Starting phenix.real_space_refine on Sun Feb 8 01:58:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb3_40289/02_2026/8sb3_40289_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb3_40289/02_2026/8sb3_40289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sb3_40289/02_2026/8sb3_40289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb3_40289/02_2026/8sb3_40289.map" model { file = "/net/cci-nas-00/data/ceres_data/8sb3_40289/02_2026/8sb3_40289_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb3_40289/02_2026/8sb3_40289_neut_trim.cif" } resolution = 4.1 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= 0.002 sd= 0.064 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: 5 Type Number sf(0) Gaussians S 129 5.16 5 C 12543 2.51 5 N 3309 2.21 5 O 4109 1.98 5 H 18600 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38690 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7145 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1919 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "C" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1942 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1577 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 7145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7145 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1919 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "H" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1942 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1577 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 7145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7145 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1919 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "M" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1942 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "N" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1577 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" 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: "J" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} 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: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "Q" 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: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} 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: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: "V" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} 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: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" 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 Time building chain proxies: 6.45, per 1000 atoms: 0.17 Number of scatterers: 38690 At special positions: 0 Unit cell: (159.43, 160.5, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 O 4109 8.00 N 3309 7.00 C 12543 6.00 H 18600 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.04 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN J 10 " - " MAN J 11 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN S 4 " - " MAN S 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " " MAN V 10 " - " MAN V 11 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 10 " " BMA O 3 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 10 " " BMA W 3 " - " MAN W 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 42 sheets defined 21.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.950A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 150 removed outlier: 4.117A pdb=" N ASN A 138 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.951A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.675A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 580 removed outlier: 3.601A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.630A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.800A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.991A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'F' and resid 58 through 61 Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.971A pdb=" N ASP F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 4.104A pdb=" N ASN F 138 " --> pdb=" O THR F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.960A pdb=" N HIS F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 474 through 482 removed outlier: 3.944A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.523A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 580 removed outlier: 3.511A pdb=" N GLN G 575 " --> pdb=" O TRP G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 596 Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.500A pdb=" N ASN G 625 " --> pdb=" O GLU G 621 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.599A pdb=" N TRP G 631 " --> pdb=" O THR G 627 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 662 removed outlier: 3.989A pdb=" N GLN G 658 " --> pdb=" O GLU G 654 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP G 659 " --> pdb=" O LYS G 655 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU G 660 " --> pdb=" O ASN G 656 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'K' and resid 58 through 61 Processing