Starting phenix.real_space_refine on Fri Jul 3 21:04:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8y_23240/07_2026/7l8y_23240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8y_23240/07_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_23240/07_2026/7l8y_23240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8y_23240/07_2026/7l8y_23240.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l8y_23240/07_2026/7l8y_23240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8y_23240/07_2026/7l8y_23240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8y_23240/07_2026/7l8y_23240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8y_23240/07_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-6108/lib/python3.11/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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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 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 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 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 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 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 chiralities: 1 Time building chain proxies: 3.80, per 1000 atoms: 0.24 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: 1.58 Conformation dependent library (CDL) restraints added in 736.7 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: 0.84 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: 3.32 Time building geometry restraints manager: 2.09 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 - 17.20: 8789 17.20 - 34.40: 226 34.40 - 51.60: 75 51.60 - 68.80: 32 68.80 - 86.00: 12 Dihedral angle restraints: 9134 sinusoidal: 3478 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 9131 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.870 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 10.194 85.998 5349 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/Z covalent geometry : bond 0.02098 / 1.13 (16174) covalent geometry : angle 1.67360 / 1.09 (22001) SS BOND : bond 0.00954 / 0.49 ( 35) SS BOND : angle 2.94546 / 1.46 ( 70) hydrogen bonds : bond 0.17236 / 9.55 ( 627) hydrogen bonds : angle 7.39201 / 4.11 ( 1845) link_ALPHA1-3 : bond 0.08453 / 4.22 ( 3) link_ALPHA1-3 : angle 4.38100 / 2.19 ( 9) link_ALPHA1-6 : bond 0.06087 / 3.07 ( 3) link_ALPHA1-6 : angle 4.01011 / 1.98 ( 9) link_BETA1-4 : bond 0.06390 / 3.60 ( 16) link_BETA1-4 : angle 4.35316 / 2.17 ( 48) link_NAG-ASN : bond 0.07147 / 4.01 ( 58) link_NAG-ASN : angle 2.71935 / 1.37 ( 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 : 0.624 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: 0.1329 time to fit residues: 101.5451 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 : 0.549 ------------------------------------------------------------------------------- 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... 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 = 0.3480 r_free = 0.3480 target = 0.104096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.086895 restraints weight = 43717.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089101 restraints weight = 26937.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090609 restraints weight = 19332.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091623 restraints weight = 15313.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.092372 restraints weight = 12975.566| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16289 Z= 0.170 Angle : 0.793 12.549 22311 Z= 0.387 Chirality : 0.048 0.286 2774 Planarity : 0.004 0.044 2718 Dihedral : 4.880 22.974 2054 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 1.06 (0.20), residues: 1709 helix: 1.18 (0.25), residues: 449 sheet: 0.76 (0.23), residues: 439 loop : 0.56 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 456 TYR 0.024 0.002 TYR D 638 PHE 0.025 0.003 PHE F 522 TRP 0.029 0.002 TRP F 610 HIS 0.012 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (16174) covalent geometry : angle 0.73460 / 0.37 (22001) SS BOND : bond 0.00404 / 0.23 ( 35) SS BOND : angle 0.98317 / 0.52 ( 70) hydrogen bonds : bond 0.06315 / 3.52 ( 627) hydrogen bonds : angle 5.52413 / 3.11 ( 1845) link_ALPHA1-3 : bond 0.00781 / 0.39 ( 3) link_ALPHA1-3 : angle 1.38373 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00706 / 0.35 ( 3) link_ALPHA1-6 : angle 1.58574 / 0.85 ( 9) link_BETA1-4 : bond 0.00561 / 0.32 ( 16) link_BETA1-4 : angle 2.50839 / 1.33 ( 48) link_NAG-ASN : bond 0.00526 / 0.28 ( 58) link_NAG-ASN : angle 3.15978 / 1.55 ( 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 370 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 0.594 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: 0.7895 (m-40) cc_final: 0.7513 (p0) REVERT: C 104 MET cc_start: 0.8894 (ttm) cc_final: 0.8513 (tpp) REVERT: C 112 TRP cc_start: 0.8984 (t-100) cc_final: 0.8483 (t-100) REVERT: C 122 LEU cc_start: 0.8949 (mp) cc_final: 0.8624 (tt) REVERT: C 180 ASP cc_start: 0.8266 (m-30) cc_final: 0.7753 (m-30) REVERT: C 259 LEU cc_start: 0.9505 (mp) cc_final: 0.9205 (mm) REVERT: C 434 MET cc_start: 0.8723 (ttm) cc_final: 0.8458 (ttm) REVERT: C 468 PHE cc_start: 0.8004 (m-80) cc_final: 0.7609 (m-80) REVERT: C 492 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7881 (mm-30) REVERT: D 548 ILE cc_start: 0.8892 (mt) cc_final: 0.8434 (mm) REVERT: D 550 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7464 (tm-30) REVERT: D 554 ASN cc_start: 0.7618 (m-40) cc_final: 0.7364 (m-40) REVERT: A 35 TRP cc_start: 0.7990 (m100) cc_final: 0.7348 (m100) REVERT: A 125 LEU cc_start: 0.8758 (mt) cc_final: 0.8548 (mt) REVERT: A 166 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7787 (mmt180) REVERT: A 217 TYR cc_start: 0.8883 (m-80) cc_final: 0.8170 (m-80) REVERT: A 315 GLN cc_start: 0.8383 (mp10) cc_final: 0.7974 (mp10) REVERT: B 565 LEU cc_start: 0.8556 (mt) cc_final: 0.7894 (tt) REVERT: B 648 GLU cc_start: 0.8105 (tp30) cc_final: 0.7746 (tp30) REVERT: B 655 LYS cc_start: 0.8548 (tptp) cc_final: 0.8180 (tptm) REVERT: E 232 LYS cc_start: 0.7996 (mttp) cc_final: 0.7496 (tttt) REVERT: E 430 ILE cc_start: 0.8611 (pt) cc_final: 0.8354 (mt) REVERT: E 435 TYR cc_start: 0.8670 (t80) cc_final: 0.8042 (t80) REVERT: F 577 GLN cc_start: 0.8147 (tp40) cc_final: 0.7770 (tm-30) REVERT: F 631 TRP cc_start: 0.8244 (t-100) cc_final: 0.8025 (t-100) REVERT: F 638 TYR cc_start: 0.7609 (m-80) cc_final: 0.7173 (m-10) REVERT: F 650 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8227 (tm-30) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 0.1159 time to fit residues: 63.9835 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 : 0.590 ------------------------------------------------------------------------------- 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: 0.6980 chunk 112 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 315 GLN D 552 GLN D 563 GLN D 630 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 374 HIS F 552 GLN F 640 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082825 restraints weight = 44993.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.084915 restraints weight = 27906.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.086362 restraints weight = 20182.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087241 restraints weight = 16078.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.087989 restraints weight = 13777.876| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16289 Z= 0.200 Angle : 0.717 14.064 22311 Z= 0.350 Chirality : 0.046 0.279 2774 Planarity : 0.004 0.037 2718 Dihedral : 4.685 21.670 2054 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.48 % 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: 0.97 (0.20), residues: 1709 helix: 1.47 (0.25), residues: 450 sheet: 0.59 (0.24), residues: 427 loop : 0.35 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 298 TYR 0.025 0.002 TYR D 638 PHE 0.025 0.002 PHE B 522 TRP 0.038 0.002 TRP F 610 HIS 0.011 0.002 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (16174) covalent geometry : angle 0.66289 / 0.34 (22001) SS BOND : bond 0.00336 / 0.18 ( 35) SS BOND : angle 1.15974 / 0.58 ( 70) hydrogen bonds : bond 0.05349 / 2.98 ( 627) hydrogen bonds : angle 5.22866 / 2.93 ( 1845) link_ALPHA1-3 : bond 0.00651 / 0.33 ( 3) link_ALPHA1-3 : angle 1.51275 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00699 / 0.36 ( 3) link_ALPHA1-6 : angle 1.56137 / 0.78 ( 9) link_BETA1-4 : bond 0.00385 / 0.24 ( 16) link_BETA1-4 : angle 1.85247 / 0.96 ( 48) link_NAG-ASN : bond 0.00412 / 0.23 ( 58) link_NAG-ASN : angle 2.92140 / 1.41 ( 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 320 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.560 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: 0.8994 (ttm) cc_final: 0.8432 (tpp) REVERT: C 112 TRP cc_start: 0.8973 (t-100) cc_final: 0.8576 (t-100) REVERT: C 122 LEU cc_start: 0.9022 (mp) cc_final: 0.8568 (tt) REVERT: C 180 ASP cc_start: 0.8343 (m-30) cc_final: 0.7818 (m-30) REVERT: C 468 PHE cc_start: 0.8026 (m-80) cc_final: 0.7412 (m-80) REVERT: C 491 ILE cc_start: 0.9026 (tp) cc_final: 0.8736 (tp) REVERT: C 492 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7940 (mm-30) REVERT: D 542 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8839 (ttp80) REVERT: D 548 ILE cc_start: 0.8967 (mt) cc_final: 0.8683 (mm) REVERT: D 550 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7743 (tm-30) REVERT: D 574 LYS cc_start: 0.9408 (mmtp) cc_final: 0.9022 (mmtm) REVERT: A 35 TRP cc_start: 0.7995 (m100) cc_final: 0.7353 (m100) REVERT: A 315 GLN cc_start: 0.8641 (mp10) cc_final: 0.8325 (mp10) REVERT: A 467 THR cc_start: 0.9656 (m) cc_final: 0.9440 (m) REVERT: A 491 ILE cc_start: 0.9075 (mm) cc_final: 0.8785 (mt) REVERT: B 542 ARG cc_start: 0.8616 (ttp-110) cc_final: 0.8239 (tmt-80) REVERT: B 565 LEU cc_start: 0.8669 (mt) cc_final: 0.8042 (tt) REVERT: B 655 LYS cc_start: 0.8596 (tptp) cc_final: 0.8363 (tptp) REVERT: E 426 MET cc_start: 0.7594 (ttm) cc_final: 0.6888 (ttp) REVERT: E 430 ILE cc_start: 0.8687 (pt) cc_final: 0.8451 (mt) REVERT: E 435 TYR cc_start: 0.8905 (t80) cc_final: 0.8669 (t80) REVERT: E 494 LEU cc_start: 0.9323 (tp) cc_final: 0.8834 (tp) REVERT: F 523 