Starting phenix.real_space_refine on Wed Mar 4 20:38:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8y_23240/03_2026/7l8y_23240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8y_23240/03_2026/7l8y_23240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l8y_23240/03_2026/7l8y_23240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8y_23240/03_2026/7l8y_23240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8y_23240/03_2026/7l8y_23240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8y_23240/03_2026/7l8y_23240.map" } resolution = 4.2 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9901 2.51 5 N 2711 2.21 5 O 3186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15903 Number of models: 1 Model: "" Number of chains: 27 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3447 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 20, 'TRANS': 416} Chain breaks: 3 Chain: "D" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1131 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "A" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3460 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "E" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3434 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.45, per 1000 atoms: 0.22 Number of scatterers: 15903 At special positions: 0 Unit cell: (133.9, 161.71, 123.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3186 8.00 N 2711 7.00 C 9901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.01 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 295 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 160 " " NAG A 610 " - " ASN A 197 " " NAG A 611 " - " ASN A 133 " " NAG A 612 " - " ASN A 355 " " NAG A 613 " - " ASN A 289 " " NAG A 614 " - " ASN A 462 " " NAG A 615 " - " ASN A 339 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 332 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 197 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 289 " " NAG C 611 " - " ASN C 137 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 448 " " NAG E 609 " - " ASN E 301 " " NAG E 610 " - " ASN E 160 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 133 " " NAG E 613 " - " ASN E 355 " " NAG E 614 " - " ASN E 289 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN C 392 " " NAG I 1 " - " ASN C 386 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 156 " " NAG M 1 " - " ASN C 160 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN E 156 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 584.8 milliseconds 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 34 sheets defined 31.8% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'L' and resid 27 through 31 Processing helix chain 'L' and resid 59 through 63 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.044A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.812A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 556 removed outlier: 3.615A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 560 removed outlier: 6.702A pdb=" N GLU D 560 " --> pdb=" O ARG D 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 557 through 560' Processing helix chain 'D' and resid 561 through 566 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.719A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.041A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.935A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.590A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 556 removed outlier: 3.774A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 566 removed outlier: 4.402A pdb=" N HIS B 564 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.182A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 351 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.786A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 556 removed outlier: 4.024A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 563 Processing helix chain 'F' and resid 564 through 567 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 611 through 616 removed outlier: 4.304A pdb=" N SER F 615 " --> pdb=" O ASN F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.511A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 55 through 56 removed outlier: 3.690A pdb=" N UNK H 55 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N UNK H 33 " --> pdb=" O UNK H 93 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N UNK H 93 " --> pdb=" O UNK H 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AA4, first strand: chain 'L' and resid 46 through 47 removed outlier: 3.644A pdb=" N UNK L 85 " --> pdb=" O UNK L 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.506A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.715A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB1, first strand: chain 'C' and resid 200 through 203 Processing sheet with id=AB2, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.001A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.262A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.937A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.262A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.884A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.262A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.001A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.937A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.853A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.262A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.680A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.259A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.531A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.669A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.503A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.886A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.503A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.419A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.822A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD4, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.316A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.542A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.464A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.383A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.799A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.383A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.464A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.486A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3687 