helix chain 'K' and resid 68 through 72 Processing helix chain 'K' and resid 99 through 116 removed outlier: 3.999A pdb=" N ASP K 107 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 150 removed outlier: 4.109A pdb=" N ASN K 138 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY K 139 " --> pdb=" O VAL K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 387 through 391 Processing helix chain 'K' and resid 474 through 482 removed outlier: 3.983A pdb=" N GLU K 482 " --> pdb=" O ASN K 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 534 Processing helix chain 'L' and resid 536 through 543 removed outlier: 3.643A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 580 removed outlier: 3.599A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 582 through 596 Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 626 removed outlier: 3.592A pdb=" N ASN L 625 " --> pdb=" O GLU L 621 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 636 removed outlier: 3.937A pdb=" N TRP L 631 " --> pdb=" O THR L 627 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 662 removed outlier: 3.971A pdb=" N GLN L 658 " --> pdb=" O GLU L 654 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 61 through 65 Processing helix chain 'N' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.623A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.750A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.742A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 176 removed outlier: 4.096A pdb=" N SER A 158 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 130 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.805A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.149A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.069A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.112A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.069A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.696A pdb=" N LEU C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.617A pdb=" N ALA C 92 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR C 33 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'D' and resid 47 through 49 Processing sheet with id=AB5, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.586A pdb=" N TYR D 88 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.036A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.727A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'F' and resid 91 through 92 removed outlier: 3.722A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 170 through 176 removed outlier: 3.541A pdb=" N LYS F 155 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER F 158 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 130 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.828A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 259 through 261 removed outlier: 4.093A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.095A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.096A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.095A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AC6, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.782A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.641A pdb=" N ALA H 92 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR H 33 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AC9, first strand: chain 'I' and resid 47 through 49 Processing sheet with id=AD1, first strand: chain 'I' and resid 47 through 49 removed outlier: 3.598A pdb=" N TYR I 88 " --> pdb=" O THR I 105 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.165A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AD4, first strand: chain 'K' and resid 84 through 85 removed outlier: 3.723A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 91 through 92 removed outlier: 3.712A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 170 through 176 removed outlier: 3.614A pdb=" N LYS K 155 " --> pdb=" O PHE K 176 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER K 158 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K 130 " --> pdb=" O SER K 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.808A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.151A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 292 " --> pdb=" O ILE K 449 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 11.974A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.144A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.093A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA K 329 " --> pdb=" O CYS K 418 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.093A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 12.144A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 11.974A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 292 " --> pdb=" O ILE K 449 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AE2, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.671A pdb=" N LEU M 83 " --> pdb=" O VAL M 18 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.619A pdb=" N ALA M 92 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR M 