Starting phenix.real_space_refine on Thu Sep 18 09:31:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhh_49411/09_2025/9nhh_49411.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhh_49411/09_2025/9nhh_49411.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 { model { file = "/net/cci-nas-00/data/ceres_data/9nhh_49411/09_2025/9nhh_49411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhh_49411/09_2025/9nhh_49411.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nhh_49411/09_2025/9nhh_49411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhh_49411/09_2025/9nhh_49411.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.034 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 106 5.16 5 C 9715 2.51 5 N 2594 2.21 5 O 3191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15606 Number of models: 1 Model: "" Number of chains: 32 Chain: "H" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 665 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'TRANS': 128} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 537 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 103} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3457 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "B" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 945 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" 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: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3347 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 3.83, per 1000 atoms: 0.25 Number of scatterers: 15606 At special positions: 0 Unit cell: (136.895, 123.31, 146.3, 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 106 16.00 O 3191 8.00 N 2594 7.00 C 9715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 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 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 664 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 664 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.02 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA T 3 " - " MAN T 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 U 2 " - " BMA U 3 " " 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-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 130 " " NAG A 605 " - " ASN A 197 " " NAG A 606 " - " ASN A 230 " " NAG A 607 " - " ASN A 289 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 392 " " NAG A 611 " - " ASN A 398 " " NAG B 701 " - " ASN B 656 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 616 " " NAG B 705 " - " ASN B 637 " " NAG C 701 " - " ASN C 656 " " NAG C 702 " - " ASN C 611 " " NAG C 703 " - " ASN C 625 " " NAG C 704 " - " ASN C 616 " " NAG C 705 " - " ASN C 637 " " NAG D 701 " - " ASN D 625 " " NAG D 702 " - " ASN D 616 " " NAG D 703 " - " ASN D 637 " " NAG D 704 " - " ASN D 611 " " NAG E 601 " - " ASN E 301 " " NAG E 602 " - " ASN E 295 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 130 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 230 " " NAG E 607 " - " ASN E 289 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 386 " " NAG E 610 " - " ASN E 392 " " NAG E 611 " - " ASN E 398 " " NAG E 612 " - " ASN E 234 " " NAG E 613 " - " ASN E 276 " " NAG F 601 " - " ASN F 301 " " NAG F 602 " - " ASN F 295 " " NAG F 603 " - " ASN F 160 " " NAG F 604 " - " ASN F 130 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 230 " " NAG F 607 " - " ASN F 289 " " NAG F 608 " - " ASN F 339 " " NAG F 609 " - " ASN F 386 " " NAG F 610 " - " ASN F 392 " " NAG F 611 " - " ASN F 241 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 413 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN E 88 " " NAG P 1 " - " ASN E 156 " " NAG Q 1 " - " ASN E 332 " " NAG R 1 " - " ASN E 413 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN F 88 " " NAG V 1 " - " ASN F 156 " " NAG W 1 " - " ASN F 332 " " NAG X 1 " - " ASN F 413 " " NAG Y 1 " - " ASN F 448 " " NAG Z 1 " - " ASN F 262 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 593.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3562 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 25 sheets defined 27.9% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'H' and resid 65 through 69 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'L' and resid 78 through 81 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.828A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.501A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.917A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.363A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.421A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.417A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 545 removed outlier: 4.066A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 658 Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.363A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.808A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 659 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.874A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 480 Processing helix chain 'E' and resid 481 through 484 removed outlier: 4.932A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 481 through 484' Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 98 through 116 removed outlier: 3.790A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 353 removed outlier: 3.922A pdb=" N GLU F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.558A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU F 429 " --> pdb=" O LEU F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.892A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 8 removed outlier: 5.989A pdb=" N UNK H 16 " --> pdb=" O UNK H 86 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N UNK H 86 " --> pdb=" O UNK H 16 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N UNK H 84 " --> pdb=" O UNK