1.32 - 1.46: 5040 1.46 - 1.60: 7295 1.60 - 1.74: 18 1.74 - 1.88: 134 Bond restraints: 16174 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.393 0.104 1.40e-02 5.10e+03 5.54e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.395 -0.069 1.10e-02 8.26e+03 3.98e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.72e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.650 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 16169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 17980 2.02 - 4.05: 3308 4.05 - 6.07: 609 6.07 - 8.09: 89 8.09 - 10.12: 15 Bond angle restraints: 22001 Sorted by residual: angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.44 -8.88 1.02e+00 9.61e-01 7.58e+01 angle pdb=" C LEU F 523 " pdb=" N GLY F 524 " pdb=" CA GLY F 524 " ideal model delta sigma weight residual 120.10 128.29 -8.19 9.50e-01 1.11e+00 7.42e+01 angle pdb=" N ILE F 622 " pdb=" CA ILE F 622 " pdb=" C ILE F 622 " ideal model delta sigma weight residual 111.67 103.60 8.07 9.50e-01 1.11e+00 7.21e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.34 -7.78 1.01e+00 9.80e-01 5.93e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.32 -7.76 1.01e+00 9.80e-01 5.90e+01 ... (remaining 21996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 10484 21.29 - 42.58: 194 42.58 - 63.88: 73 63.88 - 85.17: 32 85.17 - 106.46: 13 Dihedral angle restraints: 10796 sinusoidal: 5140 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.02 -66.02 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.31 -60.31 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.22 -60.22 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 10793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 2317 0.169 - 0.338: 353 0.338 - 0.507: 102 0.507 - 0.676: 1 0.676 - 0.845: 1 Chirality restraints: 2774 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 2771 not shown) Planarity restraints: 2776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 610 " -0.349 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG C 610 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C 610 " -0.128 2.00e-02 2.50e+03 pdb=" N2 NAG C 610 " 0.535 2.00e-02 2.50e+03 pdb=" O7 NAG C 610 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 606 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG E 606 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG E 606 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG E 606 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG E 606 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B 702 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.074 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " 0.185 2.00e-02 2.50e+03 ... (remaining 2773 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1761 2.73 - 3.27: 15138 3.27 - 3.82: 24705 3.82 - 4.36: 31661 4.36 - 4.90: 49452 Nonbonded interactions: 122717 Sorted by model distance: nonbonded pdb=" O3 NAG A 614 " pdb=" O7 NAG A 614 " model vdw 2.188 3.040 nonbonded pdb=" O3 NAG I 2 " pdb=" O7 NAG I 2 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR C 240 " pdb=" O6 NAG C 602 " model vdw 2.413 3.040 nonbonded pdb=" C ASN A 195 " pdb=" OD1 ASN A 195 " model vdw 2.475 3.270 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.491 3.120 ... (remaining 122712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 66 through 397 or resid 414 through \ 611)) selection = (chain 'C' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 611)) selection = (chain 'E' and resid 33 through 611) } ncs_group { reference = (chain 'B' and (resid 521 through 662 or resid 702)) selection = (chain 'D' and (resid 521 through 662 or resid 702)) selection = (chain 'F' and (resid 521 through 662 or resid 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = (chain 'H' and resid 16 through 114) selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'T' } 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.021 0.128 16289 Z= 1.155 Angle : 1.703 10.118 22311 Z= 1.092 Chirality : 0.136 0.845 2774 Planarity : 0.018 0.301 2718 Dihedral : 11.267 106.459 7011 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1709 helix: 0.16 (0.23), residues: 463 sheet: 1.04 (0.23), residues: 454 loop : 1.01 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 308 TYR 0.031 0.006 TYR E 318 PHE 0.044 0.006 PHE A 383 TRP 0.069 0.009 TRP C 35 HIS 0.008 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.02098 (16174) covalent geometry : angle 1.67360 (22001) SS BOND : bond 0.00954 ( 35) SS BOND : angle 2.94546 ( 70) hydrogen bonds : bond 0.17236 ( 627) hydrogen bonds : angle 7.39201 ( 1845) link_ALPHA1-3 : bond 0.08453 ( 3) link_ALPHA1-3 : angle 4.38100 ( 9) link_ALPHA1-6 : bond 0.06087 ( 3) link_ALPHA1-6 : angle 4.01011 ( 9) link_BETA1-4 : bond 0.06390 ( 16) link_BETA1-4 : angle 4.35316 ( 48) link_NAG-ASN : bond 0.07147 ( 58) link_NAG-ASN : angle 2.71935 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 0.554 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: C 104 MET cc_start: 0.8953 (ttm) cc_final: 0.8617 (tpp) REVERT: C 199 SER cc_start: 0.8873 (p) cc_final: 0.7716 (m) REVERT: C 349 LEU cc_start: 0.9538 (mt) cc_final: 0.9325 (mp) REVERT: C 368 ASP cc_start: 0.7771 (t70) cc_final: 0.7165 (p0) REVERT: C 376 PHE cc_start: 0.6707 (t80) cc_final: 0.6144 (t80) REVERT: C 435 TYR cc_start: 0.9063 (t80) cc_final: 0.8662 (t80) REVERT: C 450 THR cc_start: 0.9044 (p) cc_final: 