33 " --> pdb=" O ALA M 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.766A pdb=" N SER N 65 " --> pdb=" O THR N 76 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 47 through 49 Processing sheet with id=AE6, first strand: chain 'N' and resid 47 through 49 removed outlier: 3.629A pdb=" N TYR N 88 " --> pdb=" O THR N 105 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1737 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: 10.62 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 18597 1.04 - 1.24: 2739 1.24 - 1.44: 6287 1.44 - 1.65: 11319 1.65 - 1.85: 171 Bond restraints: 39113 Sorted by residual: bond pdb=" C1 MAN J 11 " pdb=" O5 MAN J 11 " ideal model delta sigma weight residual 1.399 1.490 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C1 MAN R 11 " pdb=" O5 MAN R 11 " ideal model delta sigma weight residual 1.399 1.489 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C2 MAN V 8 " pdb=" O2 MAN V 8 " ideal model delta sigma weight residual 1.407 1.490 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C2 MAN R 8 " pdb=" O2 MAN R 8 " ideal model delta sigma weight residual 1.407 1.485 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 MAN R 11 " pdb=" C2 MAN R 11 " ideal model delta sigma weight residual 1.526 1.601 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 39108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 68969 2.79 - 5.57: 958 5.57 - 8.36: 104 8.36 - 11.14: 13 11.14 - 13.93: 3 Bond angle restraints: 70047 Sorted by residual: angle pdb=" N CYS K 131 " pdb=" CA CYS K 131 " pdb=" C CYS K 131 " ideal model delta sigma weight residual 108.49 116.53 -8.04 1.15e+00 7.56e-01 4.89e+01 angle pdb=" N CYS F 131 " pdb=" CA CYS F 131 " pdb=" C CYS F 131 " ideal model delta sigma weight residual 108.49 116.46 -7.97 1.15e+00 7.56e-01 4.80e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.51 -10.81 1.80e+00 3.09e-01 3.61e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 132.43 -10.73 1.80e+00 3.09e-01 3.55e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 132.37 -10.67 1.80e+00 3.09e-01 3.52e+01 ... (remaining 70042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 18107 21.57 - 43.14: 1111 43.14 - 64.70: 348 64.70 - 86.27: 134 86.27 - 107.84: 53 Dihedral angle restraints: 19753 sinusoidal: 11422 harmonic: 8331 Sorted by residual: dihedral pdb=" CA CYS A 131 " pdb=" C CYS A 131 " pdb=" N SER A 132 " pdb=" CA SER A 132 " ideal model delta harmonic sigma weight residual -180.00 -131.52 -48.48 0 5.00e+00 4.00e-02 9.40e+01 dihedral pdb=" CA CYS K 131 " pdb=" C CYS K 131 " pdb=" N SER K 132 " pdb=" CA SER K 132 " ideal model delta harmonic sigma weight residual 180.00 -131.55 -48.45 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA CYS F 131 " pdb=" C CYS F 131 " pdb=" N SER F 132 " pdb=" CA SER F 132 " ideal model delta harmonic sigma weight residual 180.00 -131.80 -48.20 0 5.00e+00 4.00e-02 9.29e+01 ... (remaining 19750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2729 0.062 - 0.123: 523 0.123 - 0.185: 100 0.185 - 0.246: 13 0.246 - 0.308: 12 Chirality restraints: 3377 Sorted by residual: chirality pdb=" C1 MAN J 11 " pdb=" O2 MAN J 10 " pdb=" C2 MAN J 11 " pdb=" O5 MAN J 11 " both_signs ideal model delta sigma weight residual False 2.40 2.45 -0.05 2.00e-02 2.50e+03 5.97e+00 chirality pdb=" C1 MAN R 11 " pdb=" O2 MAN R 10 " pdb=" C2 MAN R 11 " pdb=" O5 MAN R 11 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.57e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 3374 not shown) Planarity restraints: 5793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 628 " -0.015 2.00e-02 2.50e+03 2.29e-02 2.10e+01 pdb=" CG TRP L 628 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP L 628 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP L 628 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP L 628 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP L 628 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 628 " 0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 628 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 628 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 628 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP L 628 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP L 628 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP L 628 " -0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 628 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 628 " 0.013 2.00e-02 2.50e+03 pdb=" HH2 TRP L 628 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 124 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 123 " 0.069 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO F 124 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO F 124 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 124 " 0.057 5.00e-02 4.00e+02 ... (remaining 5790 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4848 2.26 - 2.84: 83567 2.84 - 3.43: 93051 3.43 - 4.01: 129156 4.01 - 4.60: 195973 Nonbonded interactions: 506595 Sorted by model distance: nonbonded pdb=" O GLU N 52 " pdb=" H SER N 54 " model vdw 1.672 2.450 nonbonded