H 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 33 through 40 removed outlier: 5.718A pdb=" N UNK H 39 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N UNK H 48 " --> pdb=" O UNK H 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 61 current: chain 'H' and resid 111 through 113 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.798A pdb=" N UNK L 49 " --> pdb=" O UNK L 52 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N UNK L 44 " --> pdb=" O UNK L 36 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TRP L 34 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N UNK L 48 " --> pdb=" O UNK L 32 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N UNK L 32 " --> pdb=" O UNK L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.037A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.494A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA9, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB1, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.901A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 7.045A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AB3, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.207A pdb=" N CYS B 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR F 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR B 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL F 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL B 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 603 through 609 removed outlier: 5.054A pdb=" N VAL E 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.497A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB9, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.940A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.910A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ARG E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC2, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.422A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 75 through 76 removed outlier: 7.016A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'F' and resid 200 through 203 removed outlier: 5.873A pdb=" N VAL F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR F 435 " --> pdb=" O VAL F 200 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 6.825A pdb=" N ASN F 301 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 323A current: chain 'F' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 382 through 385 current: chain 'F' and resid 465 through 470 467 hydrogen bonds defined for protein. 1275 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: 2.70 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4810 1.34 - 1.47: 4043 1.47 - 1.59: 6876 1.59 - 1.72: 0 1.72 - 1.84: 139 Bond restraints: 15868 Sorted by residual: bond pdb=" N UNK H 1 " pdb=" CA UNK H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N UNK L 1 " pdb=" CA UNK L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" CB TRP E 479 " pdb=" CG TRP E 479 " ideal model delta sigma weight residual 1.498 1.544 -0.046 3.10e-02 1.04e+03 2.17e+00 bond pdb=" CB ILE F 184 " pdb=" CG2 ILE F 184 " ideal model delta sigma weight residual 1.521 1.569 -0.048 3.30e-02 9.18e+02 2.09e+00 bond pdb=" CB ILE B 622 " pdb=" CG2 ILE B 622 " ideal model delta sigma weight residual 1.521 1.566 -0.045 3.30e-02 9.18e+02 1.89e+00 ... (remaining 15863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 19146 1.48 - 2.96: 2110 2.96 - 4.45: 264 4.45 - 5.93: 55 5.93 - 7.41: 2 Bond angle restraints: 21577 Sorted by residual: angle pdb=" N GLY E 41 " pdb=" CA GLY E 41 " pdb=" C GLY E 41 " ideal model delta sigma weight residual 116.01 110.37 5.64 1.64e+00 3.72e-01 1.18e+01 angle pdb=" N GLY F 41 " pdb=" CA GLY F 41 " pdb=" C GLY F 41 " ideal model delta sigma weight residual 116.01 110.54 5.47 1.64e+00 3.72e-01 1.11e+01 angle pdb=" C UNK H 121 " pdb=" N UNK H 122 " pdb=" CA UNK H 122 " ideal model delta sigma weight residual 121.70 127.41 -5.71 1.80e+00 3.09e-01 1.01e+01 angle pdb=" N ILE A 194 " pdb=" CA ILE A 194 " pdb=" C ILE A 194 " ideal model delta sigma weight residual 110.62 114.23 -3.61 1.14e+00 7.69e-01 1.01e+01 angle pdb=" C UNK L 92 " pdb=" CA UNK L 92 " pdb=" CB UNK L 92 " ideal model delta sigma weight residual 110.08 115.84 -5.76 1.90e+00 2.77e-01 9.19e+00 ... (remaining 21572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.03: 10440 21.03 - 42.06: 236 42.06 - 63.08: 56 63.08 - 84.11: 44 84.11 - 105.14: 31 Dihedral angle restraints: 10807 sinusoidal: 5334 harmonic: 5473 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 87 " pdb=" CB CYS L 87 " ideal model delta sinusoidal sigma weight residual 93.00 137.64 -44.64 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -122.70 36.70 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 664 " pdb=" CB CYS B 664 " ideal model delta sinusoidal sigma weight residual -86.00 -122.30 36.30 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 10804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2385 0.089 - 0.178: 360 0.178 - 0.267: 21 0.267 - 0.356: 2 0.356 - 0.445: 1 Chirality restraints: 2769 Sorted by residual: chirality pdb=" C1 NAG E 605 " pdb=" ND2 ASN E 197 " pdb=" C2 NAG E 605 " pdb=" O5 NAG E 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" C1 NAG E 607 " pdb=" ND2 ASN E 289 " pdb=" C2 NAG E 607 " pdb=" O5 NAG E 607 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG A 607 " pdb=" ND2 ASN A 289 " pdb=" C2 NAG A 607 " pdb=" O5 NAG A 607 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 2766 not shown) Planarity restraints: 2701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 640 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ASN B 640 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN B 640 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 641 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 636 