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: 5.33 Time building geometry restraints manager: 8.17 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 - 17.78: 9329 17.78 - 35.56: 221 35.56 - 53.34: 85 53.34 - 71.12: 29 71.12 - 88.91: 11 Dihedral angle restraints: 9675 sinusoidal: 4088 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 9672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 2655 0.278 - 0.557: 165 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 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. 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: 2.610 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: 11.160 Check model and map are aligned: 0.230 Process input model: 43.250 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 0.175 16257 Z= 1.483 Angle : 1.720 18.072 22098 Z= 1.178 Chirality : 0.146 1.392 2823 Planarity : 0.010 0.242 2699 Dihedral : 10.266 88.906 5939 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 % 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 *********************** 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 : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.3159 time to fit residues: 189.7251 Evaluate side-chains 198 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5000 ------------------------------------------------------------------------------- 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: 1.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 658 GLN C 72 HIS E 564 HIS E 577 GLN D 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2587 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= 0.270 Angle : 0.699 8.283 22098 Z= 0.383 Chirality : 0.049 0.483 2823 Planarity : 0.004 0.045 2699 Dihedral : 5.939 55.073 2646 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 2.79 % 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: 0.90 (0.20), residues: 1700 helix: 0.89 (0.26), residues: 413 sheet: 0.83 (0.23), residues: 459 loop : 0.47 (0.22), residues: 828 *********************** 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 282 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 27 residues processed: 261 average time/residue: 0.2807 time to fit residues: 109.5025 Evaluate side-chains 214 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1352 time to fit residues: 9.3415 ------------------------------------------------------------------------------- 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: 7.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 136 ASN A 422 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.080 16257 Z= 0.635 Angle : 0.852 8.682 22098 Z= 0.456 Chirality : 0.054 0.483 2823 Planarity : 0.006 0.107 2699 Dihedral : 6.367 53.604 2646 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 3.63 % 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: 0.08 (0.20), residues: 1700 helix: 0.50 (0.26), residues: 411 sheet: 0.27 (0.23), residues: 456 loop : -0.19 (0.22), residues: 833 *********************** 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 246 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 190 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 37 residues processed: 232 average time/residue: 0.2870 time to fit residues: 99.9193 Evaluate side-chains 204 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1635 time to fit residues: 13.1592 ------------------------------------------------------------------------------- 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: 0.5980 chunk 128 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 chunk 89 optimal weight: 0.0040 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 258 GLN C 428 GLN E 577 GLN D 99 ASN D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16257 Z= 0.174 Angle : 0.575 8.670 22098 Z= 0.312 Chirality : 0.045 0.532 2823 Planarity : 0.004 0.039 2699 Dihedral : 5.879 53.057 2646 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 1.69 % 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: 0.37 (0.21), residues: 1700 helix: 1.04 (0.27), residues: 397 sheet: 0.37 (0.23), residues: 464 loop : -0.10 (0.23), residues: 839 *********************** 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 240 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 232 average time/residue: 0.2767 time to fit residues: 96.7096 Evaluate side-chains 188 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 1.830 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1386 time to fit residues: 5.3127 ------------------------------------------------------------------------------- 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: 2.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 625 ASN B 658 GLN C 72 HIS E 564 HIS E 577 GLN ** 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: 0.8454 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 16257 Z= 0.394 Angle : 0.659 10.389 22098 Z= 0.355 Chirality : 0.052 1.076 2823 Planarity : 0.004 0.047 2699 Dihedral : 6.035 52.612 2646 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer Outliers : 2.98 % 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: 0.15 (0.21), residues: 1700 helix: 0.88 (0.27), residues: 405 sheet: 0.27 (0.24), residues: 437 loop : -0.28 (0.22), residues: 858 *********************** 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 232 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 27 residues processed: 213 average time/residue: 0.2959 time to fit residues: 93.0693 Evaluate side-chains 194 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.917 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.1907 time to fit residues: 10.9904 ------------------------------------------------------------------------------- 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: 1.9990 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 16257 Z= 0.206 Angle : 0.564 8.521 22098 Z= 0.305 Chirality : 0.048 0.797 2823 Planarity : 0.004 0.039 2699 Dihedral : 5.845 56.410 2646 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.00 % Favored : 95.88 % Rotamer Outliers : 1.43 % 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: 0.28 (0.21), residues: 1700 helix: 1.10 (0.27), residues: 403 sheet: 0.33 (0.24), residues: 440 loop : -0.25 (0.22), residues: 857 *********************** 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 212 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 203 average time/residue: 0.2972 time to fit residues: 88.8677 Evaluate side-chains 185 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 1.667 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1354 time to fit residues: 4.5544 ------------------------------------------------------------------------------- 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: 6.9990 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN E 577 GLN E 656 ASN D 88 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.090 16257 Z= 0.490 Angle : 0.715 10.770 22098 Z= 0.380 Chirality : 0.051 0.637 2823 Planarity : 0.005 0.054 2699 Dihedral : 6.202 54.619 2646 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.65 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.18 % 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: -0.14 (0.20), residues: 1700 helix: 0.65 (0.27), residues: 410 sheet: 0.13 (0.24), residues: 421 loop : -0.50 (0.22), residues: 869 *********************** 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 212 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 28 residues processed: 193 average time/residue: 0.3085 time to fit residues: 88.6168 Evaluate side-chains 185 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1448 time to fit residues: 10.0201 ------------------------------------------------------------------------------- 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: 0.7980 chunk 72 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4775 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= 0.195 Angle : 0.579 10.829 22098 Z= 0.310 Chirality : 0.046 0.588 2823 Planarity : 0.004 0.038 2699 Dihedral : 5.879 59.723 2646 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.94 % Favored : 95.94 % Rotamer Outliers : 0.58 % 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: 0.19 (0.21), residues: 1700 helix: 1.07 (0.28), residues: 403 sheet: 0.26 (0.25), residues: 413 loop : -0.31 (0.22), residues: 884 *********************** 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 204 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 198 average time/residue: 0.3073 time to fit residues: 90.0916 Evaluate side-chains 173 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1550 time to fit residues: 3.4010 ------------------------------------------------------------------------------- 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: 6.9990 chunk 168 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 178 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 478 ASN 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: 0.8409 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 16257 Z= 0.222 Angle : 0.572 10.303 22098 Z= 0.305 Chirality : 0.045 0.514 2823 Planarity : 0.004 0.038 2699 Dihedral : 5.743 59.030 2646 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.88 % Favored : 95.00 % Rotamer Outliers : 0.78 % 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: 0.21 (0.21), residues: 1700 helix: 1.07 (0.28), residues: 407 sheet: 0.19 (0.24), residues: 416 loop : -0.25 (0.22), residues: 877 *********************** 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 197 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 190 average time/residue: 0.2956 time to fit residues: 83.3422 Evaluate side-chains 182 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 176 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1323 time to fit residues: 3.6651 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 91 optimal weight: 0.0070 chunk 118 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- 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 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: 0.8404 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 16257 Z= 0.226 Angle : 0.572 10.197 22098 Z= 0.304 Chirality : 0.045 0.518 2823 Planarity : 0.004 0.038 2699 Dihedral : 5.676 57.458 2646 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer Outliers : 0.39 % 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: 0.23 (0.21), residues: 1700 helix: 1.06 (0.28), residues: 413 sheet: 0.26 (0.25), residues: 402 loop : -0.25 (0.22), residues: 885 ********************** 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 186 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 184 average time/residue: 0.3009 time to fit residues: 81.2824 Evaluate side-chains 178 residues out of total 1543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1317 time to fit residues: 3.0347 ------------------------------------------------------------------------------- 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: 4.9990 chunk 137 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 478 ASN B 550 GLN B 658 GLN E 563 GLN E 577 GLN D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.095342 restraints weight = 29401.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098031 restraints weight = 17586.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099823 restraints weight = 12716.926| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 16257 Z= 0.404 Angle : 0.672 12.682 22098 Z= 0.356 Chirality : 0.048 0.505 2823 Planarity : 0.005 0.050 2699 Dihedral : 5.955 59.567 2646 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.47 % Favored : 94.35 % Rotamer Outliers : 0.52 % 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: -0.04 (0.21), residues: 1700 helix: 0.80 (0.27), residues: 409 sheet: 0.11 (0.25), residues: 393 loop : -0.40 (0.21), residues: 898 =============================================================================== Job complete usr+sys time: 2924.08 seconds wall clock time: 54 minutes 22.12 seconds (3262.12 seconds total)