pdb=" O GLU I 52 " pdb=" H SER I 54 " model vdw 1.681 2.450 nonbonded pdb=" O GLU D 52 " pdb=" H SER D 54 " model vdw 1.685 2.450 nonbonded pdb=" OD1 ASN F 300 " pdb=" H LYS F 327 " model vdw 1.689 2.450 nonbonded pdb=" OD1 ASN F 463 " pdb=" H THR F 465 " model vdw 1.693 2.450 ... (remaining 506590 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' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = (chain 'O' and (resid 2 or resid 5 through 7)) selection = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'W' and (resid 1 or resid 4 through 6)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.290 Extract box with map and model: 0.620 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 36.250 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.007 0.091 20634 Z= 0.319 Angle : 1.106 13.926 28224 Z= 0.539 Chirality : 0.055 0.308 3377 Planarity : 0.006 0.103 3435 Dihedral : 17.069 107.838 8605 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.59 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.16), residues: 2436 helix: -1.35 (0.23), residues: 408 sheet: -1.26 (0.19), residues: 651 loop : -1.46 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 87 TYR 0.034 0.002 TYR K 395 PHE 0.017 0.002 PHE K 233 TRP 0.054 0.003 TRP A 427 HIS 0.010 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00682 (20513) covalent geometry : angle 1.04077 (27903) SS BOND : bond 0.00505 ( 42) SS BOND : angle 1.54547 ( 84) hydrogen bonds : bond 0.21898 ( 646) hydrogen bonds : angle 9.62075 ( 1737) link_ALPHA1-2 : bond 0.01753 ( 16) link_ALPHA1-2 : angle 4.16073 ( 48) link_ALPHA1-3 : bond 0.01228 ( 14) link_ALPHA1-3 : angle 4.82995 ( 42) link_ALPHA1-6 : bond 0.01358 ( 13) link_ALPHA1-6 : angle 3.51693 ( 39) link_BETA1-4 : bond 0.00925 ( 24) link_BETA1-4 : angle 4.50257 ( 72) link_NAG-ASN : bond 0.00956 ( 12) link_NAG-ASN : angle 3.04146 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.6119 (mmt) cc_final: 0.5632 (mmm) REVERT: H 101 TYR cc_start: 0.8252 (t80) cc_final: 0.7991 (t80) REVERT: K 322 ILE cc_start: 0.9101 (mt) cc_final: 0.8849 (mt) REVERT: M 111 TYR cc_start: 0.8283 (m-10) cc_final: 0.8018 (m-10) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.3791 time to fit residues: 191.2079 Evaluate side-chains 178 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN C 115 ASN F 461 ASN H 115 ASN K 461 ASN L 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.080382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.062922 restraints weight = 235616.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065771 restraints weight = 103648.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.067661 restraints weight = 62721.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068866 restraints weight = 45763.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.069634 restraints weight = 37398.267| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20634 Z= 0.190 Angle : 0.756 11.427 28224 Z= 0.383 Chirality : 0.045 0.205 3377 Planarity : 0.005 0.096 3435 Dihedral : 13.256 77.891 4201 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.49 % Favored : 93.02 % Rotamer: Outliers : 0.14 % Allowed : 2.49 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2436 helix: -0.98 (0.25), residues: 405 sheet: -1.23 (0.19), residues: 687 loop : -1.55 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 419 TYR 0.012 0.001 TYR K 484 PHE 0.013 0.001 PHE K 391 TRP 0.014 0.001 TRP L 571 HIS 0.008 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00413 (20513) covalent geometry : angle 0.73078 (27903) SS BOND : bond 0.00339 ( 42) SS BOND : angle 1.11942 ( 84) hydrogen bonds : bond 0.05286 ( 646) hydrogen bonds : angle 7.14727 ( 1737) link_ALPHA1-2 : bond 0.00695 ( 16) link_ALPHA1-2 : angle 1.87022 ( 48) link_ALPHA1-3 : bond 0.00606 ( 14) link_ALPHA1-3 : angle 2.11318 ( 42) link_ALPHA1-6 : bond 0.00420 ( 13) link_ALPHA1-6 : angle 1.79079 ( 39) link_BETA1-4 : bond 0.00339 ( 24) link_BETA1-4 : angle 2.53784 ( 72) link_NAG-ASN : bond 0.00466 ( 12) link_NAG-ASN : angle 2.12138 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 217 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7471 (tmm) cc_final: 0.7097 (tmm) REVERT: A 434 MET cc_start: 0.8001 (ttm) cc_final: 0.7796 (ttp) REVERT: B 626 MET cc_start: 0.8161 (tpp) cc_final: 0.7936 (tpp) REVERT: C 13 GLU cc_start: 0.8749 (pm20) cc_final: 0.8485 (pm20) REVERT: F 95 MET cc_start: 0.7928 (ttp) cc_final: 0.6706 (tpp) REVERT: G 654 GLU cc_start: 0.8833 (tp30) cc_final: 0.8551 (tm-30) REVERT: H 101 TYR cc_start: 0.8997 (t80) cc_final: 0.8664 (t80) REVERT: M 13 GLU cc_start: 0.8789 (pm20) cc_final: 0.8516 (pm20) outliers start: 3 outliers final: 1 residues processed: 220 average time/residue: 0.3501 time to fit residues: 115.1157 Evaluate side-chains 164 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.0070 chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN B 543 ASN B 656 ASN G 656 ASN ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.079002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.061632 restraints weight = 239683.