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C SER B 636 " -0.066 2.00e-02 2.50e+03 pdb=" O SER B 636 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN B 637 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 480 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C ARG F 480 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG F 480 " 0.024 2.00e-02 2.50e+03 pdb=" N SER F 481 " 0.021 2.00e-02 2.50e+03 ... (remaining 2698 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3337 2.79 - 3.32: 13824 3.32 - 3.85: 25529 3.85 - 4.37: 30249 4.37 - 4.90: 50782 Nonbonded interactions: 123721 Sorted by model distance: nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 432 " model vdw 2.267 3.120 nonbonded pdb=" OE2 GLU B 647 " pdb=" NE ARG C 542 " model vdw 2.345 3.120 nonbonded pdb=" OD1 ASP F 113 " pdb=" NZ LYS F 432 " model vdw 2.371 3.120 nonbonded pdb=" OD1 ASP F 133 " pdb=" NZ LYS F 155 " model vdw 2.415 3.120 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR C 606 " model vdw 2.473 3.040 ... (remaining 123716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 77 or resid 82 through 396 or resid 413 through \ 457 or resid 464 through 611)) selection = (chain 'E' and (resid 33 through 396 or resid 413 through 457 or resid 464 throu \ gh 611)) selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 521 through 704) selection = (chain 'C' and resid 521 through 704) selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'T' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.160 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16000 Z= 0.220 Angle : 0.991 7.409 21938 Z= 0.528 Chirality : 0.062 0.445 2769 Planarity : 0.006 0.040 2634 Dihedral : 12.341 105.140 7140 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.19), residues: 1614 helix: 0.31 (0.24), residues: 377 sheet: 0.97 (0.21), residues: 477 loop : 0.38 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 192 TYR 0.016 0.003 TYR A 191 PHE 0.024 0.003 PHE E 383 TRP 0.035 0.004 TRP F 427 HIS 0.005 0.002 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00498 (15868) covalent geometry : angle 0.96217 (21577) SS BOND : bond 0.00433 ( 35) SS BOND : angle 1.85478 ( 70) hydrogen bonds : bond 0.12052 ( 467) hydrogen bonds : angle 7.41089 ( 1275) link_ALPHA1-3 : bond 0.00205 ( 3) link_ALPHA1-3 : angle 1.78389 ( 9) link_ALPHA1-6 : bond 0.00650 ( 3) link_ALPHA1-6 : angle 1.25324 ( 9) link_BETA1-4 : bond 0.00559 ( 24) link_BETA1-4 : angle 1.88222 ( 72) link_NAG-ASN : bond 0.00370 ( 67) link_NAG-ASN : angle 2.28577 ( 201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8410 (mppt) REVERT: A 106 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7644 (mp0) REVERT: A 109 ILE cc_start: 0.8795 (mm) cc_final: 0.8171 (mp) REVERT: A 178 LYS cc_start: 0.8404 (ttmt) cc_final: 0.8071 (ttmm) REVERT: A 302 ASN cc_start: 0.7874 (m-40) cc_final: 0.7650 (m110) REVERT: A 500 LYS cc_start: 0.8340 (mttt) cc_final: 0.7455 (mtmt) REVERT: B 534 SER cc_start: 0.9127 (p) cc_final: 0.8778 (m) REVERT: C 647 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8199 (mt-10) REVERT: C 660 ASN cc_start: 0.8261 (t0) cc_final: 0.7838 (t0) REVERT: D 543 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7456 (tm-30) REVERT: D 636 SER cc_start: 0.8385 (t) cc_final: 0.8063 (p) REVERT: E 169 MET cc_start: 0.6932 (mmm) cc_final: 0.5092 (tmm) REVERT: E 207 LYS cc_start: 0.8597 (mmtt) cc_final: 0.7786 (tptt) REVERT: E 371 ILE cc_start: 0.8738 (mt) cc_final: 0.8344 (pt) REVERT: E 500 LYS cc_start: 0.7655 (tttp) cc_final: 0.7372 (pttp) REVERT: F 46 LYS cc_start: 0.8820 (pttt) cc_final: 0.8576 (pttp) REVERT: F 49 THR cc_start: 0.9073 (m) cc_final: 0.8862 (p) REVERT: F 87 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7717 (mp0) REVERT: F 106 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7602 (mp0) REVERT: F 207 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8169 (tptt) REVERT: F 211 GLU cc_start: 0.8571 (tt0) cc_final: 0.8220 (tm-30) REVERT: F 428 GLN cc_start: 0.8410 (mp10) cc_final: 0.8159 (mp10) outliers start: 0 outliers final: 3 residues processed: 312 average time/residue: 0.7359 time to fit residues: 249.5090 Evaluate side-chains 172 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain E residue 325 ASN Chi-restraints excluded: chain F residue 184 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 461 ASN C 650 GLN C 652 GLN D 652 GLN E 340 ASN F 356 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.106857 restraints weight = 21648.720| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.79 r_work: 0.3110 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16000 Z= 0.201 Angle : 0.643 10.249 21938 Z= 0.313 Chirality : 0.047 0.316 2769 Planarity : 0.004 0.034 2634 Dihedral : 9.028 82.343 3996 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.82 % Allowed : 8.70 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.20), residues: 1614 helix: 1.38 (0.26), residues: 383 sheet: 0.76 (0.21), residues: 475 loop : 0.51 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 327 TYR 0.014 0.002 TYR B 638 PHE 0.015 0.002 PHE A 233 TRP 0.022 0.002 TRP E 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00475 (15868) covalent geometry : angle 0.59872 (21577) SS BOND : bond 0.00366 ( 35) SS BOND : angle 1.28847 ( 70) hydrogen bonds : bond 0.04770 ( 467) hydrogen bonds : angle 5.55690 ( 1275) link_ALPHA1-3 : bond 0.00604 ( 3) link_ALPHA1-3 : angle 2.25374 ( 9) link_ALPHA1-6 : bond 0.00292 ( 3) link_ALPHA1-6 : angle 1.75372 ( 9) link_BETA1-4 : bond 0.00388 ( 24) link_BETA1-4 : angle 1.92582 ( 72) link_NAG-ASN : bond 0.00328 ( 67) link_NAG-ASN : angle 2.10627 ( 201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7980 (mp0) REVERT: A 178 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8175 (ttmm) REVERT: A 500 LYS cc_start: 0.8629 (mttt) cc_final: 0.7863 (mtmt) REVERT: B 534 SER cc_start: 0.9191 (p) cc_final: 0.8878 (m) REVERT: B 544 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7440 (tp) REVERT: B 632 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: C 574 LYS cc_start: 0.7961 (tttt) cc_final: 0.7630 (pmtt) REVERT: C 636 SER cc_start: 0.8672 (t) cc_final: 0.8346 (p) REVERT: C 647 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8391 (mt-10) REVERT: C 657 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7728 (mm-30) REVERT: D 543 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7743 (tm-30) REVERT: D 636 SER cc_start: 0.8938 (t) cc_final: 0.8597 (p) REVERT: E 169 MET cc_start: 0.6827 (mmm) cc_final: 0.5234 (tmm) REVERT: E 207 LYS cc_start: 0.8520 (mmtt) cc_final: 0.7772 (tptt) REVERT: F 46 LYS cc_start: 0.8931 (pttt) cc_final: 0.8692 (pttp) REVERT: F 87 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7902 (mp0) REVERT: F 106 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7821 (mp0) REVERT: F 207 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8205 (tptt) outliers start: 27 outliers final: 10 residues processed: 188 average time/residue: 0.7714 time to fit residues: 157.1947 Evaluate side-chains 156 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 128 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 130 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 A 302 ASN A 461 ASN B 653 GLN D 652 GLN F 103 GLN F 356 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108108 restraints weight = 21830.972| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.83 r_work: 0.3104 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16000 Z= 0.126 Angle : 0.543 6.671 21938 Z= 0.265 Chirality : 0.044 0.276 2769 Planarity : 0.003 0.048 2634 Dihedral : 7.447 73.741 3990 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.75 % Allowed : 10.05 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.20), residues: 1614 helix: 1.57 (0.27), residues: 385 sheet: 0.79 (0.22), residues: 443 loop : 0.26 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 542 TYR 0.016 0.001 TYR B 638 PHE 0.013 0.001 PHE F 53 TRP 0.017 0.001 TRP A 479 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00292 (15868) covalent geometry : angle 0.50248 (21577) SS BOND : bond 0.00488 ( 35) SS BOND : angle 1.20846 ( 70) hydrogen bonds : bond 0.03959 ( 467) hydrogen bonds : angle 5.02763 ( 1275) link_ALPHA1-3 : bond 0.00947 ( 3) link_ALPHA1-3 : angle 1.74174 ( 9) link_ALPHA1-6 : bond 0.00525 ( 3) link_ALPHA1-6 : angle 1.67848 ( 9) link_BETA1-4 : bond 0.00457 ( 24) link_BETA1-4 : angle 1.62773 ( 72) link_NAG-ASN : bond 0.00273 ( 67) link_NAG-ASN : angle 1.82134 ( 201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8616 (mppt) REVERT: A 106 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8031 (mp0) REVERT: A 169 MET cc_start: 0.8548 (mtp) cc_final: 0.8282 (mtt) REVERT: A 178 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8112 (ttmm) REVERT: A 500 LYS cc_start: 0.8589 (mttt) cc_final: 0.7854 (mtmt) REVERT: B 534 SER cc_start: 0.9074 (p) cc_final: 0.8737 (m) REVERT: B 535 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7820 (mtp) REVERT: B 588 LYS cc_start: 0.7729 (mttt) cc_final: 0.6919 (mmtt) REVERT: B 632 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: C 574 LYS cc_start: 0.7954 (tttt) cc_final: 0.7689 (pmtt) REVERT: C 647 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8382 (mt-10) REVERT: D 543 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7803 (tm-30) REVERT: D 636 SER cc_start: 0.8930 (t) cc_final: 0.8635 (p) REVERT: E 99 ASN cc_start: 0.8867 (t0) cc_final: 0.8526 (t0) REVERT: E 169 MET cc_start: 0.6920 (mmm) cc_final: 0.5290 (tmm) REVERT: E 207 LYS cc_start: 0.8603 (mmtt) cc_final: 0.7864 (tptt) REVERT: E 477 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8558 (m-30) REVERT: F 87 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7916 (mp0) REVERT: F 106 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7876 (mp0) REVERT: F 207 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8221 (tptt) outliers start: 26 outliers final: 9 residues processed: 174 average time/residue: 0.7579 time to fit residues: 143.1390 Evaluate side-chains 146 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 348 LYS Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 461 ASN B 653 GLN C 652 GLN D 652 GLN E 340 ASN F 356 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106386 restraints weight = 21711.890| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.83 r_work: 0.3095 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16000 Z= 0.153 Angle : 0.552 6.804 21938 Z= 0.269 Chirality : 0.045 0.272 2769 Planarity : 0.003 0.086 2634 Dihedral : 6.635 65.982 3990 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.89 % Allowed : 10.32 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1614 helix: 1.59 (0.27), residues: 385 sheet: 0.63 (0.22), residues: 443 loop : 0.15 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 166 TYR 0.014 0.001 TYR B 638 PHE 0.011 0.002 PHE E 53 TRP 0.014 0.001 TRP F 69 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00360 (15868) covalent geometry : angle 0.51441 (21577) SS BOND : bond 0.00443 ( 35) SS BOND : angle 1.08858 ( 70) hydrogen bonds : bond 0.03903 ( 467) hydrogen bonds : angle 4.86901 ( 1275) link_ALPHA1-3 : bond 0.00903 ( 3) link_ALPHA1-3 : angle 2.00506 ( 9) link_ALPHA1-6 : bond 0.00629 ( 3) link_ALPHA1-6 : angle 1.68467 ( 9) link_BETA1-4 : bond 0.00443 ( 24) link_BETA1-4 : angle 1.57496 ( 72) link_NAG-ASN : bond 0.00267 ( 67) link_NAG-ASN : angle 1.80077 ( 201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8584 (mppt) REVERT: A 99 ASN cc_start: 0.8530 (t0) cc_final: 0.8146 (t0) REVERT: A 106 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8037 (mp0) REVERT: A 178 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8139 (ttmm) REVERT: A 207 LYS cc_start: 0.8520 (mmpt) cc_final: 