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8500 (mp) REVERT: F 577 GLN cc_start: 0.8188 (tp40) cc_final: 0.7834 (tm-30) REVERT: F 657 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8034 (tm-30) REVERT: F 658 GLN cc_start: 0.9023 (tp40) cc_final: 0.8760 (tp40) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.1161 time to fit residues: 55.9619 Evaluate side-chains 229 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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: 0.9990 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 203 GLN D 552 GLN D 651 ASN A 72 HIS A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** F 540 GLN ** 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 = 0.3406 r_free = 0.3406 target = 0.099499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.082613 restraints weight = 44600.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.084694 restraints weight = 27866.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.086102 restraints weight = 20196.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087078 restraints weight = 16141.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.087676 restraints weight = 13739.661| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16289 Z= 0.155 Angle : 0.641 14.808 22311 Z= 0.314 Chirality : 0.044 0.260 2774 Planarity : 0.003 0.033 2718 Dihedral : 4.598 20.048 2054 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.99 (0.20), residues: 1709 helix: 1.75 (0.25), residues: 443 sheet: 0.70 (0.24), residues: 440 loop : 0.11 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 298 TYR 0.025 0.002 TYR B 643 PHE 0.022 0.002 PHE A 53 TRP 0.044 0.002 TRP F 610 HIS 0.009 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (16174) covalent geometry : angle 0.59152 / 0.30 (22001) SS BOND : bond 0.00364 / 0.20 ( 35) SS BOND : angle 0.87168 / 0.42 ( 70) hydrogen bonds : bond 0.04599 / 2.54 ( 627) hydrogen bonds : angle 4.99587 / 2.82 ( 1845) link_ALPHA1-3 : bond 0.00591 / 0.30 ( 3) link_ALPHA1-3 : angle 1.45997 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00554 / 0.28 ( 3) link_ALPHA1-6 : angle 1.52826 / 0.78 ( 9) link_BETA1-4 : bond 0.00331 / 0.20 ( 16) link_BETA1-4 : angle 1.53088 / 0.80 ( 48) link_NAG-ASN : bond 0.00397 / 0.21 ( 58) link_NAG-ASN : angle 2.69701 / 1.28 ( 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 298 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.587 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 104 MET cc_start: 0.8948 (ttm) cc_final: 0.8267 (tpp) REVERT: C 112 TRP cc_start: 0.8877 (t-100) cc_final: 0.8522 (t-100) REVERT: C 122 LEU cc_start: 0.9053 (mp) cc_final: 0.8625 (tt) REVERT: C 180 ASP cc_start: 0.8373 (m-30) cc_final: 0.7809 (m-30) REVERT: C 194 ILE cc_start: 0.9275 (tp) cc_final: 0.9036 (tp) REVERT: C 434 MET cc_start: 0.8719 (ttm) cc_final: 0.8500 (ttm) REVERT: C 491 ILE cc_start: 0.9028 (tp) cc_final: 0.8738 (mm) REVERT: C 492 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7915 (mm-30) REVERT: D 574 LYS cc_start: 0.9405 (mmtp) cc_final: 0.9114 (mmtm) REVERT: A 35 TRP cc_start: 0.8082 (m100) cc_final: 0.7236 (m100) REVERT: A 217 TYR cc_start: 0.8960 (m-80) cc_final: 0.7980 (m-80) REVERT: A 315 GLN cc_start: 0.8609 (mp10) cc_final: 0.8340 (mp10) REVERT: A 491 ILE cc_start: 0.9087 (mm) cc_final: 0.8739 (mt) REVERT: A 494 LEU cc_start: 0.9250 (mm) cc_final: 0.8928 (mm) REVERT: A 502 LYS cc_start: 0.8247 (tmmt) cc_final: 0.7880 (tttm) REVERT: B 542 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8230 (tmt-80) REVERT: B 565 LEU cc_start: 0.8644 (mt) cc_final: 0.7962 (tt) REVERT: B 655 LYS cc_start: 0.8595 (tptp) cc_final: 0.8348 (tptm) REVERT: E 69 TRP cc_start: 0.8933 (m-90) cc_final: 0.8481 (m-90) REVERT: E 249 HIS cc_start: 0.8210 (p-80) cc_final: 0.7982 (p90) REVERT: E 426 MET cc_start: 0.7290 (ttm) cc_final: 0.6774 (ttp) REVERT: E 430 ILE cc_start: 0.8725 (pt) cc_final: 0.8473 (mt) REVERT: F 552 GLN cc_start: 0.8120 (pt0) cc_final: 0.7709 (pt0) REVERT: F 577 GLN cc_start: 0.8185 (tp40) cc_final: 0.7857 (tm-30) REVERT: F 631 TRP cc_start: 0.8151 (t-100) cc_final: 0.7913 (t-100) REVERT: F 658 GLN cc_start: 0.9036 (tp40) cc_final: 0.8808 (tp40) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1166 time to fit residues: 52.4247 Evaluate side-chains 229 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 10.0000 chunk 148 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 174 optimal weight: 0.2980 chunk 162 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 99 optimal weight: 0.0060 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 564 HIS B 575 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.099245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082317 restraints weight = 44413.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084409 restraints weight = 27581.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.085833 restraints weight = 19925.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.086824 restraints weight = 15887.