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064435 restraints weight = 106473.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066274 restraints weight = 64951.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.067457 restraints weight = 47682.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.068217 restraints weight = 39119.946| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20634 Z= 0.212 Angle : 0.725 10.177 28224 Z= 0.368 Chirality : 0.044 0.220 3377 Planarity : 0.005 0.090 3435 Dihedral : 11.522 67.702 4201 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.27 % Favored : 92.24 % Rotamer: Outliers : 0.09 % Allowed : 2.16 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.16), residues: 2436 helix: -0.99 (0.25), residues: 405 sheet: -1.33 (0.19), residues: 657 loop : -1.57 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 38 TYR 0.015 0.001 TYR K 217 PHE 0.013 0.001 PHE K 391 TRP 0.021 0.002 TRP F 427 HIS 0.008 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00459 (20513) covalent geometry : angle 0.69980 (27903) SS BOND : bond 0.00393 ( 42) SS BOND : angle 1.61419 ( 84) hydrogen bonds : bond 0.04693 ( 646) hydrogen bonds : angle 6.57574 ( 1737) link_ALPHA1-2 : bond 0.00907 ( 16) link_ALPHA1-2 : angle 1.90390 ( 48) link_ALPHA1-3 : bond 0.00706 ( 14) link_ALPHA1-3 : angle 1.76895 ( 42) link_ALPHA1-6 : bond 0.00494 ( 13) link_ALPHA1-6 : angle 1.89031 ( 39) link_BETA1-4 : bond 0.00325 ( 24) link_BETA1-4 : angle 2.02894 ( 72) link_NAG-ASN : bond 0.00822 ( 12) link_NAG-ASN : angle 2.32692 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7508 (tmm) cc_final: 0.7159 (tmm) REVERT: C 13 GLU cc_start: 0.8774 (pm20) cc_final: 0.8466 (pm20) REVERT: F 95 MET cc_start: 0.7919 (ttp) cc_final: 0.6715 (tpp) REVERT: H 101 TYR cc_start: 0.8996 (t80) cc_final: 0.8646 (t80) REVERT: I 62 LYS cc_start: 0.7772 (mmpt) cc_final: 0.7478 (mmmt) REVERT: M 13 GLU cc_start: 0.8729 (pm20) cc_final: 0.8439 (pm20) outliers start: 2 outliers final: 0 residues processed: 197 average time/residue: 0.3344 time to fit residues: 100.5701 Evaluate side-chains 149 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 240 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.078317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.060976 restraints weight = 238864.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.063731 restraints weight = 107180.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065556 restraints weight = 65768.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066716 restraints weight = 48450.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067390 restraints weight = 39852.088| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20634 Z= 0.202 Angle : 0.701 10.115 28224 Z= 0.355 Chirality : 0.044 0.220 3377 Planarity : 0.005 0.092 3435 Dihedral : 9.955 59.734 4201 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.02 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.16), residues: 2436 helix: -0.86 (0.25), residues: 408 sheet: -1.37 (0.19), residues: 639 loop : -1.66 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 84 TYR 0.012 0.001 TYR M 101 PHE 0.025 0.001 PHE C 64 TRP 0.012 0.001 TRP B 571 HIS 0.012 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00437 (20513) covalent geometry : angle 0.67786 (27903) SS BOND : bond 0.00444 ( 42) SS BOND : angle 1.40505 ( 84) hydrogen bonds : bond 0.03999 ( 646) hydrogen bonds : angle 6.20914 ( 1737) link_ALPHA1-2 : bond 0.00735 ( 16) link_ALPHA1-2 : angle 1.93012 ( 48) link_ALPHA1-3 : bond 0.00696 ( 14) link_ALPHA1-3 : angle 1.94441 ( 42) link_ALPHA1-6 : bond 0.00473 ( 13) link_ALPHA1-6 : angle 1.72912 ( 39) link_BETA1-4 : bond 0.00276 ( 24) link_BETA1-4 : angle 1.93982 ( 72) link_NAG-ASN : bond 0.00664 ( 12) link_NAG-ASN : angle 2.07124 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7505 (tmm) cc_final: 0.7145 (tmm) REVERT: C 13 GLU cc_start: 0.8850 (pm20) cc_final: 0.8496 (pm20) REVERT: F 95 MET cc_start: 0.7886 (ttp) cc_final: 0.6673 (tpp) REVERT: G 654 GLU cc_start: 0.8869 (tp30) cc_final: 0.8561 (tm-30) REVERT: H 101 TYR cc_start: 0.9026 (t80) cc_final: 0.8739 (t80) REVERT: K 33 ASN cc_start: 0.7563 (m-40) cc_final: 0.6893 (t0) REVERT: M 13 GLU cc_start: 0.8768 (pm20) cc_final: 0.8424 (pm20) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3386 time to fit residues: 96.9903 Evaluate side-chains 143 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 591 GLN ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.076993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059711 restraints weight = 239718.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.062407 restraints weight = 107417.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.064185 restraints weight = 66141.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065314 restraints weight = 48900.