0.8280 (tppp) REVERT: A 304 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7485 (mtm-85) REVERT: A 500 LYS cc_start: 0.8636 (mttt) cc_final: 0.7814 (mtmt) REVERT: B 534 SER cc_start: 0.9053 (p) cc_final: 0.8765 (m) REVERT: B 535 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7869 (mtp) REVERT: B 588 LYS cc_start: 0.7762 (mttt) cc_final: 0.6998 (tptp) REVERT: B 632 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: C 574 LYS cc_start: 0.8079 (tttt) cc_final: 0.7713 (pmtt) REVERT: C 588 LYS cc_start: 0.8350 (mttt) cc_final: 0.7900 (tptt) REVERT: C 636 SER cc_start: 0.8759 (t) cc_final: 0.8466 (p) REVERT: C 647 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8441 (mt-10) REVERT: C 654 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7819 (mt-10) REVERT: D 543 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7863 (tm-30) REVERT: D 632 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7150 (tp30) REVERT: D 636 SER cc_start: 0.8966 (t) cc_final: 0.8724 (p) REVERT: E 99 ASN cc_start: 0.8817 (t0) cc_final: 0.8420 (t0) REVERT: E 169 MET cc_start: 0.6910 (mmm) cc_final: 0.5318 (tmm) REVERT: E 207 LYS cc_start: 0.8502 (mmtt) cc_final: 0.7839 (tptt) REVERT: F 87 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7958 (mp0) REVERT: F 106 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7840 (mp0) REVERT: F 207 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8200 (tptt) REVERT: F 370 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7058 (mm-30) outliers start: 28 outliers final: 11 residues processed: 162 average time/residue: 0.7631 time to fit residues: 134.3853 Evaluate side-chains 147 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 588 LYS Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 348 LYS Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 163 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 461 ASN B 653 GLN C 652 GLN D 652 GLN E 103 GLN E 460 ASN F 356 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102587 restraints weight = 21698.765| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.74 r_work: 0.3021 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16000 Z= 0.260 Angle : 0.651 7.430 21938 Z= 0.314 Chirality : 0.048 0.283 2769 Planarity : 0.004 0.067 2634 Dihedral : 6.890 62.690 3990 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.70 % Allowed : 10.11 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.20), residues: 1614 helix: 1.22 (0.27), residues: 391 sheet: 0.23 (0.23), residues: 441 loop : -0.13 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 480 TYR 0.024 0.002 TYR B 638 PHE 0.014 0.002 PHE A 233 TRP 0.014 0.002 TRP E 479 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00626 (15868) covalent geometry : angle 0.61135 (21577) SS BOND : bond 0.00562 ( 35) SS BOND : angle 1.32023 ( 70) hydrogen bonds : bond 0.04532 ( 467) hydrogen bonds : angle 5.09154 ( 1275) link_ALPHA1-3 : bond 0.00676 ( 3) link_ALPHA1-3 : angle 1.96672 ( 9) link_ALPHA1-6 : bond 0.00616 ( 3) link_ALPHA1-6 : angle 1.54735 ( 9) link_BETA1-4 : bond 0.00457 ( 24) link_BETA1-4 : angle 1.64103 ( 72) link_NAG-ASN : bond 0.00387 ( 67) link_NAG-ASN : angle 2.07720 ( 201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8606 (t0) cc_final: 0.8171 (t0) REVERT: A 178 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8206 (ttmm) REVERT: A 207 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8322 (tppp) REVERT: A 304 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7426 (mtm-85) REVERT: A 315 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7249 (mmp-170) REVERT: A 500 LYS cc_start: 0.8663 (mttt) cc_final: 0.7799 (mtmt) REVERT: B 534 SER cc_start: 0.9090 (p) cc_final: 0.8824 (m) REVERT: B 535 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: B 588 LYS cc_start: 0.7791 (mttt) cc_final: 0.7102 (tptt) REVERT: C 574 LYS cc_start: 0.8059 (tttt) cc_final: 0.7678 (pmtt) REVERT: C 636 SER cc_start: 0.8851 (t) cc_final: 0.8585 (p) REVERT: C 647 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8462 (mt-10) REVERT: D 543 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7815 (tm-30) REVERT: D 632 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: D 636 SER cc_start: 0.9014 (t) cc_final: 0.8775 (p) REVERT: E 169 MET cc_start: 0.6763 (mmm) cc_final: 0.5217 (tmm) REVERT: E 207 LYS cc_start: 0.8600 (mmtt) cc_final: 0.7940 (tptt) REVERT: F 87 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8034 (mp0) REVERT: F 207 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8252 (tptt) REVERT: F 370 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7300 (mm-30) outliers start: 40 outliers final: 14 residues processed: 162 average time/residue: 0.7227 time to fit residues: 127.4872 Evaluate side-chains 145 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 588 LYS Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 160 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN B 651 ASN B 653 GLN C 652 GLN D 652 GLN F 356 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104804 restraints weight = 21606.902| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.74 r_work: 0.3054 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16000 Z= 0.149 Angle : 0.543 6.836 21938 Z= 0.264 Chirality : 0.044 0.272 2769 Planarity : 0.003 0.047 2634 Dihedral : 6.322 58.997 3990 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.02 % Allowed : 10.92 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 1614 helix: 1.34 (0.27), residues: 396 sheet: 0.17 (0.23), residues: 441 loop : -0.19 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 327 TYR 0.014 0.001 TYR B 638 PHE 0.012 0.001 PHE E 53 TRP 0.014 0.001 TRP A 479 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00352 (15868) covalent geometry : angle 0.50665 (21577) SS BOND : bond 0.00413 ( 35) SS BOND : angle 1.07987 ( 70) hydrogen bonds : bond 