Starting phenix.real_space_refine on Sat Jun 14 15:18:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8y_23240/06_2025/7l8y_23240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8y_23240/06_2025/7l8y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8y_23240/06_2025/7l8y_23240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8y_23240/06_2025/7l8y_23240.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8y_23240/06_2025/7l8y_23240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8y_23240/06_2025/7l8y_23240.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15903 Number of models: 1 Model: "" Number of chains: 27 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3447 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 20, 'TRANS': 416} Chain breaks: 3 Chain: "D" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1131 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "A" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3460 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "E" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3434 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 20, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.94, per 1000 atoms: 0.63 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: 4.41 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.15 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: 5.43 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3687 1.32 - 1.46: 5040 1.46 - 1.60: 7295 1.60 - 1.74: 18 1.74 - 1.88: 134 Bond restraints: 16174 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.393 0.104 1.40e-02 5.10e+03 5.54e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.395 -0.069 1.10e-02 8.26e+03 3.98e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.72e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.650 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 16169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 17980 2.02 - 4.05: 3308 4.05 - 6.07: 609 6.07 - 8.09: 89 8.09 - 10.12: 15 Bond angle restraints: 22001 Sorted by residual: angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.44 -8.88 1.02e+00 9.61e-01 7.58e+01 angle pdb=" C LEU F 523 " pdb=" N GLY F 524 " pdb=" CA GLY F 524 " ideal model delta sigma weight residual 120.10 128.29 -8.19 9.50e-01 1.11e+00 7.42e+01 angle pdb=" N ILE F 622 " pdb=" CA ILE F 622 " pdb=" C ILE F 622 " ideal model delta sigma weight residual 111.67 103.60 8.07 9.50e-01 1.11e+00 7.21e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.34 -7.78 1.01e+00 9.80e-01 5.93e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.32 -7.76 1.01e+00 9.80e-01 5.90e+01 ... (remaining 21996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 10484 21.29 - 42.58: 194 42.58 - 63.88: 73 63.88 - 85.17: 32 85.17 - 106.46: 13 Dihedral angle restraints: 10796 sinusoidal: 5140 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.02 -66.02 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.31 -60.31 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.22 -60.22 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 10793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 2317 0.169 - 0.338: 353 0.338 - 0.507: 102 0.507 - 0.676: 1 0.676 - 0.845: 1 Chirality restraints: 2774 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 2771 not shown) Planarity restraints: 2776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 610 " -0.349 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG C 610 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C 610 " -0.128 2.00e-02 2.50e+03 pdb=" N2 NAG C 610 " 0.535 2.00e-02 