0.8801 (p) REVERT: C 468 PHE cc_start: 0.8564 (m-80) cc_final: 0.8141 (m-80) REVERT: C 492 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8102 (mm-30) REVERT: D 548 ILE cc_start: 0.9194 (mt) cc_final: 0.8597 (mm) REVERT: D 590 GLN cc_start: 0.9365 (mm-40) cc_final: 0.9103 (tp40) REVERT: D 591 GLN cc_start: 0.8930 (tt0) cc_final: 0.8547 (tt0) REVERT: D 603 ILE cc_start: 0.9239 (mt) cc_final: 0.8820 (tt) REVERT: D 623 TRP cc_start: 0.8555 (m100) cc_final: 0.8339 (m100) REVERT: A 78 ASP cc_start: 0.8329 (t0) cc_final: 0.8040 (t0) REVERT: A 196 CYS cc_start: 0.8284 (m) cc_final: 0.7900 (m) REVERT: A 217 TYR cc_start: 0.9182 (m-80) cc_final: 0.8859 (m-80) REVERT: A 377 ASN cc_start: 0.8464 (t0) cc_final: 0.8247 (t0) REVERT: A 399 THR cc_start: 0.6395 (t) cc_final: 0.6075 (m) REVERT: B 565 LEU cc_start: 0.8369 (mt) cc_final: 0.7792 (tt) REVERT: B 586 TYR cc_start: 0.9599 (t80) cc_final: 0.9399 (t80) REVERT: B 622 ILE cc_start: 0.8636 (mt) cc_final: 0.8258 (mt) REVERT: B 642 ILE cc_start: 0.9218 (mt) cc_final: 0.8589 (tt) REVERT: B 648 GLU cc_start: 0.8027 (tp30) cc_final: 0.7791 (tp30) REVERT: E 107 ASP cc_start: 0.8794 (m-30) cc_final: 0.8162 (t0) REVERT: E 122 LEU cc_start: 0.9257 (mt) cc_final: 0.9042 (mm) REVERT: E 295 ASN cc_start: 0.8395 (m-40) cc_final: 0.7627 (t0) REVERT: F 563 GLN cc_start: 0.8674 (pt0) cc_final: 0.8382 (pt0) REVERT: F 631 TRP cc_start: 0.8388 (t-100) cc_final: 0.8093 (t-100) REVERT: F 638 TYR cc_start: 0.8172 (m-80) cc_final: 0.7873 (m-10) REVERT: F 656 ASN cc_start: 0.8793 (m-40) cc_final: 0.8580 (m-40) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.1343 time to fit residues: 102.2977 Evaluate side-chains 281 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN D 551 GLN D 552 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS F 552 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.086663 restraints weight = 43783.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088878 restraints weight = 27093.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090384 restraints weight = 19416.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091380 restraints weight = 15360.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.092133 restraints weight = 13057.684| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16289 Z= 0.179 Angle : 0.807 11.830 22311 Z= 0.394 Chirality : 0.049 0.354 2774 Planarity : 0.004 0.046 2718 Dihedral : 8.481 85.910 3716 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.06 % Allowed : 2.07 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1709 helix: 1.20 (0.25), residues: 449 sheet: 0.83 (0.23), residues: 425 loop : 0.63 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 456 TYR 0.023 0.002 TYR D 638 PHE 0.023 0.003 PHE F 522 TRP 0.027 0.002 TRP F 610 HIS 0.012 0.002 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00380 (16174) covalent geometry : angle 0.74142 (22001) SS BOND : bond 0.00331 ( 35) SS BOND : angle 1.06477 ( 70) hydrogen bonds : bond 0.06665 ( 627) hydrogen bonds : angle 5.58513 ( 1845) link_ALPHA1-3 : bond 0.01134 ( 3) link_ALPHA1-3 : angle 1.49824 ( 9) link_ALPHA1-6 : bond 0.00670 ( 3) link_ALPHA1-6 : angle 1.84522 ( 9) link_BETA1-4 : bond 0.00863 ( 16) link_BETA1-4 : angle 2.76698 ( 48) link_NAG-ASN : bond 0.00507 ( 58) link_NAG-ASN : angle 3.32721 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 0.588 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: C 80 ASN cc_start: 0.7903 (m-40) cc_final: 0.7510 (p0) REVERT: C 104 MET cc_start: 0.8905 (ttm) cc_final: 0.8554 (tpp) REVERT: C 112 TRP cc_start: 0.8959 (t-100) cc_final: 0.8481 (t-100) REVERT: C 122 LEU cc_start: 0.8964 (mp) cc_final: 0.8636 (tt) REVERT: C 180 ASP cc_start: 0.8246 (m-30) cc_final: 0.7900 (m-30) REVERT: C 259 LEU cc_start: 0.9507 (mp) cc_final: 0.9208 (mm) REVERT: C 468 PHE cc_start: 0.8024 (m-80) cc_final: 0.7601 (m-80) REVERT: C 492 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7874 (mm-30) REVERT: D 548 ILE cc_start: 0.8866 (mt) cc_final: 0.8393 (mm) REVERT: D 550 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7560 (tm-30) REVERT: A 35 TRP cc_start: 0.8054 (m100) cc_final: 0.7410 (m100) REVERT: A 166 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7957 (mmt180) REVERT: A 217 TYR cc_start: 0.8935 (m-80) cc_final: 0.8276 (m-80) REVERT: A 315 GLN cc_start: 0.8407 (mp10) cc_final: 0.7989 (mp10) REVERT: B 565 LEU cc_start: 0.8606 (mt) cc_final: 0.7942 (tt) REVERT: B 648 GLU cc_start: 0.8097 (tp30) cc_final: 0.7738 (tp30) REVERT: B 655 LYS cc_start: 0.8580 (tptp) cc_final: 0.8206 (tptm) REVERT: E 430 ILE cc_start: 0.8589 (pt) cc_final: 0.8308 (mt) REVERT: E 435 TYR cc_start: 0.8635 (t80) cc_final: 0.7998 (t80) REVERT: F 577 GLN cc_start: 0.8105 (tp40) cc_final: 0.7751 (tm-30) REVERT: F 631 TRP cc_start: 0.8232 (t-100) cc_final: 0.8002 (t-100) REVERT: F 638 TYR cc_start: 0.7664 (m-80) cc_final: 0.7167 (m-10) REVERT: F 650 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8349 (tm-30) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1172 time to fit residues: 62.9013 Evaluate side-chains 253 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 17 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN D 563 GLN D 630 GLN A 72 HIS A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.103212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086065 restraints weight = 44427.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.088299 restraints weight = 27331.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.089708 restraints weight = 19480.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090816 restraints weight = 15511.