0.03803 ( 467) hydrogen bonds : angle 4.82419 ( 1275) link_ALPHA1-3 : bond 0.00881 ( 3) link_ALPHA1-3 : angle 1.77905 ( 9) link_ALPHA1-6 : bond 0.00826 ( 3) link_ALPHA1-6 : angle 1.52017 ( 9) link_BETA1-4 : bond 0.00420 ( 24) link_BETA1-4 : angle 1.41487 ( 72) link_NAG-ASN : bond 0.00236 ( 67) link_NAG-ASN : angle 1.79831 ( 201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8530 (t0) cc_final: 0.8091 (t0) REVERT: A 109 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8529 (mp) REVERT: A 113 ASP cc_start: 0.8108 (m-30) cc_final: 0.7636 (m-30) REVERT: A 178 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8132 (ttmm) REVERT: A 207 LYS cc_start: 0.8600 (mmpt) cc_final: 0.8365 (tppp) REVERT: A 304 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7358 (mtm-85) REVERT: A 500 LYS cc_start: 0.8726 (mttt) cc_final: 0.7858 (mtmt) REVERT: B 534 SER cc_start: 0.9071 (p) cc_final: 0.8788 (m) REVERT: B 535 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8089 (mtt) REVERT: B 588 LYS cc_start: 0.7797 (mttt) cc_final: 0.6952 (tptp) REVERT: C 588 LYS cc_start: 0.8321 (mttt) cc_final: 0.7849 (tptt) REVERT: C 636 SER cc_start: 0.8821 (t) cc_final: 0.8559 (p) REVERT: C 647 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8383 (mt-10) REVERT: D 543 GLN cc_start: 0.8445 (mm-40) cc_final: 0.7830 (tm-30) REVERT: D 632 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7066 (tp30) REVERT: D 636 SER cc_start: 0.9010 (t) cc_final: 0.8763 (p) REVERT: E 99 ASN cc_start: 0.8965 (t0) cc_final: 0.8558 (t0) REVERT: E 169 MET cc_start: 0.6820 (mmm) cc_final: 0.5220 (tmm) REVERT: E 207 LYS cc_start: 0.8595 (mmtt) cc_final: 0.7923 (tptt) REVERT: F 49 THR cc_start: 0.9139 (m) cc_final: 0.8820 (p) REVERT: F 87 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7973 (mp0) REVERT: F 207 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8172 (tptt) REVERT: F 293 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: F 370 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7353 (mm-30) outliers start: 30 outliers final: 11 residues processed: 155 average time/residue: 0.7343 time to fit residues: 123.9288 Evaluate side-chains 144 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 289 ASN Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 121 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 461 ASN B 653 GLN D 652 GLN F 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105406 restraints weight = 21613.499| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.80 r_work: 0.3067 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16000 Z= 0.146 Angle : 0.538 6.877 21938 Z= 0.262 Chirality : 0.044 0.268 2769 Planarity : 0.003 0.041 2634 Dihedral : 5.952 50.645 3990 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.69 % Allowed : 11.67 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.20), residues: 1614 helix: 1.43 (0.27), residues: 394 sheet: 0.19 (0.23), residues: 441 loop : -0.23 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.016 0.001 TYR B 638 PHE 0.011 0.001 PHE E 53 TRP 0.013 0.001 TRP F 69 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00347 (15868) covalent geometry : angle 0.50261 (21577) SS BOND : bond 0.00413 ( 35) SS BOND : angle 1.06980 ( 70) hydrogen bonds : bond 0.03757 ( 467) hydrogen bonds : angle 4.68458 ( 1275) link_ALPHA1-3 : bond 0.00876 ( 3) link_ALPHA1-3 : angle 1.77905 ( 9) link_ALPHA1-6 : bond 0.00900 ( 3) link_ALPHA1-6 : angle 1.50400 ( 9) link_BETA1-4 : bond 0.00437 ( 24) link_BETA1-4 : angle 1.39783 ( 72) link_NAG-ASN : bond 0.00254 ( 67) link_NAG-ASN : angle 1.75907 ( 201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8705 (t0) cc_final: 0.8321 (t0) REVERT: A 109 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8631 (mp) REVERT: A 113 ASP cc_start: 0.8300 (m-30) cc_final: 0.7843 (m-30) REVERT: A 178 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8235 (ttmm) REVERT: A 207 LYS cc_start: 0.8569 (mmpt) cc_final: 0.8301 (tppp) REVERT: A 304 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7412 (mtm-85) REVERT: A 434 MET cc_start: 0.9136 (ttp) cc_final: 0.8905 (ttt) REVERT: A 500 LYS cc_start: 0.8872 (mttt) cc_final: 0.7949 (mtmt) REVERT: B 534 SER cc_start: 0.9097 (p) cc_final: 0.8827 (m) REVERT: B 535 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8200 (mtt) REVERT: B 588 LYS cc_start: 0.7951 (mttt) cc_final: 0.7089 (tptp) REVERT: C 588 LYS cc_start: 0.8539 (mttt) cc_final: 0.7970 (tptt) REVERT: C 636 SER cc_start: 0.8952 (t) cc_final: 0.8674 (p) REVERT: C 647 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8573 (mt-10) REVERT: D 543 GLN cc_start: 0.8607 (mm-40) cc_final: 0.7604 (tm-30) REVERT: D 632 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: D 636 SER cc_start: 0.9065 (t) cc_final: 0.8802 (p) REVERT: E 99 ASN cc_start: 0.9121 (t0) cc_final: 0.8664 (t0) REVERT: E 169 MET cc_start: 0.6892 (mmm) cc_final: 0.5204 (tmm) REVERT: E 207 LYS cc_start: 0.8668 (mmtt) cc_final: 0.7924 (tptt) REVERT: F 49 THR cc_start: 0.9203 (m) cc_final: 0.8894 (p) REVERT: F 87 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8147 (mp0) REVERT: F 207 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8205 (tptt) REVERT: F 370 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7481 (mm-30) outliers start: 25 outliers final: 13 residues processed: 154 average time/residue: 0.7175 time to fit residues: 120.3894 Evaluate side-chains 147 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 289 ASN Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 85 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 652 GLN F 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103602 restraints weight = 21784.508| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.73 r_work: 0.3035 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16000 Z= 0.193 Angle : 0.578 7.249 21938 Z= 0.279 Chirality : 0.045 0.272 2769 