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087515 restraints weight = 13500.029| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16289 Z= 0.149 Angle : 0.631 14.302 22311 Z= 0.308 Chirality : 0.044 0.279 2774 Planarity : 0.003 0.030 2718 Dihedral : 4.527 20.518 2054 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.06 % Allowed : 1.42 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1709 helix: 1.82 (0.25), residues: 440 sheet: 0.65 (0.24), residues: 448 loop : 0.05 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 617 TYR 0.023 0.002 TYR B 643 PHE 0.024 0.002 PHE A 53 TRP 0.047 0.002 TRP F 610 HIS 0.007 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16174) covalent geometry : angle 0.58331 / 0.30 (22001) SS BOND : bond 0.00333 / 0.18 ( 35) SS BOND : angle 1.20998 / 0.60 ( 70) hydrogen bonds : bond 0.04399 / 2.42 ( 627) hydrogen bonds : angle 4.84449 / 2.73 ( 1845) link_ALPHA1-3 : bond 0.00595 / 0.30 ( 3) link_ALPHA1-3 : angle 1.43314 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00542 / 0.28 ( 3) link_ALPHA1-6 : angle 1.49962 / 0.78 ( 9) link_BETA1-4 : bond 0.00319 / 0.18 ( 16) link_BETA1-4 : angle 1.43431 / 0.75 ( 48) link_NAG-ASN : bond 0.00395 / 0.21 ( 58) link_NAG-ASN : angle 2.58378 / 1.20 ( 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 301 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.586 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: 0.8937 (ttm) cc_final: 0.8221 (tpp) REVERT: C 112 TRP cc_start: 0.8896 (t-100) cc_final: 0.8674 (t-100) REVERT: C 180 ASP cc_start: 0.8354 (m-30) cc_final: 0.7826 (m-30) REVERT: C 194 ILE cc_start: 0.9261 (tp) cc_final: 0.9021 (tp) REVERT: C 491 ILE cc_start: 0.8983 (tp) cc_final: 0.8515 (mm) REVERT: C 492 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7960 (mm-30) REVERT: D 538 THR cc_start: 0.8866 (p) cc_final: 0.8588 (p) REVERT: D 550 GLN cc_start: 0.8486 (mm110) cc_final: 0.7578 (tm-30) REVERT: D 574 LYS cc_start: 0.9341 (mmtp) cc_final: 0.9088 (mmtm) REVERT: D 603 ILE cc_start: 0.8624 (mt) cc_final: 0.8296 (tt) REVERT: A 35 TRP cc_start: 0.8160 (m100) cc_final: 0.6270 (m100) REVERT: A 173 TYR cc_start: 0.8543 (p90) cc_final: 0.8007 (p90) REVERT: A 180 ASP cc_start: 0.8771 (m-30) cc_final: 0.8570 (m-30) REVERT: A 315 GLN cc_start: 0.8561 (mp10) cc_final: 0.8329 (mp10) REVERT: A 494 LEU cc_start: 0.9263 (mm) cc_final: 0.8894 (mm) REVERT: B 542 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8253 (tmt-80) REVERT: B 565 LEU cc_start: 0.8553 (mt) cc_final: 0.8033 (tt) REVERT: B 651 ASN cc_start: 0.8407 (m-40) cc_final: 0.7409 (m-40) REVERT: B 654 GLU cc_start: 0.8885 (tp30) cc_final: 0.8548 (tp30) REVERT: B 655 LYS cc_start: 0.8527 (tptp) cc_final: 0.8299 (tptm) REVERT: E 249 HIS cc_start: 0.8333 (p-80) cc_final: 0.8046 (p90) REVERT: E 426 MET cc_start: 0.7234 (ttm) cc_final: 0.6781 (ttp) REVERT: F 577 GLN cc_start: 0.8215 (tp40) cc_final: 0.7835 (tm-30) REVERT: F 631 TRP cc_start: 0.8169 (t-100) cc_final: 0.7879 (t-100) REVERT: F 642 ILE cc_start: 0.9417 (pt) cc_final: 0.9150 (pt) REVERT: F 654 GLU cc_start: 0.8909 (tp30) cc_final: 0.8691 (tp30) REVERT: F 656 ASN cc_start: 0.8794 (m-40) cc_final: 0.8142 (t0) REVERT: F 658 GLN cc_start: 0.9082 (tp40) cc_final: 0.8826 (tp40) outliers start: 1 outliers final: 1 residues processed: 301 average time/residue: 0.1161 time to fit residues: 52.3889 Evaluate side-chains 229 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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: 0.9980 chunk 108 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS C 170 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN D 630 GLN A 348 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN E 67 ASN E 103 GLN E 114 GLN E 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.074682 restraints weight = 46443.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076484 restraints weight = 29692.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.077700 restraints weight = 21923.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.078471 restraints weight = 17790.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.079078 restraints weight = 15450.609| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.092 16289 Z= 0.420 Angle : 1.016 13.419 22311 Z= 0.491 Chirality : 0.055 0.313 2774 Planarity : 0.006 0.063 2718 Dihedral : 5.690 26.482 2054 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1709 helix: 0.71 (0.24), residues: 443 sheet: -0.03 (0.22), residues: 479 loop : -0.56 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 298 TYR 0.035 0.003 TYR E 191 PHE 0.043 0.004 PHE E 361 TRP 0.063 0.003 TRP D 571 HIS 0.009 0.003 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00954 / 0.42 (16174) covalent geometry : angle 0.97931 / 0.48 (22001) SS BOND : bond 0.00868 / 0.47 ( 35) SS BOND : angle 1.69113 / 0.80 ( 70) hydrogen bonds : bond 0.05992 / 3.29 ( 627) hydrogen bonds : angle 5.78036 / 3.20 ( 1845) link_ALPHA1-3 : bond 0.00680 / 0.34 ( 3) link_ALPHA1-3 : angle 1.86695 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00391 / 0.20 ( 3) link_ALPHA1-6 : angle 1.64117 / 0.84 ( 9) link_BETA1-4 : bond 0.00464 / 0.26 ( 16) link_BETA1-4 : angle 2.10027 / 1.05 ( 48) link_NAG-ASN : bond 0.00808 / 0.46 ( 58) link_NAG-ASN : angle 2.90234 / 1.34 ( 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 240 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.566 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: 0.9070 (ttm) cc_final: 0.8478 (tpp) REVERT: C 112 TRP cc_start: 0.8961 (t-100) cc_final: 0.8759 (t-100) REVERT: C 180 ASP cc_start: 0.8646 (m-30) cc_final: 0.8049 (m-30) REVERT: C 342 LEU cc_start: 0.9533 (mt) cc_final: 0.9306 (mt) REVERT: D 542 ARG cc_start: 0.8966 (ttp80) cc_final: 0.8430 (ttm170) REVERT: D 574 LYS cc_start: 0.9418 (mmtp) cc_final: 0.9072 (mmtm) REVERT: D 603 ILE cc_start: 0.8837 (mt) cc_final: 0.8513 (tt) REVERT: D 656 ASN cc_start: 0.8432 (m-40) cc_final: 0.8180 (m110) REVERT: A 35 TRP cc_start: 0.7759 (m100) cc_final: 0.7456 (m100) REVERT: B 530 MET cc_start: 0.8417 (mtp) cc_final: 0.8192 (mtp) REVERT: B 565 LEU cc_start: 0.8636 (mt) cc_final: 0.8137 (tp) REVERT: B 648 GLU cc_start: 0.8434 (tp30) cc_final: 0.8233 (tp30) REVERT: B 655 LYS cc_start: 0.8449 (tptp) cc_final: 0.8201 (tptp) REVERT: E 426 MET cc_start: 0.7421 (ttm) cc_final: 0.6905 (ttt) REVERT: E 490 LYS cc_start: 0.9071 (pttt) cc_final: 0.8866 (pttp) REVERT: F 601 LYS cc_start: 0.9457 (mmtp) cc_final: 0.9251 (mmmm) REVERT: F 603 ILE cc_start: 0.8429 (pt) cc_final: 0.7724 (tt) REVERT: F 642 ILE cc_start: 0.9536 (pt) cc_final: 0.9299 (pt) REVERT: F 653 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8616 (tm-30) outliers start: 1 outliers final: 1 residues processed: 240 average time/residue: 0.1238 time to fit residues: 44.7634 Evaluate side-chains 194 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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: 0.6980 chunk 121 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 0.0070 chunk 177 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS C 258 GLN D 552 GLN D 554 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN E 72 HIS ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** 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 = 0.3362 r_free = 0.3362 target = 0.097010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080580 restraints weight = 44461.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.082592 restraints weight = 27577.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.083998 restraints weight = 19823.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.084927 restraints weight = 15736.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085518 restraints weight = 13412.283| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16289 Z= 0.127 Angle : 0.667 12.909 22311 Z= 0.325 Chirality : 0.045 0.313 2774 Planarity : 0.004 0.045 2718 Dihedral : 4.935 26.070 2054 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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 : 0.00 % 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: 0.41 (0.20), residues: 1709 helix: 1.54 (0.25), residues: 443 sheet: 0.30 (0.24), residues: 449 loop : -0.40 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 273 TYR 0.025 0.002 TYR D 638 PHE 0.017 0.002 PHE B 522 TRP 0.057 0.002 TRP F 610 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (16174) covalent geometry : angle 0.62551 / 0.32 (22001) SS BOND : bond 0.00246 / 0.13 ( 35) SS BOND : angle 1.08348 / 0.54 ( 70) hydrogen bonds : bond 0.04488 / 2.47 ( 627) hydrogen bonds : angle 4.98958 / 2.81 ( 1845) link_ALPHA1-3 : bond 0.00666 / 0.33 ( 3) link_ALPHA1-3 : angle 1.48493 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00330 / 0.17 ( 3) link_ALPHA1-6 : angle 1.51634 / 0.83 ( 9) link_BETA1-4 : bond 0.00260 / 0.15 ( 16) link_BETA1-4 : angle 1.38534 / 0.71 ( 48) link_NAG-ASN : bond 0.00370 / 0.19 ( 58) link_NAG-ASN : angle 2.51718 / 1.18 ( 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 282 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 TRP cc_start: 0.8829 (t-100) cc_final: 0.8600 (t-100) REVERT: C 180 ASP cc_start: 0.8545 (m-30) cc_final: 0.7994 (m-30) REVERT: D 542 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8340 (ttm170) REVERT: D 550 GLN cc_start: 0.8490 (mm-40) cc_final: 0.7891 (tm-30) REVERT: D 574 LYS cc_start: 0.9352 (mmtp) cc_final: 0.9085 (mmtm) REVERT: D 603 ILE cc_start: 0.8652 (mt) cc_final: 0.8327 (tt) REVERT: D 656 ASN cc_start: 0.8490 (m-40) cc_final: 0.8259 (m110) REVERT: A 53 PHE cc_start: 0.9134 (p90) cc_final: 0.8895 (p90) REVERT: A 173 TYR cc_start: 0.8559 (p90) cc_final: 0.8079 (p90) REVERT: A 217 TYR cc_start: 0.8992 (m-80) cc_final: 0.8362 (m-80) REVERT: A 494 LEU cc_start: 0.9231 (mm) cc_final: 0.8881 (mm) REVERT: B 530 MET cc_start: 0.8366 (mtp) cc_final: 0.8099 (mtp) REVERT: B 542 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.8100 (tmt-80) REVERT: B 565 LEU cc_start: 0.8581 (mt) cc_final: 0.8016 (tt) REVERT: B 617 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7825 (ttm110) REVERT: B 648 GLU cc_start: 0.8392 (tp30) cc_final: 0.8040 (tp30) REVERT: B 651 ASN cc_start: 0.8567 (m-40) cc_final: 0.8033 (m-40) REVERT: B 655 LYS cc_start: 0.8299 (tptp) cc_final: 0.7969 (tptm) REVERT: E 414 ILE cc_start: 0.9461 (mm) cc_final: 0.8979 (tp) REVERT: E 426 MET cc_start: 