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066052 restraints weight = 40407.020| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20634 Z= 0.241 Angle : 0.721 10.730 28224 Z= 0.364 Chirality : 0.044 0.239 3377 Planarity : 0.005 0.093 3435 Dihedral : 9.699 57.851 4201 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.17 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.16), residues: 2436 helix: -0.98 (0.25), residues: 405 sheet: -1.50 (0.20), residues: 621 loop : -1.67 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 84 TYR 0.015 0.001 TYR F 318 PHE 0.016 0.001 PHE K 391 TRP 0.012 0.002 TRP C 47 HIS 0.014 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00523 (20513) covalent geometry : angle 0.69379 (27903) SS BOND : bond 0.00421 ( 42) SS BOND : angle 1.79701 ( 84) hydrogen bonds : bond 0.03996 ( 646) hydrogen bonds : angle 6.16904 ( 1737) link_ALPHA1-2 : bond 0.00727 ( 16) link_ALPHA1-2 : angle 1.95870 ( 48) link_ALPHA1-3 : bond 0.00634 ( 14) link_ALPHA1-3 : angle 2.15607 ( 42) link_ALPHA1-6 : bond 0.00534 ( 13) link_ALPHA1-6 : angle 1.71683 ( 39) link_BETA1-4 : bond 0.00345 ( 24) link_BETA1-4 : angle 1.84661 ( 72) link_NAG-ASN : bond 0.01010 ( 12) link_NAG-ASN : angle 2.41964 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7588 (tmm) cc_final: 0.7223 (tmm) REVERT: C 13 GLU cc_start: 0.8855 (pm20) cc_final: 0.8448 (pm20) REVERT: F 95 MET cc_start: 0.7825 (ttp) cc_final: 0.7272 (tmm) REVERT: H 101 TYR cc_start: 0.8943 (t80) cc_final: 0.8681 (t80) REVERT: I 75 LEU cc_start: 0.9213 (tp) cc_final: 0.8982 (tp) REVERT: K 33 ASN cc_start: 0.7490 (m-40) cc_final: 0.6779 (t0) REVERT: L 626 MET cc_start: 0.7313 (tpp) cc_final: 0.7009 (tpp) REVERT: M 13 GLU cc_start: 0.8850 (pm20) cc_final: 0.8448 (pm20) REVERT: N 75 LEU cc_start: 0.9219 (tp) cc_final: 0.8983 (tp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3533 time to fit residues: 97.3638 Evaluate side-chains 135 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 151 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 214 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.077561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.060335 restraints weight = 242602.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.063037 restraints weight = 111589.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.064792 restraints weight = 69640.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.065912 restraints weight = 51988.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066622 restraints weight = 43139.123| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20634 Z= 0.178 Angle : 0.667 11.393 28224 Z= 0.338 Chirality : 0.044 0.223 3377 Planarity : 0.005 0.096 3435 Dihedral : 9.221 56.617 4201 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.35 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.16), residues: 2436 helix: -0.81 (0.25), residues: 408 sheet: -1.42 (0.19), residues: 639 loop : -1.68 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 588 TYR 0.011 0.001 TYR C 95 PHE 0.017 0.001 PHE K 391 TRP 0.012 0.001 TRP B 571 HIS 0.012 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00391 (20513) covalent geometry : angle 0.64350 (27903) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.44858 ( 84) hydrogen bonds : bond 0.03623 ( 646) hydrogen bonds : angle 5.97153 ( 1737) link_ALPHA1-2 : bond 0.00767 ( 16) link_ALPHA1-2 : angle 1.89546 ( 48) link_ALPHA1-3 : bond 0.00662 ( 14) link_ALPHA1-3 : angle 2.04466 ( 42) link_ALPHA1-6 : bond 0.00508 ( 13) link_ALPHA1-6 : angle 1.68622 ( 39) link_BETA1-4 : bond 0.00278 ( 24) link_BETA1-4 : angle 1.74811 ( 72) link_NAG-ASN : bond 0.00591 ( 12) link_NAG-ASN : angle 1.95080 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.8762 (pm20) cc_final: 0.8393 (pm20) REVERT: F 95 MET cc_start: 0.7849 (ttp) cc_final: 0.7266 (tmm) REVERT: G 654 GLU cc_start: 0.8698 (tp30) cc_final: 0.8488 (tm-30) REVERT: H 101 TYR cc_start: 0.8886 (t80) cc_final: 0.8638 (t80) REVERT: K 154 MET cc_start: 0.8438 (ptm) cc_final: 0.8198 (ptm) REVERT: M 13 GLU cc_start: 0.8746 (pm20) cc_final: 0.8373 (pm20) REVERT: N 75 LEU cc_start: 0.9171 (tp) cc_final: 0.8947 (tp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3560 time to fit residues: 100.9253 Evaluate side-chains 137 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 27 optimal weight: 0.0040 chunk 168 optimal weight: 5.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.077149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.059888 restraints weight = 239495.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.062599 restraints weight = 107646.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.064353 restraints weight = 66441.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.065495 restraints weight = 49368.