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091464 restraints weight = 13034.143| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16289 Z= 0.139 Angle : 0.663 12.683 22311 Z= 0.324 Chirality : 0.046 0.298 2774 Planarity : 0.004 0.038 2718 Dihedral : 7.310 75.942 3716 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1709 helix: 1.50 (0.25), residues: 452 sheet: 0.70 (0.23), residues: 447 loop : 0.40 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 298 TYR 0.020 0.002 TYR B 643 PHE 0.028 0.002 PHE B 522 TRP 0.032 0.002 TRP F 610 HIS 0.008 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00294 (16174) covalent geometry : angle 0.60921 (22001) SS BOND : bond 0.00199 ( 35) SS BOND : angle 1.01093 ( 70) hydrogen bonds : bond 0.05108 ( 627) hydrogen bonds : angle 5.13968 ( 1845) link_ALPHA1-3 : bond 0.01186 ( 3) link_ALPHA1-3 : angle 1.39572 ( 9) link_ALPHA1-6 : bond 0.00766 ( 3) link_ALPHA1-6 : angle 1.85478 ( 9) link_BETA1-4 : bond 0.00562 ( 16) link_BETA1-4 : angle 1.90783 ( 48) link_NAG-ASN : bond 0.00481 ( 58) link_NAG-ASN : angle 2.78529 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.445 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: C 104 MET cc_start: 0.8943 (ttm) cc_final: 0.8356 (tpp) REVERT: C 112 TRP cc_start: 0.8941 (t-100) cc_final: 0.8590 (t-100) REVERT: C 122 LEU cc_start: 0.8955 (mp) cc_final: 0.8610 (tt) REVERT: C 180 ASP cc_start: 0.8265 (m-30) cc_final: 0.7777 (m-30) REVERT: C 434 MET cc_start: 0.8706 (ttm) cc_final: 0.8501 (ttm) REVERT: C 468 PHE cc_start: 0.8008 (m-80) cc_final: 0.7631 (m-80) REVERT: C 491 ILE cc_start: 0.9020 (tp) cc_final: 0.8586 (mm) REVERT: C 500 ARG cc_start: 0.2651 (ptt-90) cc_final: 0.2323 (ptt-90) REVERT: D 550 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7677 (tm-30) REVERT: D 574 LYS cc_start: 0.9427 (mmtp) cc_final: 0.9050 (mmtm) REVERT: A 35 TRP cc_start: 0.7972 (m100) cc_final: 0.7280 (m100) REVERT: A 217 TYR cc_start: 0.8967 (m-80) cc_final: 0.8012 (m-80) REVERT: A 315 GLN cc_start: 0.8564 (mp10) cc_final: 0.8050 (mp10) REVERT: A 467 THR cc_start: 0.9633 (m) cc_final: 0.9418 (m) REVERT: B 542 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8232 (tmt-80) REVERT: B 565 LEU cc_start: 0.8656 (mt) cc_final: 0.8042 (tt) REVERT: B 622 ILE cc_start: 0.8769 (mt) cc_final: 0.8499 (mt) REVERT: E 376 PHE cc_start: 0.7918 (t80) cc_final: 0.7656 (t80) REVERT: E 426 MET cc_start: 0.7283 (ttm) cc_final: 0.6696 (ttp) REVERT: E 474 ASP cc_start: 0.7334 (t0) cc_final: 0.7018 (m-30) REVERT: E 494 LEU cc_start: 0.9292 (tp) cc_final: 0.8871 (tp) REVERT: F 577 GLN cc_start: 0.8086 (tp40) cc_final: 0.7778 (tm-30) REVERT: F 650 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8263 (tm-30) REVERT: F 657 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8138 (tm-30) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1205 time to fit residues: 58.8906 Evaluate side-chains 227 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 141 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN A 72 HIS A 85 HIS A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN F 552 GLN F 640 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.079133 restraints weight = 44682.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081050 restraints weight = 28682.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082330 restraints weight = 21204.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083259 restraints weight = 17194.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.083826 restraints weight = 14779.127| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 16289 Z= 0.264 Angle : 0.790 13.988 22311 Z= 0.382 Chirality : 0.049 0.264 2774 Planarity : 0.004 0.044 2718 Dihedral : 7.369 66.012 3716 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1709 helix: 1.38 (0.25), residues: 455 sheet: 0.57 (0.24), residues: 446 loop : 0.03 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 298 TYR 0.027 0.002 TYR B 643 PHE 0.036 0.003 PHE F 522 TRP 0.041 0.003 TRP F 610 HIS 0.014 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00603 (16174) covalent geometry : angle 0.74341 (22001) SS BOND : bond 0.00521 ( 35) SS BOND : angle 0.94548 ( 70) hydrogen bonds : bond 0.05132 ( 627) hydrogen bonds : angle 5.22097 ( 1845) link_ALPHA1-3 : bond 0.00986 ( 3) link_ALPHA1-3 : angle 2.17008 ( 9) link_ALPHA1-6 : bond 0.00884 ( 3) link_ALPHA1-6 : angle 1.92314 ( 9) link_BETA1-4 : bond 0.00400 ( 16) link_BETA1-4 : angle 1.92270 ( 48) link_NAG-ASN : bond 0.00567 ( 58) link_NAG-ASN : angle 2.88515 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.416 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: C 104 MET cc_start: 0.8932 (ttm) cc_final: 0.8297 (tpp) REVERT: C 112 TRP cc_start: 0.8882 (t-100) cc_final: 0.8596 (t-100) REVERT: C 122 LEU cc_start: 0.9078 (mp) cc_final: 0.8711 (tt) REVERT: C 180 ASP cc_start: 0.8459 (m-30) cc_final: 0.7820 (m-30) REVERT: C 194 ILE cc_start: 0.9395 (tp) cc_final: 0.9155 (tp) REVERT: C 491 ILE cc_start: 0.8992 (tp) cc_final: 0.8739 (tp) REVERT: C 492 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8019 (mm-30) REVERT: D 574 LYS cc_start: 0.9398 (mmtp) cc_final: 0.9082 (mmtm) REVERT: D 603 ILE cc_start: 0.8763 (mt) cc_final: 0.8381 (tt) REVERT: D 656 ASN cc_start: 0.8624 (m-40) cc_final: 0.8390 (m110) REVERT: A 491 ILE cc_start: 0.9108 (mm) cc_final: 0.8706 (mt) REVERT: A 494 LEU cc_start: 0.9249 (mm) cc_final: 0.8870 (mm) REVERT: B 542 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8271 (tmt-80) REVERT: B 565 LEU cc_start: 0.8611 (mt) cc_final: 0.7976 (tt) REVERT: B 654 GLU cc_start: 0.8949 (tp30) cc_final: 0.8566 (tp30) REVERT: B 655 LYS cc_start: 0.8492 (tptp) cc_final: 0.8270 (tptp) REVERT: E 426 MET cc_start: 0.7328 (ttm) cc_final: 0.6575 (ttt) REVERT: F 551 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7939 (pp30) REVERT: F 577 GLN cc_start: 0.8308 (tp40) cc_final: 0.7942 (tm-30) REVERT: F 601 LYS cc_start: 0.9381 (mmtp) cc_final: 0.9179 (mmmm) REVERT: F 642 ILE cc_start: 0.9422 (pt) cc_final: 0.9175 (pt) REVERT: F 658 GLN cc_start: 0.9134 (tp40) cc_final: 0.8889 (tp40) outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.1239 time to fit residues: 52.4828 Evaluate side-chains 218 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 80 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 GLN D 552 GLN D 651 ASN A 72 HIS A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS B 575 GLN E 72 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 551 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.097165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080463 restraints weight = 44503.