0.6739 (ttm) cc_final: 0.6169 (ttt) REVERT: F 535 MET cc_start: 0.8748 (mmm) cc_final: 0.8515 (mmp) REVERT: F 549 VAL cc_start: 0.7641 (t) cc_final: 0.7129 (m) REVERT: F 577 GLN cc_start: 0.8447 (tp40) cc_final: 0.8009 (tm-30) REVERT: F 603 ILE cc_start: 0.8391 (pt) cc_final: 0.7736 (tt) REVERT: F 642 ILE cc_start: 0.9473 (pt) cc_final: 0.9197 (pt) REVERT: F 653 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8568 (tm-30) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1153 time to fit residues: 48.8622 Evaluate side-chains 217 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 4.9990 chunk 72 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 106 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 258 GLN D 651 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 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 = 0.3353 r_free = 0.3353 target = 0.096548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.080143 restraints weight = 45241.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082121 restraints weight = 28197.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.083477 restraints weight = 20428.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084415 restraints weight = 16323.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085077 restraints weight = 13914.391| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16289 Z= 0.149 Angle : 0.662 12.084 22311 Z= 0.326 Chirality : 0.045 0.330 2774 Planarity : 0.004 0.051 2718 Dihedral : 4.755 23.045 2054 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.44 (0.20), residues: 1709 helix: 1.68 (0.25), residues: 435 sheet: 0.30 (0.23), residues: 457 loop : -0.42 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 588 TYR 0.024 0.002 TYR D 638 PHE 0.020 0.002 PHE F 522 TRP 0.057 0.002 TRP F 610 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (16174) covalent geometry : angle 0.61814 / 0.32 (22001) SS BOND : bond 0.00298 / 0.16 ( 35) SS BOND : angle 1.64397 / 0.82 ( 70) hydrogen bonds : bond 0.04359 / 2.40 ( 627) hydrogen bonds : angle 4.93497 / 2.77 ( 1845) link_ALPHA1-3 : bond 0.00597 / 0.30 ( 3) link_ALPHA1-3 : angle 1.43275 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00440 / 0.23 ( 3) link_ALPHA1-6 : angle 1.52892 / 0.83 ( 9) link_BETA1-4 : bond 0.00224 / 0.14 ( 16) link_BETA1-4 : angle 1.36649 / 0.70 ( 48) link_NAG-ASN : bond 0.00425 / 0.22 ( 58) link_NAG-ASN : angle 2.46546 / 1.16 ( 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 273 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.423 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: 0.9039 (ttm) cc_final: 0.8762 (ttm) REVERT: C 180 ASP cc_start: 0.8468 (m-30) cc_final: 0.7930 (m-30) REVERT: C 252 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8420 (mtmt) REVERT: C 500 ARG cc_start: 0.2375 (ptt-90) cc_final: 0.1899 (ptt-90) REVERT: D 542 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8304 (ttm170) REVERT: D 550 GLN cc_start: 0.8508 (mm-40) cc_final: 0.7857 (tm-30) REVERT: D 574 LYS cc_start: 0.9374 (mmtp) cc_final: 0.9088 (mmtm) REVERT: D 603 ILE cc_start: 0.8675 (mt) cc_final: 0.8257 (tt) REVERT: D 626 MET cc_start: 0.6272 (mtm) cc_final: 0.5594 (mtt) REVERT: D 638 TYR cc_start: 0.7386 (m-10) cc_final: 0.7083 (m-10) REVERT: D 647 GLU cc_start: 0.8887 (pm20) cc_final: 0.8674 (pm20) REVERT: D 656 ASN cc_start: 0.8455 (m-40) cc_final: 0.8231 (m110) REVERT: A 173 TYR cc_start: 0.8528 (p90) cc_final: 0.8128 (p90) REVERT: A 195 ASN cc_start: 0.8962 (p0) cc_final: 0.8707 (p0) REVERT: A 426 MET cc_start: 0.7272 (ttm) cc_final: 0.6605 (ttp) REVERT: A 484 TYR cc_start: 0.9221 (p90) cc_final: 0.9008 (p90) REVERT: A 502 LYS cc_start: 0.8299 (tttt) cc_final: 0.7797 (mtpt) REVERT: B 534 SER cc_start: 0.9509 (p) cc_final: 0.9079 (p) REVERT: B 535 MET cc_start: 0.8841 (mmp) cc_final: 0.8604 (mmp) REVERT: B 542 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.7942 (ttt180) REVERT: B 565 LEU cc_start: 0.8576 (mt) cc_final: 0.7989 (tt) REVERT: B 615 SER cc_start: 0.8954 (t) cc_final: 0.8724 (t) REVERT: B 617 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7644 (ttm110) REVERT: B 648 GLU cc_start: 0.8399 (tp30) cc_final: 0.8089 (tp30) REVERT: B 651 ASN cc_start: 0.8091 (m-40) cc_final: 0.7764 (m-40) REVERT: B 655 LYS cc_start: 0.8264 (tptp) cc_final: 0.7986 (tptm) REVERT: E 414 ILE cc_start: 0.9480 (mm) cc_final: 0.9007 (tp) REVERT: E 426 MET cc_start: 0.6711 (ttm) cc_final: 0.6130 (ttt) REVERT: F 549 VAL cc_start: 0.7440 (t) cc_final: 0.7047 (m) REVERT: F 577 GLN cc_start: 0.8503 (tp40) cc_final: 0.8020 (tm-30) REVERT: F 603 ILE cc_start: 0.8308 (pt) cc_final: 0.7683 (tt) REVERT: F 642 ILE cc_start: 0.9444 (pt) cc_final: 0.9208 (pt) REVERT: F 653 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8490 (tm-30) REVERT: F 654 GLU cc_start: 0.8990 (tp30) cc_final: 0.8540 (tp30) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1206 time to fit residues: 48.9796 Evaluate side-chains 211 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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: 3.9990 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 554 ASN ** 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** ** F 552 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 = 0.3372 r_free = 0.3372 target = 0.097773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081288 restraints weight = 44614.