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066237 restraints weight = 40755.276| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20634 Z= 0.194 Angle : 0.668 11.534 28224 Z= 0.339 Chirality : 0.043 0.223 3377 Planarity : 0.005 0.095 3435 Dihedral : 8.976 59.283 4201 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.13 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2436 helix: -0.76 (0.25), residues: 408 sheet: -1.39 (0.20), residues: 588 loop : -1.74 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 588 TYR 0.013 0.001 TYR A 318 PHE 0.016 0.001 PHE K 391 TRP 0.013 0.001 TRP G 628 HIS 0.012 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00426 (20513) covalent geometry : angle 0.64556 (27903) SS BOND : bond 0.00386 ( 42) SS BOND : angle 1.26442 ( 84) hydrogen bonds : bond 0.03573 ( 646) hydrogen bonds : angle 5.90231 ( 1737) link_ALPHA1-2 : bond 0.00755 ( 16) link_ALPHA1-2 : angle 1.95198 ( 48) link_ALPHA1-3 : bond 0.00643 ( 14) link_ALPHA1-3 : angle 2.13024 ( 42) link_ALPHA1-6 : bond 0.00516 ( 13) link_ALPHA1-6 : angle 1.59571 ( 39) link_BETA1-4 : bond 0.00312 ( 24) link_BETA1-4 : angle 1.69081 ( 72) link_NAG-ASN : bond 0.00726 ( 12) link_NAG-ASN : angle 2.08302 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.8833 (pm20) cc_final: 0.8383 (pm20) REVERT: D 22 CYS cc_start: 0.3555 (t) cc_final: 0.3049 (t) REVERT: F 95 MET cc_start: 0.7847 (ttp) cc_final: 0.7397 (tmm) REVERT: H 101 TYR cc_start: 0.8827 (t80) cc_final: 0.8605 (t80) REVERT: H 122 LEU cc_start: 0.9094 (pp) cc_final: 0.8875 (tt) REVERT: L 626 MET cc_start: 0.7159 (tpp) cc_final: 0.6629 (tpp) REVERT: M 13 GLU cc_start: 0.8832 (pm20) cc_final: 0.8383 (pm20) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3601 time to fit residues: 99.3926 Evaluate side-chains 130 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 176 optimal weight: 0.5980 chunk 237 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.078357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061171 restraints weight = 236834.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.063952 restraints weight = 106895.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065764 restraints weight = 65832.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.066911 restraints weight = 48647.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.067647 restraints weight = 40147.977| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20634 Z= 0.120 Angle : 0.614 11.686 28224 Z= 0.312 Chirality : 0.043 0.202 3377 Planarity : 0.004 0.096 3435 Dihedral : 8.355 59.775 4201 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.32 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.16), residues: 2436 helix: -0.55 (0.26), residues: 408 sheet: -1.09 (0.20), residues: 594 loop : -1.70 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 588 TYR 0.010 0.001 TYR A 39 PHE 0.017 0.001 PHE K 391 TRP 0.013 0.001 TRP G 571 HIS 0.008 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00263 (20513) covalent geometry : angle 0.59590 (27903) SS BOND : bond 0.00298 ( 42) SS BOND : angle 1.04127 ( 84) hydrogen bonds : bond 0.03294 ( 646) hydrogen bonds : angle 5.68042 ( 1737) link_ALPHA1-2 : bond 0.00884 ( 16) link_ALPHA1-2 : angle 1.79851 ( 48) link_ALPHA1-3 : bond 0.00775 ( 14) link_ALPHA1-3 : angle 1.87106 ( 42) link_ALPHA1-6 : bond 0.00558 ( 13) link_ALPHA1-6 : angle 1.60179 ( 39) link_BETA1-4 : bond 0.00288 ( 24) link_BETA1-4 : angle 1.47574 ( 72) link_NAG-ASN : bond 0.00162 ( 12) link_NAG-ASN : angle 1.54855 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.8806 (pm20) cc_final: 0.8438 (pm20) REVERT: F 95 MET cc_start: 0.7773 (ttp) cc_final: 0.7397 (tmm) REVERT: H 101 TYR cc_start: 0.8789 (t80) cc_final: 0.8561 (t80) REVERT: H 122 LEU cc_start: 0.9128 (pp) cc_final: 0.8919 (tt) REVERT: L 626 MET cc_start: 0.7177 (tpp) cc_final: 0.6640 (tpp) REVERT: M 13 GLU cc_start: 0.8792 (pm20) cc_final: 0.8372 (pm20) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3571 time to fit residues: 101.5583 Evaluate side-chains 137 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 131 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 0.0770 chunk 94 optimal weight: 0.5980 chunk 226 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.078437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.061215 restraints weight = 239156.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.064020 restraints weight = 107170.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065852 restraints weight = 65577.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067030 restraints weight = 48231.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.067786 restraints weight = 39634.902| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20634 Z= 0.122 Angle : 0.606 12.201 28224 Z= 0.308 Chirality : 0.042 0.197 3377 Planarity : 0.004 0.096 3435 Dihedral : 8.014 58.371 4201 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.32 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.16), residues: 2436 helix: -0.49 (0.26), residues: 408 sheet: -1.17 (0.20), residues: 624 loop : -1.58 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 588 TYR 0.015 0.001 TYR M 101 PHE 0.015 0.001 PHE K 391 TRP 0.014 0.001 TRP G 628 HIS 0.008 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00271 (20513) covalent geometry : angle 0.58752 (27903) SS BOND : bond 0.00324 ( 42) SS BOND : angle 1.06771 ( 84) hydrogen bonds : bond 0.03212 ( 646) hydrogen bonds : angle 5.60632 ( 1737) link_ALPHA1-2 : bond 0.00854 ( 16) link_ALPHA1-2 : angle 1.81254 ( 48) link_ALPHA1-3 : bond 0.00749 ( 14) link_ALPHA1-3 : angle 1.85901 ( 42) link_ALPHA1-6 : bond 0.00569 ( 13) link_ALPHA1-6 : angle 1.53058 ( 