Planarity : 0.003 0.040 2634 Dihedral : 5.971 58.860 3990 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.55 % Allowed : 11.94 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.20), residues: 1614 helix: 1.34 (0.27), residues: 394 sheet: 0.09 (0.23), residues: 443 loop : -0.30 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 469 TYR 0.014 0.001 TYR B 638 PHE 0.010 0.002 PHE A 383 TRP 0.012 0.001 TRP A 69 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00462 (15868) covalent geometry : angle 0.54100 (21577) SS BOND : bond 0.00412 ( 35) SS BOND : angle 1.19009 ( 70) hydrogen bonds : bond 0.04016 ( 467) hydrogen bonds : angle 4.77081 ( 1275) link_ALPHA1-3 : bond 0.00788 ( 3) link_ALPHA1-3 : angle 1.79612 ( 9) link_ALPHA1-6 : bond 0.00887 ( 3) link_ALPHA1-6 : angle 1.52291 ( 9) link_BETA1-4 : bond 0.00436 ( 24) link_BETA1-4 : angle 1.45063 ( 72) link_NAG-ASN : bond 0.00292 ( 67) link_NAG-ASN : angle 1.88084 ( 201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8580 (t0) cc_final: 0.8187 (t0) REVERT: A 109 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8578 (mp) REVERT: A 113 ASP cc_start: 0.8127 (m-30) cc_final: 0.7645 (m-30) REVERT: A 178 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8167 (ttmm) REVERT: A 207 LYS cc_start: 0.8641 (mmpt) cc_final: 0.8427 (tppp) REVERT: A 304 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7354 (mtm-85) REVERT: A 315 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7081 (mmp-170) REVERT: A 500 LYS cc_start: 0.8737 (mttt) cc_final: 0.7857 (mtmt) REVERT: B 534 SER cc_start: 0.9064 (p) cc_final: 0.8808 (m) REVERT: B 535 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8149 (mtt) REVERT: B 588 LYS cc_start: 0.7816 (mttt) cc_final: 0.6930 (mmtt) REVERT: C 574 LYS cc_start: 0.8040 (tttt) cc_final: 0.7732 (pmmt) REVERT: C 588 LYS cc_start: 0.8380 (mttt) cc_final: 0.7866 (tptt) REVERT: C 636 SER cc_start: 0.8882 (t) cc_final: 0.8619 (p) REVERT: C 647 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8445 (mt-10) REVERT: D 543 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7820 (tm-30) REVERT: D 632 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: D 636 SER cc_start: 0.9038 (t) cc_final: 0.8728 (p) REVERT: E 169 MET cc_start: 0.6791 (mmm) cc_final: 0.5231 (tmm) REVERT: E 207 LYS cc_start: 0.8570 (mmtt) cc_final: 0.7927 (tptt) REVERT: F 49 THR cc_start: 0.9153 (m) cc_final: 0.8849 (p) REVERT: F 87 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8037 (mp0) REVERT: F 207 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8184 (tptt) REVERT: F 370 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7273 (mm-30) outliers start: 23 outliers final: 14 residues processed: 149 average time/residue: 0.7554 time to fit residues: 122.3012 Evaluate side-chains 150 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 289 ASN Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 154 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 0.0670 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 652 GLN F 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105402 restraints weight = 21660.443| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.79 r_work: 0.3064 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16000 Z= 0.143 Angle : 0.538 7.886 21938 Z= 0.262 Chirality : 0.044 0.266 2769 Planarity : 0.003 0.040 2634 Dihedral : 5.657 55.121 3990 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.55 % Allowed : 12.20 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.20), residues: 1614 helix: 1.44 (0.27), residues: 395 sheet: 0.13 (0.23), residues: 441 loop : -0.30 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 542 TYR 0.013 0.001 TYR B 638 PHE 0.011 0.001 PHE E 53 TRP 0.013 0.001 TRP A 479 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00339 (15868) covalent geometry : angle 0.50416 (21577) SS BOND : bond 0.00373 ( 35) SS BOND : angle 0.98415 ( 70) hydrogen bonds : bond 0.03696 ( 467) hydrogen bonds : angle 4.65866 ( 1275) link_ALPHA1-3 : bond 0.00869 ( 3) link_ALPHA1-3 : angle 1.63059 ( 9) link_ALPHA1-6 : bond 0.00964 ( 3) link_ALPHA1-6 : angle 1.57937 ( 9) link_BETA1-4 : bond 0.00431 ( 24) link_BETA1-4 : angle 1.36068 ( 72) link_NAG-ASN : bond 0.00242 ( 67) link_NAG-ASN : angle 1.75308 ( 201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8714 (t0) cc_final: 0.8281 (t0) REVERT: A 109 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8691 (mp) REVERT: A 113 ASP cc_start: 0.8295 (m-30) cc_final: 0.7861 (m-30) REVERT: A 178 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8252 (ttmm) REVERT: A 207 LYS cc_start: 0.8636 (mmpt) cc_final: 0.8369 (tppp) REVERT: A 304 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7434 (mtm-85) REVERT: A 315 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7137 (mmp-170) REVERT: A 500 LYS cc_start: 0.8877 (mttt) cc_final: 0.7955 (mtmt) REVERT: B 534 SER cc_start: 0.9099 (p) cc_final: 0.8846 (m) REVERT: B 535 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8211 (mtt) REVERT: B 588 LYS cc_start: 0.7954 (mttt) cc_final: 0.7054 (mmtt) REVERT: C 588 LYS cc_start: 0.8536 (mttt) cc_final: 0.7975 (tptt) REVERT: C 636 SER cc_start: 0.9013 (t) cc_final: 0.8732 (p) REVERT: C 647 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8606 (mt-10) REVERT: D 543 GLN cc_start: 0.8619 (mm-40) cc_final: 0.7845 (tm-30) REVERT: D 632 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7480 (tp30) REVERT: D 633 LYS cc_start: 0.8646 (mttt) cc_final: 0.8092 (mptt) REVERT: D 636 SER cc_start: 0.9080 (t) cc_final: 0.8760 (p) REVERT: E 99 ASN cc_start: 0.9051 (t0) cc_final: 0.8773 (t0) REVERT: E 169 MET cc_start: 0.6852 (mmm) cc_final: 0.5191 (tmm) REVERT: E 207 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8066 (tmtt) REVERT: F 49 THR cc_start: 0.9208 (m) cc_final: 0.8907 (p) REVERT: F 87 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8176 (mp0) REVERT: F 207 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8188 (tptt) REVERT: F 246 GLN cc_start: 0.7992 (pm20) cc_final: 0.7727 (tp-100) REVERT: F 370 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7247 (mm-30) outliers start: 23 outliers final: 16 residues processed: 151 average time/residue: 0.8139 time to fit residues: 133.4067 Evaluate side-chains 154 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 588 LYS Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 289 ASN Chi-restraints excluded: chain F residue 348 LYS Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 150 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 141 optimal weight: 0.3980 chunk 123 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 652 GLN F 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106029 restraints weight = 21555.644| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.84 r_work: 0.3082 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16000 Z= 0.121 Angle : 0.531 10.141 21938 Z= 0.260 Chirality : 0.044 0.264 2769 Planarity : 0.003 0.038 2634 Dihedral : 5.431 49.521 3990 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.42 % Allowed : 12.14 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.20), residues: 1614 helix: 1.63 (0.27), residues: 387 sheet: 0.24 (0.23), residues: 442 loop : -0.27 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.017 0.001 TYR B 638 PHE 0.012 0.001 PHE E 53 TRP 0.023 0.001 TRP E 69 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00285 (15868) covalent geometry : angle 0.49863 (21577) SS BOND : bond 0.00416 ( 35) SS BOND : angle 1.06450 ( 70) hydrogen bonds : bond 0.03543 ( 467) hydrogen bonds : angle 4.58463 ( 1275) link_ALPHA1-3 : bond 0.00899 ( 3) link_ALPHA1-3 : angle 1.57394 ( 9) link_ALPHA1-6 : bond 0.01020 ( 3) link_ALPHA1-6 : angle 1.61406 ( 9) link_BETA1-4 : bond 0.00439 ( 24) link_BETA1-4 : angle 1.32444 ( 72) link_NAG-ASN : bond 0.00239 ( 67) link_NAG-ASN : angle 1.69739 ( 201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8691 (t0) cc_final: 0.8293 (t0) REVERT: A 109 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8648 (mp) REVERT: A 113 ASP cc_start: 0.8290 (m-30) cc_final: 0.7855 (m-30) REVERT: A 178 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8229 (ttmm) REVERT: A 207 LYS cc_start: 0.8547 (mmpt) cc_final: 0.8283 (tppp) REVERT: A 304 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7393 (mtm-85) REVERT: A 315 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7117 (mmp-170) REVERT: A 500 LYS cc_start: 0.8855 (mttt) cc_final: 0.7945 (mtmt) REVERT: B 534 SER cc_start: 0.9081 (p) cc_final: 0.8828 (m) REVERT: B 535 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8188 (mtt) REVERT: B 588 LYS cc_start: 0.7937 (mttt) cc_final: 0.7041 (mmtt) REVERT: C 588 LYS cc_start: 0.8508 (mttt) cc_final: 0.7944 (tptt) REVERT: C 636 SER cc_start: 0.8924 (t) cc_final: 0.8654 (p) REVERT: C 647 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8532 (mt-10) REVERT: D 543 GLN cc_start: 0.8599 (mm-40) cc_final: 0.7634 (tm-30) REVERT: D 632 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: D 633 LYS cc_start: 0.8645 (mttt) cc_final: 0.8081 (mptt) REVERT: D 636 SER cc_start: 0.9052 (t) cc_final: 0.8744 (p) REVERT: E 99 ASN cc_start: 0.9076 (t0) cc_final: 0.8570 (t0) REVERT: E 169 MET cc_start: 0.6858 (mmm) cc_final: 0.5250 (tmm) REVERT: E 207 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8064 (tmtt) REVERT: F 49 THR cc_start: 0.9185 (m) cc_final: 0.8891 (p) REVERT: F 87 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8195 (mp0) REVERT: F 207 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8165 (tptt) REVERT: F 246 GLN cc_start: 0.7911 (pm20) cc_final: 0.7699 (tp-100) REVERT: F 370 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7188 (mm-30) outliers start: 21 outliers final: 16 residues processed: 153 average time/residue: 0.7894 time to fit residues: 131.5708 Evaluate side-chains 158 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain D residue 588 LYS Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 289 ASN Chi-restraints excluded: chain F residue 348 LYS Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 12 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 156 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.0270 chunk 140 optimal weight: 0.7980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 652 GLN E 103 GLN F 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.138469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107756 restraints weight = 21501.721| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.76 r_work: 0.3089 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16000 Z= 0.102 Angle : 0.500 10.804 21938 Z= 0.245 Chirality : 0.043 0.261 2769 Planarity : 0.003 0.040 2634 Dihedral : 4.914 42.032 3990 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.08 % Allowed : 12.34 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.21), residues: 1614 helix: 1.76 (0.27), residues: 386 sheet: 0.36 (0.23), residues: 447 loop : -0.22 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 456 TYR 0.011 0.001 TYR B 638 PHE 0.013 0.001 PHE E 53 TRP 0.024 0.001 TRP E 69 HIS 0.002 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00235 (15868) covalent geometry : angle 0.46998 (21577) SS BOND : bond 0.00354 ( 35) SS BOND : angle 0.91888 ( 70) hydrogen bonds : bond 0.03248 ( 467) hydrogen bonds : angle 4.40615 ( 1275) link_ALPHA1-3 : bond 0.00935 ( 3) link_ALPHA1-3 : angle 1.45997 ( 9) link_ALPHA1-6 : bond 0.01055 ( 3) link_ALPHA1-6 : angle 1.66743 ( 9) link_BETA1-4 : bond 0.00459 ( 24) link_BETA1-4 : angle 1.24233 ( 72) link_NAG-ASN : bond 0.00235 ( 67) link_NAG-ASN : angle 1.57755 ( 201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5083.77 seconds wall clock time: 87 minutes 35.86 seconds (5255.86 seconds total)