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083287 restraints weight = 27843.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.084678 restraints weight = 20102.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.085612 restraints weight = 15995.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.086245 restraints weight = 13647.382| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5668 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= 0.125 Angle : 0.616 12.111 22311 Z= 0.307 Chirality : 0.045 0.337 2774 Planarity : 0.003 0.053 2718 Dihedral : 4.603 22.778 2054 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.44 (0.20), residues: 1709 helix: 1.60 (0.25), residues: 441 sheet: 0.36 (0.24), residues: 453 loop : -0.42 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 588 TYR 0.021 0.001 TYR F 643 PHE 0.022 0.002 PHE A 53 TRP 0.052 0.002 TRP C 112 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (16174) covalent geometry : angle 0.57723 / 0.30 (22001) SS BOND : bond 0.00266 / 0.15 ( 35) SS BOND : angle 1.20715 / 0.62 ( 70) hydrogen bonds : bond 0.04033 / 2.22 ( 627) hydrogen bonds : angle 4.78327 / 2.69 ( 1845) link_ALPHA1-3 : bond 0.00595 / 0.30 ( 3) link_ALPHA1-3 : angle 1.44532 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00432 / 0.22 ( 3) link_ALPHA1-6 : angle 1.50381 / 0.82 ( 9) link_BETA1-4 : bond 0.00257 / 0.15 ( 16) link_BETA1-4 : angle 1.29027 / 0.67 ( 48) link_NAG-ASN : bond 0.00380 / 0.20 ( 58) link_NAG-ASN : angle 2.30819 / 1.08 ( 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 273 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9018 (ttm) cc_final: 0.8718 (ttm) REVERT: C 161 MET cc_start: 0.9062 (tpp) cc_final: 0.8657 (tpt) REVERT: C 180 ASP cc_start: 0.8372 (m-30) cc_final: 0.7863 (m-30) REVERT: C 195 ASN cc_start: 0.7834 (t0) cc_final: 0.7475 (t0) REVERT: C 252 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8399 (mtmt) REVERT: C 309 ILE cc_start: 0.8654 (tt) cc_final: 0.8364 (tt) REVERT: D 542 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8326 (ttm170) REVERT: D 550 GLN cc_start: 0.8493 (mm-40) cc_final: 0.7844 (tm-30) REVERT: D 574 LYS cc_start: 0.9328 (mmtp) cc_final: 0.9085 (mmtm) REVERT: D 603 ILE cc_start: 0.8540 (mt) cc_final: 0.7864 (tt) REVERT: D 626 MET cc_start: 0.6362 (mtm) cc_final: 0.5927 (mtt) REVERT: D 638 TYR cc_start: 0.7213 (m-10) cc_final: 0.6930 (m-10) REVERT: A 53 PHE cc_start: 0.9229 (p90) cc_final: 0.8970 (p90) REVERT: A 173 TYR cc_start: 0.8495 (p90) cc_final: 0.8157 (p90) REVERT: A 195 ASN cc_start: 0.8942 (p0) cc_final: 0.8664 (p0) REVERT: A 217 TYR cc_start: 0.8877 (m-80) cc_final: 0.8259 (m-80) REVERT: A 426 MET cc_start: 0.7193 (ttm) cc_final: 0.6609 (ttp) REVERT: A 502 LYS cc_start: 0.8206 (tttt) cc_final: 0.7747 (mtpt) REVERT: B 530 MET cc_start: 0.7727 (mtp) cc_final: 0.7527 (mtp) REVERT: B 534 SER cc_start: 0.9504 (p) cc_final: 0.9101 (p) REVERT: B 542 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.7915 (ttt180) REVERT: B 565 LEU cc_start: 0.8663 (mt) cc_final: 0.8070 (tt) REVERT: B 615 SER cc_start: 0.9027 (t) cc_final: 0.8817 (t) REVERT: B 648 GLU cc_start: 0.8405 (tp30) cc_final: 0.8114 (tp30) REVERT: B 651 ASN cc_start: 0.8107 (m-40) cc_final: 0.7755 (m-40) REVERT: B 655 LYS cc_start: 0.8206 (tptp) cc_final: 0.7918 (tptm) REVERT: E 414 ILE cc_start: 0.9460 (mm) cc_final: 0.9009 (tp) REVERT: E 426 MET cc_start: 0.6708 (ttm) cc_final: 0.6282 (ttt) REVERT: E 500 ARG cc_start: 0.2682 (mtm180) cc_final: 0.2482 (mpp80) REVERT: F 549 VAL cc_start: 0.7346 (t) cc_final: 0.6896 (m) REVERT: F 577 GLN cc_start: 0.8413 (tp40) cc_final: 0.7943 (tm-30) REVERT: F 601 LYS cc_start: 0.9409 (mmmm) cc_final: 0.9167 (mmmm) REVERT: F 603 ILE cc_start: 0.8254 (pt) cc_final: 0.7716 (tt) REVERT: F 642 ILE cc_start: 0.9442 (pt) cc_final: 0.9141 (pt) REVERT: F 653 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8493 (tm-30) REVERT: F 654 GLU cc_start: 0.8984 (tp30) cc_final: 0.8524 (tp30) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1169 time to fit residues: 47.9801 Evaluate side-chains 217 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 41 optimal weight: 0.0070 chunk 96 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 chunk 138 optimal weight: 7.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 554 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081930 restraints weight = 44556.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083802 restraints weight = 28369.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085123 restraints weight = 20909.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086028 restraints weight = 16789.