39) link_BETA1-4 : bond 0.00299 ( 24) link_BETA1-4 : angle 1.43662 ( 72) link_NAG-ASN : bond 0.00230 ( 12) link_NAG-ASN : angle 1.55647 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8983 (ppp) cc_final: 0.8688 (ppp) REVERT: C 13 GLU cc_start: 0.8832 (pm20) cc_final: 0.8434 (pm20) REVERT: F 95 MET cc_start: 0.7765 (ttp) cc_final: 0.7395 (tmm) REVERT: G 654 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8316 (tm-30) REVERT: H 101 TYR cc_start: 0.8747 (t80) cc_final: 0.8523 (t80) REVERT: H 122 LEU cc_start: 0.9154 (pp) cc_final: 0.8907 (tt) REVERT: M 4 LEU cc_start: 0.9030 (mm) cc_final: 0.8584 (tp) REVERT: M 13 GLU cc_start: 0.8778 (pm20) cc_final: 0.8345 (pm20) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3700 time to fit residues: 101.7807 Evaluate side-chains 135 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 9 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 125 optimal weight: 0.0370 chunk 104 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.077472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.060244 restraints weight = 239092.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.062964 restraints weight = 108678.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.064744 restraints weight = 67385.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065887 restraints weight = 50109.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.066558 restraints weight = 41360.580| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20634 Z= 0.175 Angle : 0.638 12.836 28224 Z= 0.322 Chirality : 0.042 0.208 3377 Planarity : 0.005 0.093 3435 Dihedral : 7.951 58.808 4201 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.68 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.17), residues: 2436 helix: -0.49 (0.26), residues: 408 sheet: -1.42 (0.20), residues: 666 loop : -1.54 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 588 TYR 0.014 0.001 TYR F 318 PHE 0.014 0.001 PHE K 391 TRP 0.022 0.001 TRP G 628 HIS 0.010 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00382 (20513) covalent geometry : angle 0.61747 (27903) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.10006 ( 84) hydrogen bonds : bond 0.03321 ( 646) hydrogen bonds : angle 5.64429 ( 1737) link_ALPHA1-2 : bond 0.00781 ( 16) link_ALPHA1-2 : angle 1.92967 ( 48) link_ALPHA1-3 : bond 0.00641 ( 14) link_ALPHA1-3 : angle 1.97101 ( 42) link_ALPHA1-6 : bond 0.00579 ( 13) link_ALPHA1-6 : angle 1.52163 ( 39) link_BETA1-4 : bond 0.00326 ( 24) link_BETA1-4 : angle 1.51152 ( 72) link_NAG-ASN : bond 0.00636 ( 12) link_NAG-ASN : angle 1.94893 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.8822 (pm20) cc_final: 0.8436 (pm20) REVERT: F 95 MET cc_start: 0.7805 (ttp) cc_final: 0.7460 (tmm) REVERT: G 654 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8336 (tm-30) REVERT: H 101 TYR cc_start: 0.8772 (t80) cc_final: 0.8556 (t80) REVERT: H 122 LEU cc_start: 0.9158 (pp) cc_final: 0.8951 (tt) REVERT: K 154 MET cc_start: 0.8893 (ptm) cc_final: 0.8387 (ppp) REVERT: L 654 GLU cc_start: 0.8852 (tp30) cc_final: 0.8641 (tm-30) REVERT: M 13 GLU cc_start: 0.8820 (pm20) cc_final: 0.8358 (pm20) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3649 time to fit residues: 97.5494 Evaluate side-chains 134 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 183 optimal weight: 0.0770 chunk 148 optimal weight: 8.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.076713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059424 restraints weight = 240061.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062103 restraints weight = 108756.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.063879 restraints weight = 67526.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065008 restraints weight = 50139.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065731 restraints weight = 41521.695| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20634 Z= 0.197 Angle : 0.651 12.530 28224 Z= 0.328 Chirality : 0.042 0.203 3377 Planarity : 0.005 0.093 3435 Dihedral : 8.006 59.005 4201 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.09 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2436 helix: -0.53 (0.26), residues: 408 sheet: -1.52 (0.20), residues: 630 loop : -1.56 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 588 TYR 0.014 0.001 TYR A 318 PHE 0.016 0.001 PHE K 391 TRP 0.018 0.002 TRP K 112 HIS 0.010 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00432 (20513) covalent geometry : angle 0.63108 (27903) SS BOND : bond 0.00374 ( 42) SS BOND : angle 1.13855 ( 84) hydrogen bonds : bond 0.03393 ( 646) hydrogen bonds : angle 5.67803 ( 1737) link_ALPHA1-2 : bond 0.00766 ( 16) link_ALPHA1-2 : angle 1.94387 ( 48) link_ALPHA1-3 : bond 0.00599 ( 14) link_ALPHA1-3 : angle 2.00988 ( 42) link_ALPHA1-6 : bond 0.00561 ( 13) link_ALPHA1-6 : angle 1.56354 ( 39) link_BETA1-4 : bond 0.00351 ( 24) link_BETA1-4 : angle 1.51208 ( 72) link_NAG-ASN : bond 0.00719 ( 12) link_NAG-ASN : angle 1.98084 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5683.92 seconds wall clock time: 98 minutes 23.30 seconds (5903.30 seconds total)