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.082486 restraints weight = 27721.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.083765 restraints weight = 20090.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.084818 restraints weight = 16165.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085432 restraints weight = 13721.728| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16289 Z= 0.170 Angle : 0.659 14.657 22311 Z= 0.322 Chirality : 0.046 0.299 2774 Planarity : 0.003 0.028 2718 Dihedral : 6.830 61.560 3716 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.13 % Allowed : 2.00 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1709 helix: 1.52 (0.25), residues: 453 sheet: 0.54 (0.24), residues: 461 loop : -0.02 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 617 TYR 0.022 0.002 TYR B 643 PHE 0.023 0.002 PHE A 53 TRP 0.050 0.002 TRP F 610 HIS 0.009 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00384 (16174) covalent geometry : angle 0.60876 (22001) SS BOND : bond 0.00370 ( 35) SS BOND : angle 1.32181 ( 70) hydrogen bonds : bond 0.04629 ( 627) hydrogen bonds : angle 4.96983 ( 1845) link_ALPHA1-3 : bond 0.01174 ( 3) link_ALPHA1-3 : angle 1.66990 ( 9) link_ALPHA1-6 : bond 0.00733 ( 3) link_ALPHA1-6 : angle 1.87753 ( 9) link_BETA1-4 : bond 0.00310 ( 16) link_BETA1-4 : angle 1.59043 ( 48) link_NAG-ASN : bond 0.00392 ( 58) link_NAG-ASN : angle 2.65017 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.562 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: C 44 VAL cc_start: 0.9264 (m) cc_final: 0.8971 (m) REVERT: C 104 MET cc_start: 0.8930 (ttm) cc_final: 0.8184 (tpp) REVERT: C 112 TRP cc_start: 0.8868 (t-100) cc_final: 0.8454 (t-100) REVERT: C 122 LEU cc_start: 0.8971 (mp) cc_final: 0.8599 (tt) REVERT: C 180 ASP cc_start: 0.8490 (m-30) cc_final: 0.7951 (m-30) REVERT: C 194 ILE cc_start: 0.9353 (tp) cc_final: 0.9112 (tp) REVERT: C 490 LYS cc_start: 0.8676 (tptt) cc_final: 0.7823 (tptt) REVERT: D 574 LYS cc_start: 0.9360 (mmtp) cc_final: 0.9072 (mmtm) REVERT: D 656 ASN cc_start: 0.8643 (m-40) cc_final: 0.8437 (m110) REVERT: A 35 TRP cc_start: 0.8145 (m100) cc_final: 0.7464 (m100) REVERT: A 173 TYR cc_start: 0.8587 (p90) cc_final: 0.8094 (p90) REVERT: A 195 ASN cc_start: 0.8852 (p0) cc_final: 0.8597 (p0) REVERT: A 491 ILE cc_start: 0.9023 (mm) cc_final: 0.8665 (mt) REVERT: B 542 ARG cc_start: 0.8557 (ttp-110) cc_final: 0.8179 (tmt-80) REVERT: B 565 LEU cc_start: 0.8534 (mt) cc_final: 0.7988 (tt) REVERT: B 648 GLU cc_start: 0.8183 (tp30) cc_final: 0.7887 (tp30) REVERT: B 655 LYS cc_start: 0.8337 (tptp) cc_final: 0.8049 (tptm) REVERT: E 103 GLN cc_start: 0.8769 (tp40) cc_final: 0.8180 (tp-100) REVERT: E 376 PHE cc_start: 0.8169 (t80) cc_final: 0.7724 (t80) REVERT: E 426 MET cc_start: 0.7073 (ttm) cc_final: 0.6400 (ttt) REVERT: E 491 ILE cc_start: 0.8884 (mp) cc_final: 0.8667 (mt) REVERT: F 551 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7774 (pp30) REVERT: F 642 ILE cc_start: 0.9455 (pt) cc_final: 0.9217 (pt) REVERT: F 658 GLN cc_start: 0.9155 (tp40) cc_final: 0.8947 (tp40) outliers start: 2 outliers final: 0 residues processed: 294 average time/residue: 0.1232 time to fit residues: 53.8955 Evaluate side-chains 226 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 160 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN E 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.078203 restraints weight = 45438.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.080154 restraints weight = 28792.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.081479 restraints weight = 21032.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082384 restraints weight = 16951.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082998 restraints weight = 14545.068| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16289 Z= 0.244 Angle : 0.741 13.854 22311 Z= 0.360 Chirality : 0.048 0.295 2774 Planarity : 0.004 0.069 2718 Dihedral : 7.088 57.794 3716 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1709 helix: 1.45 (0.25), residues: 447 sheet: 0.41 (0.24), residues: 462 loop : -0.33 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 617 TYR 0.020 0.002 TYR B 643 PHE 0.021 0.002 PHE A 53 TRP 0.056 0.002 TRP F 610 HIS 0.007 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00555 (16174) covalent geometry : angle 0.69553 (22001) SS BOND : bond 0.00532 ( 35) SS BOND : angle 1.25332 ( 70) hydrogen bonds : bond 0.04729 ( 627) hydrogen bonds : angle 5.08593 ( 1845) link_ALPHA1-3 : bond 0.01081 ( 3) link_ALPHA1-3 : angle 2.00373 ( 9) link_ALPHA1-6 : bond 0.00828 ( 3) link_ALPHA1-6 : angle 1.92915 ( 9) link_BETA1-4 : bond 0.00278 ( 16) link_BETA1-4 : angle 1.74329 ( 48) link_NAG-ASN : bond 0.00468 ( 58) link_NAG-ASN : angle 2.70002 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8979 (ttm) cc_final: 0.8251 (tpp) REVERT: C 112 TRP cc_start: 0.8889 (t-100) cc_final: 0.8687 (t-100) REVERT: C 180 ASP cc_start: 0.8560 (m-30) cc_final: 0.7981 (m-30) REVERT: C 252 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8420 (mtmt) REVERT: C 342 LEU cc_start: 0.9465 (mt) cc_final: 0.9259 (mt) REVERT: C 491 ILE cc_start: 0.9219 (pt) cc_final: 0.8556 (pt) REVERT: D 574 LYS cc_start: 0.9411 (mmtp) cc_final: 0.9112 (mmtm) REVERT: D 656 ASN cc_start: 0.8642 (m-40) cc_final: 0.8416 (m110) REVERT: A 173 TYR cc_start: 0.8593 (p90) cc_final: 0.8044 (p90) REVERT: A 494 LEU cc_start: 0.9294 (mm) cc_final: 0.8839 (mm) REVERT: B 542 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8261 (tmt-80) REVERT: B 565 LEU cc_start: 0.8585 (mt) cc_final: 0.7989 (tt) REVERT: B 648 GLU cc_start: 0.8270 (tp30) cc_final: 0.7909 (tp30) REVERT: B 655 LYS cc_start: 0.8521 (tptp) cc_final: 0.8163 (tptm) REVERT: E 103 GLN cc_start: 0.8764 (tp40) cc_final: 0.8414 (tp40) REVERT: E 264 SER cc_start: 0.8693 (m) cc_final: 0.8241 (p) REVERT: E 426 MET cc_start: 0.6956 (ttm) cc_final: 0.6348 (ttt) REVERT: E 491 ILE cc_start: 0.8731 (mp) cc_final: 0.8514 (mt) REVERT: F 577 GLN cc_start: 0.8448 (tp40) cc_final: 0.7975 (tm-30) REVERT: F 601 LYS cc_start: 0.9476 (mmtp) cc_final: 0.9253 (mmmm) REVERT: F 603 ILE cc_start: 0.8422 (pt) cc_final: 0.7728 (tt) REVERT: F 626 MET cc_start: 0.6643 (ttm) cc_final: 0.6338 (ttm) REVERT: F 642 ILE cc_start: 0.9490 (pt) cc_final: 0.9243 (pt) REVERT: F 653 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8348 (tm-30) REVERT: F 658 GLN cc_start: 0.9187 (tp40) cc_final: 0.8930 (tp40) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1234 time to fit residues: 48.8807 Evaluate side-chains 215 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 177 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** F 540 GLN ** 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 = 0.3343 r_free = 0.3343 target = 0.096024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.079594 restraints weight = 44710.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081555 restraints weight = 28171.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082903 restraints weight = 20522.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.083836 restraints weight = 16447.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084474 restraints weight = 14035.762| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16289 Z= 0.179 Angle : 0.665 13.995 22311 Z= 0.324 Chirality : 0.046 0.298 2774 Planarity : 0.004 0.051 2718 Dihedral : 6.791 54.834 3716 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1709 helix: 1.61 (0.25), residues: 447 sheet: 0.35 (0.24), residues: 457 loop : -0.40 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 456 TYR 0.023 0.002 TYR D 638 PHE 0.017 0.002 PHE C 383 TRP 0.059 0.002 TRP D 571 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00410 (16174) covalent geometry : angle 0.61751 (22001) SS BOND : bond 0.00354 ( 35) SS BOND : angle 0.97676 ( 70) hydrogen bonds : bond 0.04385 ( 627) hydrogen bonds : angle 4.94748 ( 1845) link_ALPHA1-3 : bond 0.01154 ( 3) link_ALPHA1-3 : angle 1.66673 ( 9) link_ALPHA1-6 : bond 0.00743 ( 3) link_ALPHA1-6 : angle 1.82513 ( 9) link_BETA1-4 : bond 0.00245 ( 16) link_BETA1-4 : angle 1.60751 ( 48) link_NAG-ASN : bond 0.00371 ( 58) link_NAG-ASN : angle 2.67060 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.568 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: C 112 TRP cc_start: 0.8863 (t-100) cc_final: 0.8651 (t-100) REVERT: C 180 ASP cc_start: 0.8539 (m-30) cc_final: 0.7988 (m-30) REVERT: C 252 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8409 (mtmt) REVERT: C 491 ILE cc_start: 0.9278 (pt) cc_final: 0.8699 (pt) REVERT: D 574 LYS cc_start: 0.9372 (mmtp) cc_final: 0.9109 (mmtm) REVERT: D 656 ASN cc_start: 0.8679 (m-40) cc_final: 0.8447 (m110) REVERT: A 173 TYR cc_start: 0.8573 (p90) cc_final: 0.8085 (p90) REVERT: A 195 ASN cc_start: 0.8928 (p0) cc_final: 0.8720 (p0) REVERT: A 217 TYR cc_start: 0.8918 (m-80) cc_final: 0.7935 (m-80) REVERT: A 426 MET cc_start: 0.7396 (ttm) cc_final: 0.6757 (ttp) REVERT: A 484 TYR cc_start: 0.9275 (p90) cc_final: 0.9041 (p90) REVERT: A 491 ILE cc_start: 0.8853 (mm) cc_final: 0.8514 (mt) REVERT: B 538 THR cc_start: 0.9397 (p) cc_final: 0.8989 (p) REVERT: B 542 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.8199 (tmt-80) REVERT: B 565 LEU cc_start: 0.8590 (mt) cc_final: 0.8035 (tt) REVERT: B 648 GLU cc_start: 0.8280 (tp30) cc_final: 0.8000 (tp30) REVERT: B 655 LYS cc_start: 0.8396 (tptp) cc_final: 0.7985 (tptm) REVERT: E 264 SER cc_start: 0.8617 (m) cc_final: 0.8136 (p) REVERT: E 414 ILE cc_start: 0.9494 (mm) cc_final: 0.9043 (tp) REVERT: E 426 MET cc_start: 0.6843 (ttm) cc_final: 0.6224 (ttt) REVERT: E 490 LYS cc_start: 0.9008 (pttt) cc_final: 0.8783 (pttp) REVERT: E 491 ILE cc_start: 0.8829 (mp) cc_final: 0.8564 (mt) REVERT: F 535 MET cc_start: 0.8791 (mmm) cc_final: 0.8584 (mmp) REVERT: F 577 GLN cc_start: 0.8435 (tp40) cc_final: 0.7942 (tm-30) REVERT: F 603 ILE cc_start: 0.8345 (pt) cc_final: 0.7683 (tt) REVERT: F 642 ILE cc_start: 0.9472 (pt) cc_final: 0.9210 (pt) REVERT: F 653 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8431 (tm-30) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1250 time to fit residues: 50.9611 Evaluate side-chains 215 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 ASN A 348 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.079337 restraints weight = 45124.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.081310 restraints weight = 28314.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.082662 restraints weight = 20560.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.083571 restraints weight = 16426.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084191 restraints weight = 14035.923| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16289 Z= 0.170 Angle : 0.658 13.605 22311 Z= 0.321 Chirality : 0.046 0.313 2774 Planarity : 0.004 0.052 2718 Dihedral : 6.665 53.921 3716 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.46 (0.20), residues: 1709 helix: 1.59 (0.25), residues: 450 sheet: 0.35 (0.24), residues: 453 loop : -0.40 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 617 TYR 0.021 0.002 TYR D 638 PHE 0.021 0.002 PHE A 53 TRP 0.055 0.002 TRP D 571 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00387 (16174) covalent geometry : angle 0.61272 (22001) SS BOND : bond 0.00372 ( 35) SS BOND : angle 1.38004 ( 70) hydrogen bonds : bond 0.04264 ( 627) hydrogen bonds : angle 4.88011 ( 1845) link_ALPHA1-3 : bond 0.01151 ( 3) link_ALPHA1-3 : angle 1.68319 ( 9) link_ALPHA1-6 : bond 0.00755 ( 3) link_ALPHA1-6 : angle 1.76731 ( 9) link_BETA1-4 : bond 0.00248 ( 16) link_BETA1-4 : angle 1.59464 ( 48) link_NAG-ASN : bond 0.00395 ( 58) link_NAG-ASN : angle 2.51350 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.568 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: C 104 MET cc_start: 0.8934 (ttm) cc_final: 0.8651 (ttm) REVERT: C 180 ASP cc_start: 0.8532 (m-30) cc_final: 0.7990 (m-30) REVERT: C 252 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8415 (mtmt) REVERT: C 491 ILE cc_start: 0.9298 (pt) cc_final: 0.8681 (pt) REVERT: C 492 GLU cc_start: 0.8421 (mp0) cc_final: 0.8166 (mm-30) REVERT: C 500 ARG cc_start: 0.2631 (ptt-90) cc_final: 0.2058 (ptt-90) REVERT: D 574 LYS cc_start: 0.9395 (mmtp) cc_final: 0.9095 (mmtm) REVERT: D 656 ASN cc_start: 0.8656 (m-40) cc_final: 0.8432 (m110) REVERT: A 53 PHE cc_start: 0.9219 (p90) cc_final: 0.8972 (p90) REVERT: A 104 MET cc_start: 0.8480 (tpp) cc_final: 0.7366 (tpp) REVERT: A 173 TYR cc_start: 0.8568 (p90) cc_final: 0.8191 (p90) REVERT: A 180 ASP cc_start: 0.8925 (m-30) cc_final: 0.8580 (m-30) REVERT: A 195 ASN cc_start: 0.8962 (p0) cc_final: 0.8733 (p0) REVERT: A 217 TYR cc_start: 0.8832 (m-80) cc_final: 0.7969 (m-80) REVERT: A 426 MET cc_start: 0.7445 (ttm) cc_final: 0.6824 (ttp) REVERT: A 484 TYR cc_start: 0.9262 (p90) cc_final: 0.9019 (p90) REVERT: B 530 MET cc_start: 0.8433 (mtp) cc_final: 0.8206 (mtp) REVERT: B 542 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.8214 (tmt-80) REVERT: B 565 LEU cc_start: 0.8616 (mt) cc_final: 0.8026 (tt) REVERT: B 615 SER cc_start: 0.9093 (t) cc_final: 0.8750 (t) REVERT: B 648 GLU cc_start: 0.8309 (tp30) cc_final: 0.8039 (tp30) REVERT: B 655 LYS cc_start: 0.8316 (tptp) cc_final: 0.7997 (tptm) REVERT: E 264 SER cc_start: 0.8579 (m) cc_final: 0.8107 (p) REVERT: E 414 ILE cc_start: 0.9488 (mm) cc_final: 0.9058 (tp) REVERT: E 426 MET cc_start: 0.6850 (ttm) cc_final: 0.6242 (ttt) REVERT: F 577 GLN cc_start: 0.8390 (tp40) cc_final: 0.7929 (tm-30) REVERT: F 603 ILE cc_start: 0.8328 (pt) cc_final: 0.7654 (tt) REVERT: F 631 TRP cc_start: 0.8342 (t-100) cc_final: 0.7933 (t-100) REVERT: F 642 ILE cc_start: 0.9469 (pt) cc_final: 0.9201 (pt) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1250 time to fit residues: 48.9511 Evaluate side-chains 215 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 82 optimal weight: 6.9990 chunk 131 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 78 optimal weight: 0.0870 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN D 554 ASN D 630 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 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 = 0.3386 r_free = 0.3386 target = 0.098581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082297 restraints weight = 44241.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.084305 restraints weight = 27600.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.085675 restraints weight = 19986.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086532 restraints weight = 15944.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.087290 restraints weight = 13667.669| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16289 Z= 0.117 Angle : 0.613 13.298 22311 Z= 0.303 Chirality : 0.045 0.319 2774 Planarity : 0.003 0.054 2718 Dihedral : 6.048 52.708 3716 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1709 helix: 1.67 (0.25), residues: 455 sheet: 0.50 (0.24), residues: 437 loop : -0.39 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 585 TYR 0.034 0.002 TYR F 586 PHE 0.025 0.002 PHE A 53 TRP 0.058 0.002 TRP C 112 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00254 (16174) covalent geometry : angle 0.56939 (22001) SS BOND : bond 0.00266 ( 35) SS BOND : angle 1.35440 ( 70) hydrogen bonds : bond 0.03856 ( 627) hydrogen bonds : angle 4.67061 ( 1845) link_ALPHA1-3 : bond 0.01308 ( 3) link_ALPHA1-3 : angle 1.34135 ( 9) link_ALPHA1-6 : bond 0.00771 ( 3) link_ALPHA1-6 : angle 1.58317 ( 9) link_BETA1-4 : bond 0.00330 ( 16) link_BETA1-4 : angle 1.41715 ( 48) link_NAG-ASN : bond 0.00377 ( 58) link_NAG-ASN : angle 2.38585 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8918 (ttm) cc_final: 0.8672 (ttm) REVERT: C 180 ASP cc_start: 0.8385 (m-30) cc_final: 0.7844 (m-30) REVERT: C 195 ASN cc_start: 0.7833 (t0) cc_final: 0.7482 (t0) REVERT: C 252 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8406 (mtmt) REVERT: C 491 ILE cc_start: 0.9269 (pt) cc_final: 0.8601 (pt) REVERT: C 492 GLU cc_start: 0.8437 (mp0) cc_final: 0.8208 (mm-30) REVERT: C 500 ARG cc_start: 0.2277 (ptt-90) cc_final: 0.1867 (ptt-90) REVERT: D 574 LYS cc_start: 0.9341 (mmtp) cc_final: 0.9087 (mmtm) REVERT: D 591 GLN cc_start: 0.8771 (tt0) cc_final: 0.7915 (tt0) REVERT: A 104 MET cc_start: 0.8339 (tpp) cc_final: 0.7022 (tpp) REVERT: A 173 TYR cc_start: 0.8499 (p90) cc_final: 0.8184 (p90) REVERT: A 180 ASP cc_start: 0.8989 (m-30) cc_final: 0.8617 (m-30) REVERT: A 195 ASN cc_start: 0.8842 (p0) cc_final: 0.8571 (p0) REVERT: A 217 TYR cc_start: 0.8751 (m-80) cc_final: 0.7734 (m-80) REVERT: A 426 MET cc_start: 0.7159 (ttm) cc_final: 0.6604 (ttp) REVERT: A 484 TYR cc_start: 0.9228 (p90) cc_final: 0.9006 (p90) REVERT: A 502 LYS cc_start: 0.8153 (tmmt) cc_final: 0.7755 (ttpt) REVERT: B 530 MET cc_start: 0.8392 (mtp) cc_final: 0.8128 (mtp) REVERT: B 538 THR cc_start: 0.9337 (p) cc_final: 0.8968 (p) REVERT: B 542 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.8074 (tmt-80) REVERT: B 565 LEU cc_start: 0.8594 (mt) cc_final: 0.8019 (tt) REVERT: E 264 SER cc_start: 0.8549 (m) cc_final: 0.8098 (p) REVERT: E 414 ILE cc_start: 0.9453 (mm) cc_final: 0.9039 (tp) REVERT: E 426 MET cc_start: 0.7000 (ttm) cc_final: 0.6450 (ttt) REVERT: F 577 GLN cc_start: 0.8358 (tp40) cc_final: 0.7883 (tm-30) REVERT: F 601 LYS cc_start: 0.9391 (mmmm) cc_final: 0.9129 (mmmm) REVERT: F 631 TRP cc_start: 0.8282 (t-100) cc_final: 0.7912 (t-100) REVERT: F 642 ILE cc_start: 0.9476 (pt) cc_final: 0.9130 (pt) REVERT: F 654 GLU cc_start: 0.8973 (tp30) cc_final: 0.8768 (tp30) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1204 time to fit residues: 50.0457 Evaluate side-chains 218 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 122 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** 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 = 0.3386 r_free = 0.3386 target = 0.098586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082180 restraints weight = 44463.