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086646 restraints weight = 14372.354| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16289 Z= 0.127 Angle : 0.627 12.221 22311 Z= 0.310 Chirality : 0.044 0.307 2774 Planarity : 0.003 0.052 2718 Dihedral : 4.543 23.132 2054 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: 0.49 (0.20), residues: 1709 helix: 1.63 (0.25), residues: 446 sheet: 0.36 (0.24), residues: 461 loop : -0.38 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 588 TYR 0.043 0.002 TYR D 638 PHE 0.025 0.002 PHE A 53 TRP 0.060 0.002 TRP D 614 HIS 0.004 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16174) covalent geometry : angle 0.58345 / 0.30 (22001) SS BOND : bond 0.00240 / 0.13 ( 35) SS BOND : angle 1.12290 / 0.57 ( 70) hydrogen bonds : bond 0.04031 / 2.22 ( 627) hydrogen bonds : angle 4.71645 / 2.66 ( 1845) link_ALPHA1-3 : bond 0.00608 / 0.30 ( 3) link_ALPHA1-3 : angle 1.42915 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00387 / 0.20 ( 3) link_ALPHA1-6 : angle 1.46521 / 0.80 ( 9) link_BETA1-4 : bond 0.00261 / 0.15 ( 16) link_BETA1-4 : angle 1.29087 / 0.67 ( 48) link_NAG-ASN : bond 0.00322 / 0.17 ( 58) link_NAG-ASN : angle 2.48601 / 1.19 ( 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 270 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8993 (ttm) cc_final: 0.8716 (ttm) REVERT: C 161 MET cc_start: 0.9062 (tpp) cc_final: 0.8667 (tpt) REVERT: C 180 ASP cc_start: 0.8315 (m-30) cc_final: 0.7832 (m-30) REVERT: C 252 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8394 (mtmt) REVERT: C 309 ILE cc_start: 0.8646 (tt) cc_final: 0.8374 (tt) REVERT: D 542 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8301 (ttm170) REVERT: D 550 GLN cc_start: 0.8447 (mm-40) cc_final: 0.7850 (tm-30) REVERT: D 574 LYS cc_start: 0.9356 (mmtp) cc_final: 0.9090 (mmtm) REVERT: D 623 TRP cc_start: 0.8568 (m100) cc_final: 0.7331 (m-10) REVERT: D 626 MET cc_start: 0.6511 (mtm) cc_final: 0.6107 (mtt) REVERT: A 53 PHE cc_start: 0.9256 (p90) cc_final: 0.9012 (p90) REVERT: A 173 TYR cc_start: 0.8461 (p90) cc_final: 0.8106 (p90) REVERT: A 195 ASN cc_start: 0.8949 (p0) cc_final: 0.8670 (p0) REVERT: A 217 TYR cc_start: 0.8836 (m-80) cc_final: 0.8224 (m-80) REVERT: A 426 MET cc_start: 0.7032 (ttm) cc_final: 0.6538 (ttp) REVERT: A 484 TYR cc_start: 0.9246 (p90) cc_final: 0.9020 (p90) REVERT: A 502 LYS cc_start: 0.8179 (tttt) cc_final: 0.7706 (mtpt) REVERT: B 542 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7914 (ttt180) REVERT: B 565 LEU cc_start: 0.8594 (mt) cc_final: 0.8027 (tt) REVERT: B 648 GLU cc_start: 0.8387 (tp30) cc_final: 0.8086 (tp30) REVERT: B 651 ASN cc_start: 0.8089 (m-40) cc_final: 0.7875 (m110) REVERT: E 414 ILE cc_start: 0.9504 (mm) cc_final: 0.9067 (tp) REVERT: E 426 MET cc_start: 0.6942 (ttm) cc_final: 0.6245 (ttt) REVERT: F 549 VAL cc_start: 0.7317 (t) cc_final: 0.6988 (m) REVERT: F 577 GLN cc_start: 0.8411 (tp40) cc_final: 0.7918 (tm-30) REVERT: F 601 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9165 (mmmm) REVERT: F 631 TRP cc_start: 0.8157 (t-100) cc_final: 0.7706 (t-100) REVERT: F 642 ILE cc_start: 0.9462 (pt) cc_final: 0.9166 (pt) REVERT: F 653 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8478 (tm-30) REVERT: F 654 GLU cc_start: 0.8958 (tp30) cc_final: 0.8562 (tp30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1206 time to fit residues: 49.1146 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 : 0.593 ------------------------------------------------------------------------------- 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: 6.9990 chunk 137 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN D 554 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.082366 restraints weight = 44497.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.084346 restraints weight = 27853.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.085682 restraints weight = 20156.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086568 restraints weight = 16178.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087225 restraints weight = 13892.926| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16289 Z= 0.118 Angle : 0.606 11.356 22311 Z= 0.301 Chirality : 0.044 0.310 2774 Planarity : 0.003 0.054 2718 Dihedral : 4.462 23.311 2054 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.45 (0.20), residues: 1709 helix: 1.61 (0.25), residues: 448 sheet: 0.34 (0.24), residues: 452 loop : -0.42 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 588 TYR 0.025 0.001 TYR D 638 PHE 0.024 0.002 PHE A 53 TRP 0.055 0.002 TRP D 614 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16174) covalent geometry : angle 0.56515 / 0.29 (22001) SS BOND : bond 0.00212 / 0.11 ( 35) SS BOND : angle 1.01903 / 0.52 ( 70) hydrogen bonds : bond 0.03918 / 2.15 ( 627) hydrogen bonds : angle 4.63209 / 2.62 ( 1845) link_ALPHA1-3 : bond 0.00536 / 0.27 ( 3) link_ALPHA1-3 : angle 1.42275 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00434 / 0.22 ( 3) link_ALPHA1-6 : angle 1.47257 / 0.80 ( 9) link_BETA1-4 : bond 0.00289 / 0.17 ( 16) link_BETA1-4 : angle 1.26509 / 0.65 ( 48) link_NAG-ASN : bond 0.00418 / 0.22 ( 58) link_NAG-ASN : angle 2.36291 / 1.11 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2443.85 seconds wall clock time: 43 minutes 10.18 seconds (2590.18 seconds total)