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.084175 restraints weight = 27819.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085489 restraints weight = 20191.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086471 restraints weight = 16243.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087066 restraints weight = 13781.192| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16289 Z= 0.128 Angle : 0.634 14.256 22311 Z= 0.314 Chirality : 0.045 0.276 2774 Planarity : 0.003 0.055 2718 Dihedral : 5.956 52.931 3716 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.12 % 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: 0.48 (0.20), residues: 1709 helix: 1.51 (0.25), residues: 462 sheet: 0.47 (0.24), residues: 439 loop : -0.41 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 579 TYR 0.031 0.002 TYR D 638 PHE 0.024 0.002 PHE A 53 TRP 0.050 0.002 TRP D 571 HIS 0.006 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00288 (16174) covalent geometry : angle 0.58683 (22001) SS BOND : bond 0.00226 ( 35) SS BOND : angle 1.84891 ( 70) hydrogen bonds : bond 0.03854 ( 627) hydrogen bonds : angle 4.59772 ( 1845) link_ALPHA1-3 : bond 0.01199 ( 3) link_ALPHA1-3 : angle 1.41323 ( 9) link_ALPHA1-6 : bond 0.00850 ( 3) link_ALPHA1-6 : angle 1.64639 ( 9) link_BETA1-4 : bond 0.00311 ( 16) link_BETA1-4 : angle 1.44699 ( 48) link_NAG-ASN : bond 0.00334 ( 58) link_NAG-ASN : angle 2.41554 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3418 Ramachandran restraints generated. 1709 Oldfield, 0 Emsley, 1709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8916 (ttm) cc_final: 0.8635 (ttm) REVERT: C 161 MET cc_start: 0.9119 (tpp) cc_final: 0.8703 (tpt) REVERT: C 180 ASP cc_start: 0.8394 (m-30) cc_final: 0.7885 (m-30) REVERT: C 252 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8403 (mtmt) REVERT: C 309 ILE cc_start: 0.8638 (tt) cc_final: 0.8397 (tt) REVERT: C 491 ILE cc_start: 0.9249 (pt) cc_final: 0.8650 (pt) REVERT: C 492 GLU cc_start: 0.8472 (mp0) cc_final: 0.8160 (mm-30) REVERT: D 538 THR cc_start: 0.9111 (p) cc_final: 0.8302 (p) REVERT: D 574 LYS cc_start: 0.9381 (mmtp) cc_final: 0.9088 (mmtm) REVERT: A 53 PHE cc_start: 0.9173 (p90) cc_final: 0.8944 (p90) REVERT: A 87 GLU cc_start: 0.7971 (mp0) cc_final: 0.7415 (mp0) REVERT: A 104 MET cc_start: 0.8376 (tpp) cc_final: 0.7043 (tpp) REVERT: A 173 TYR cc_start: 0.8501 (p90) cc_final: 0.8182 (p90) REVERT: A 180 ASP cc_start: 0.8940 (m-30) cc_final: 0.8544 (m-30) REVERT: A 195 ASN cc_start: 0.8834 (p0) cc_final: 0.8591 (p0) REVERT: A 217 TYR cc_start: 0.8757 (m-80) cc_final: 0.7740 (m-80) REVERT: A 426 MET cc_start: 0.7063 (ttm) cc_final: 0.6553 (ttp) REVERT: A 484 TYR cc_start: 0.9263 (p90) cc_final: 0.9016 (p90) REVERT: B 542 ARG cc_start: 0.8445 (ttp-110) cc_final: 0.7966 (ttt180) REVERT: B 565 LEU cc_start: 0.8639 (mt) cc_final: 0.8036 (tt) REVERT: E 264 SER cc_start: 0.8501 (m) cc_final: 0.8091 (p) REVERT: E 414 ILE cc_start: 0.9459 (mm) cc_final: 0.9048 (tp) REVERT: E 426 MET cc_start: 0.6967 (ttm) cc_final: 0.6465 (ttt) REVERT: E 500 ARG cc_start: 0.2189 (mtm180) cc_final: 0.1870 (mpp80) REVERT: F 577 GLN cc_start: 0.8291 (tp40) cc_final: 0.7848 (tm-30) REVERT: F 601 LYS cc_start: 0.9386 (mmmm) cc_final: 0.9164 (mmmm) REVERT: F 626 MET cc_start: 0.6747 (ttm) cc_final: 0.6319 (ttm) REVERT: F 631 TRP cc_start: 0.8310 (t-100) cc_final: 0.7803 (t-100) REVERT: F 637 ASN cc_start: 0.7821 (p0) cc_final: 0.7461 (p0) REVERT: F 642 ILE cc_start: 0.9521 (pt) cc_final: 0.9147 (pt) REVERT: F 653 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8274 (tm-30) REVERT: F 654 GLU cc_start: 0.8913 (tp30) cc_final: 0.8601 (tp30) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1251 time to fit residues: 51.7285 Evaluate side-chains 220 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 129 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 169 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** 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 = 0.3395 r_free = 0.3395 target = 0.098903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.082441 restraints weight = 44309.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.084392 restraints weight = 27925.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.085765 restraints weight = 20391.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.086709 restraints weight = 16334.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.087381 restraints weight = 13916.570| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 16289 Z= 0.126 Angle : 0.637 19.501 22311 Z= 0.314 Chirality : 0.045 0.386 2774 Planarity : 0.003 0.052 2718 Dihedral : 5.756 52.948 3716 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1709 helix: 1.52 (0.25), residues: 464 sheet: 0.50 (0.24), residues: 446 loop : -0.41 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 588 TYR 0.019 0.001 TYR D 638 PHE 0.026 0.002 PHE A 53 TRP 0.050 0.002 TRP D 596 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00290 (16174) covalent geometry : angle 0.58878 (22001) SS BOND : bond 0.00449 ( 35) SS BOND : angle 2.13812 ( 70) hydrogen bonds : bond 0.03728 ( 627) hydrogen bonds : angle 4.55655 ( 1845) link_ALPHA1-3 : bond 0.01177 ( 3) link_ALPHA1-3 : angle 1.35983 ( 9) link_ALPHA1-6 : bond 0.00836 ( 3) link_ALPHA1-6 : angle 1.56738 ( 9) link_BETA1-4 : bond 0.00322 ( 16) link_BETA1-4 : angle 1.40705 ( 48) link_NAG-ASN : bond 0.00355 ( 58) link_NAG-ASN : angle 2.35494 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2369.35 seconds wall clock time: 41 minutes 44.59 seconds (2504.59 seconds total)