2.50e+03 pdb=" O7 NAG C 610 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 606 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG E 606 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG E 606 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG E 606 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG E 606 " -0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B 702 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.074 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " 0.185 2.00e-02 2.50e+03 ... (remaining 2773 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1761 2.73 - 3.27: 15138 3.27 - 3.82: 24705 3.82 - 4.36: 31661 4.36 - 4.90: 49452 Nonbonded interactions: 122717 Sorted by model distance: nonbonded pdb=" O3 NAG A 614 " pdb=" O7 NAG A 614 " model vdw 2.188 3.040 nonbonded pdb=" O3 NAG I 2 " pdb=" O7 NAG I 2 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR C 240 " pdb=" O6 NAG C 602 " model vdw 2.413 3.040 nonbonded pdb=" C ASN A 195 " pdb=" OD1 ASN A 195 " model vdw 2.475 3.270 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.491 3.120 ... (remaining 122712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 66 through 397 or resid 414 through \ 503 or resid 601 through 611)) selection = (chain 'C' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 503 or resid 601 through 611)) selection = (chain 'E' and (resid 33 through 503 or resid 601 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.180 Process input model: 37.160 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.128 16289 Z= 1.155 Angle : 1.703 10.118 22311 Z= 1.092 Chirality : 0.136 0.845 2774 Planarity : 0.018 0.301 2718 Dihedral : 11.267 106.459 7011 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.069 0.009 TRP C 35 HIS 0.008 0.002 HIS A 216 PHE 0.044 0.006 PHE A 383 TYR 0.031 0.006 TYR E 318 ARG 0.009 0.001 ARG A 308 Details of bonding type rmsd link_NAG-ASN : bond 0.07147 ( 58) link_NAG-ASN : angle 2.71935 ( 174) link_ALPHA1-6 : bond 0.06087 ( 3) link_ALPHA1-6 : angle 4.01011 ( 9) link_BETA1-4 : bond 0.06390 ( 16) link_BETA1-4 : angle 4.35316 ( 48) link_ALPHA1-3 : bond 0.08453 ( 3) link_ALPHA1-3 : angle 4.38100 ( 9) hydrogen bonds : bond 0.17236 ( 627) hydrogen bonds : angle 7.39201 ( 1845) SS BOND : bond 0.00954 ( 35) SS BOND : angle 2.94546 ( 70) covalent geometry : bond 0.02098 (16174) covalent geometry : angle 1.67360 (22001) *********************** 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 : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8953 (ttm) cc_final: 0.8614 (tpp) REVERT: C 199 SER cc_start: 0.8873 (p) cc_final: 0.7733 (m) REVERT: C 349 LEU cc_start: 0.9538 (mt) cc_final: 0.9319 (mp) REVERT: C 368 ASP cc_start: 0.7771 (t70) cc_final: 0.7164 (p0) REVERT: C 376 PHE cc_start: 0.6707 (t80) cc_final: 0.6148 (t80) REVERT: C 435 TYR cc_start: 0.9063 (t80) cc_final: 0.8658 (t80) REVERT: C 450 THR cc_start: 0.9044 (p) cc_final: 0.8809 (p) REVERT: C 468 PHE cc_start: 0.8564 (m-80) cc_final: 0.8201 (m-80) REVERT: C 492 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8098 (mm-30) REVERT: D 548 ILE cc_start: 0.9194 (mt) cc_final: 0.8594 (mm) REVERT: D 590 GLN cc_start: 0.9365 (mm-40) cc_final: 0.9097 (tp40) REVERT: D 591 GLN cc_start: 0.8930 (tt0) cc_final: 0.8525 (tt0) REVERT: D 603 ILE cc_start: 0.9239 (mt) cc_final: 0.8818 (tt) REVERT: D 623 TRP cc_start: 0.8555 (m100) cc_final: 0.8323 (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: 0.7898 (m) REVERT: A 217 TYR cc_start: 0.9182 (m-80) cc_final: 0.8860 (m-80) REVERT: A 377 ASN cc_start: 0.8464 (t0) cc_final: 0.8244 (t0) REVERT: A 399 THR cc_start: 0.6395 (t) cc_final: 0.6073 (m) REVERT: B 565 LEU cc_start: 0.8369 (mt) cc_final: 0.7771 (tt) REVERT: B 590 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9147 (tp40) REVERT: B 622 ILE cc_start: 0.8636 (mt) cc_final: 0.8247 (mt) REVERT: B 642 ILE cc_start: 0.9218 (mt) cc_final: 0.8585 (tt) REVERT: B 648 GLU cc_start: 0.8027 (tp30) cc_final: 0.7763 (tp30) REVERT: E 107 ASP cc_start: 0.8794 (m-30) cc_final: 0.8162 (t0) REVERT: E 295 ASN cc_start: 0.8395 (m-40) cc_final: 0.7628 (t0) REVERT: F 563 GLN cc_start: 0.8674 (pt0) cc_final: 0.8384 (pt0) REVERT: F 631 TRP cc_start: 0.8388 (t-100) cc_final: 0.8099 (t-100) REVERT: F 638 TYR cc_start: 0.8172 (m-80) cc_final: 0.7874 (m-10) REVERT: F 656 ASN cc_start: 0.8793 (m-40) cc_final: 0.8576 (m-40) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.2980 time to fit residues: 223.8430 Evaluate side-chains 286 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN D 551 GLN D 552 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS F 552 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.104080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086840 restraints weight = 43740.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.089048 restraints weight = 26887.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090551 restraints weight = 19288.050| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16289 Z= 0.168 Angle : 0.785 12.071 22311 Z= 0.384 Chirality : 0.049 0.322 2774 Planarity : 0.004 0.046 2718 Dihedral : 8.408 84.845 3716 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1709 helix: 1.31 (0.25), residues: 441 sheet: 0.82 (0.23), residues: 425 loop : 0.59 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 610 HIS 0.010 0.001 HIS C 72 PHE 0.022 0.003 PHE F 522 TYR 0.030 0.002 TYR B 643 ARG 0.004 0.001 ARG C 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 58) link_NAG-ASN : angle 3.20244 ( 174) link_ALPHA1-6 : bond 0.00668 ( 3) link_ALPHA1-6 : angle 1.89439 ( 9) link_BETA1-4 : bond 0.00777 ( 16) link_BETA1-4 : angle 2.67740 ( 48) link_ALPHA1-3 : bond 0.01253 ( 3) link_ALPHA1-3 : angle 1.76872 ( 9) hydrogen bonds : bond 0.06510 ( 627) hydrogen bonds : angle 5.52887 ( 1845) SS BOND : bond 0.00388 ( 35) SS BOND : angle 1.03625 ( 70) covalent geometry : bond 0.00350 (16174) covalent geometry : angle 0.72286 (22001) *********************** 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 365 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 1.892 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: 0.7948 (m-40) cc_final: 0.7528 (p0) REVERT: C 104 MET cc_start: 0.8880 (ttm) cc_final: 0.8512 (tpp) REVERT: C 112 TRP cc_start: 0.8976 (t-100) cc_final: 0.8496 (t-100) REVERT: C 122 LEU cc_start: 0.8961 (mp) cc_final: 0.8642 (tt) REVERT: C 180 ASP cc_start: 0.8295 (m-30) cc_final: 0.7786 (m-30) REVERT: C 259 LEU cc_start: 0.9484 (mp) cc_final: 0.9183 (mm) REVERT: C 434 MET cc_start: 0.8692 (ttm) cc_final: 0.8468 (ttm) REVERT: C 468 PHE cc_start: 0.8006 (m-80) cc_final: 0.7581 (m-80) REVERT: D 548 ILE cc_start: 0.8878 (mt) cc_final: 0.8340 (mm) REVERT: D 550 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7576 (tm-30) REVERT: A 35 TRP cc_start: 0.8040 (m100) cc_final: 0.7391 (m100) REVERT: A 166 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7991 (mmt180) REVERT: A 217 TYR cc_start: 0.8882 (m-80) cc_final: 0.8206 (m-80) REVERT: A 315 GLN cc_start: 0.8401 (mp10) cc_final: 0.8006 (mp10) REVERT: B 565 LEU cc_start: 0.8626 (mt) cc_final: 0.8005 (tt) REVERT: B 648 GLU cc_start: 0.8126 (tp30) cc_final: 0.7764 (tp30) REVERT: B 655 LYS cc_start: 0.8581 (tptp) cc_final: 0.8207 (tptm) REVERT: E 430 ILE cc_start: 0.8610 (pt) cc_final: 0.8349 (mt) REVERT: F 577 GLN cc_start: 0.8107 (tp40) cc_final: 0.7762 (tm-30) REVERT: F 631 TRP cc_start: 0.8276 (t-100) cc_final: 0.7973 (t-100) REVERT: F 638 TYR cc_start: 0.7646 (m-80) cc_final: 0.7177 (m-10) REVERT: F 650 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8276 (tm-30) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.3087 time to fit residues: 165.3121 Evaluate side-chains 250 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 158 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN D 563 GLN D 630 GLN A 85 HIS A 287 GLN A 302 ASN A 348 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 374 HIS ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.093836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.077017 restraints weight = 45164.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.078962 restraints weight = 28435.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.080300 restraints weight = 20810.343| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 16289 Z= 0.340 Angle : 0.923 13.050 22311 Z= 0.448 Chirality : 0.053 0.316 2774 Planarity : 0.005 0.060 2718 Dihedral : 8.321 71.513 3716 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1709 helix: 0.89 (0.24), residues: 453 sheet: 0.50 (0.23), residues: 463 loop : -0.07 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP F 610 HIS 0.011 0.003 HIS C 72 PHE 0.024 0.004 PHE A 376 TYR 0.021 0.003 TYR D 586 ARG 0.012 0.001 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 58) link_NAG-ASN : angle 3.00894 ( 174) link_ALPHA1-6 : bond 0.00758 ( 3) link_ALPHA1-6 : angle 2.08262 ( 9) link_BETA1-4 : bond 0.00469 ( 16) link_BETA1-4 : angle 2.13269 ( 48) link_ALPHA1-3 : bond 0.00908 ( 3) link_ALPHA1-3 : angle 2.08934 ( 9) hydrogen bonds : bond 0.06037 ( 627) hydrogen bonds : angle 5.63103 ( 1845) SS BOND : bond 0.00618 ( 35) SS BOND : angle 1.45935 ( 70) covalent geometry : bond 0.00769 (16174) covalent geometry : angle 0.87901 (22001) *********************** 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 277 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 275 time to evaluate : 1.641 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: 0.9031 (ttm) cc_final: 0.8541 (tpp) REVERT: C 112 TRP cc_start: 0.9015 (t-100) cc_final: 0.8805 (t-100) REVERT: C 122 LEU cc_start: 0.9080 (mp) cc_final: 0.8732 (tt) REVERT: C 180 ASP cc_start: 0.8631 (m-30) cc_final: 0.7997 (m-30) REVERT: C 434 MET cc_start: 0.8516 (ttm) cc_final: 0.8280 (ttp) REVERT: C 468 PHE cc_start: 0.8122 (m-80) cc_final: 0.7426 (m-80) REVERT: D 542 ARG cc_start: 0.9077 (ttp80) cc_final: 0.8845 (ttp80) REVERT: D 574 LYS cc_start: 0.9405 (mmtp) cc_final: 0.9055 (mmtm) REVERT: D 647 GLU cc_start: 0.8348 (mp0) cc_final: 0.8146 (mp0) REVERT: D 656 ASN cc_start: 0.8591 (m-40) cc_final: 0.8384 (m110) REVERT: A 35 TRP cc_start: 0.8100 (m100) cc_final: 0.7510 (m100) REVERT: A 195 ASN cc_start: 0.8950 (p0) cc_final: 0.8742 (p0) REVERT: A 315 GLN cc_start: 0.8568 (mp10) cc_final: 0.8332 (mp10) REVERT: B 530 MET cc_start: 0.8496 (mtp) cc_final: 0.8262 (mtp) REVERT: B 542 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8264 (ttt90) REVERT: B 565 LEU cc_start: 0.8637 (mt) cc_final: 0.8112 (tp) REVERT: B 622 ILE cc_start: 0.9046 (mt) cc_final: 0.8812 (mt) REVERT: B 631 TRP cc_start: 0.9099 (t-100) cc_final: 0.8774 (t-100) REVERT: B 647 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7846 (mt-10) REVERT: B 648 GLU cc_start: 0.8346 (tp30) cc_final: 0.8102 (tp30) REVERT: E 426 MET cc_start: 0.7457 (ttm) cc_final: 0.6772 (ttt) REVERT: E 435 TYR cc_start: 0.8953 (t80) cc_final: 0.8492 (t80) REVERT: F 603 ILE cc_start: 0.8332 (pt) cc_final: 0.7715 (tt) REVERT: F 658 GLN cc_start: 0.9152 (tp40) cc_final: 0.8860 (tp40) outliers start: 2 outliers final: 1 residues processed: 277 average time/residue: 0.2796 time to fit residues: 114.4075 Evaluate side-chains 217 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 13 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN D 651 ASN A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS B 575 GLN E 72 HIS ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN F 552 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.098191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081370 restraints weight = 43771.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.083401 restraints weight = 27446.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.084692 restraints weight = 19959.862| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16289 Z= 0.135 Angle : 0.656 12.720 22311 Z= 0.319 Chirality : 0.046 0.288 2774 Planarity : 0.004 0.051 2718 Dihedral : 7.225 65.991 3716 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1709 helix: 1.43 (0.25), residues: 453 sheet: 0.52 (0.24), residues: 441 loop : 0.01 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 610 HIS 0.008 0.001 HIS C 72 PHE 0.019 0.002 PHE A 53 TYR 0.025 0.002 TYR B 643 ARG 0.005 0.001 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 58) link_NAG-ASN : angle 2.78096 ( 174) link_ALPHA1-6 : bond 0.00660 ( 3) link_ALPHA1-6 : angle 1.96515 ( 9) link_BETA1-4 : bond 0.00347 ( 16) link_BETA1-4 : angle 1.61162 ( 48) link_ALPHA1-3 : bond 0.01248 ( 3) link_ALPHA1-3 : angle 1.63252 ( 9) hydrogen bonds : bond 0.04808 ( 627) hydrogen bonds : angle 5.05485 ( 1845) SS BOND : bond 0.00276 ( 35) SS BOND : angle 0.94576 ( 70) covalent geometry : bond 0.00293 (16174) covalent geometry : angle 0.60285 (22001) *********************** 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 313 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 1.606 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: 0.8922 (ttm) cc_final: 0.8299 (tpp) REVERT: C 112 TRP cc_start: 0.8914 (t-100) cc_final: 0.8602 (t-100) REVERT: C 122 LEU cc_start: 0.8977 (mp) cc_final: 0.8603 (tt) REVERT: C 180 ASP cc_start: 0.8590 (m-30) cc_final: 0.8021 (m-30) REVERT: C 194 ILE cc_start: 0.9339 (tp) cc_final: 0.9080 (tp) REVERT: C 468 PHE cc_start: 0.7880 (m-80) cc_final: 0.7533 (m-80) REVERT: D 535 MET cc_start: 0.7876 (tpp) cc_final: 0.7636 (mmp) REVERT: D 548 ILE cc_start: 0.8964 (mm) cc_final: 0.8496 (mm) REVERT: D 574 LYS cc_start: 0.9393 (mmtp) cc_final: 0.9104 (mmtm) REVERT: D 626 MET cc_start: 0.7073 (tpp) cc_final: 0.6610 (mtt) REVERT: A 35 TRP cc_start: 0.8087 (m100) cc_final: 0.7265 (m100) REVERT: A 85 HIS cc_start: 0.8511 (t70) cc_final: 0.8277 (t-90) REVERT: A 217 TYR cc_start: 0.8937 (m-80) cc_final: 0.7899 (m-80) REVERT: A 315 GLN cc_start: 0.8664 (mp10) cc_final: 0.8429 (mp10) REVERT: A 494 LEU cc_start: 0.9247 (mm) cc_final: 0.8912 (mm) REVERT: A 502 LYS cc_start: 0.8085 (tmmt) cc_final: 0.7755 (tttm) REVERT: B 530 MET cc_start: 0.8405 (mtp) cc_final: 0.8158 (mtp) REVERT: B 542 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8205 (ttt90) REVERT: B 565 LEU cc_start: 0.8628 (mt) cc_final: 0.7986 (tt) REVERT: B 631 TRP cc_start: 0.8956 (t-100) cc_final: 0.8711 (t60) REVERT: B 655 LYS cc_start: 0.8547 (tptp) cc_final: 0.8257 (tptp) REVERT: E 191 TYR cc_start: 0.9004 (m-80) cc_final: 0.8795 (m-10) REVERT: E 376 PHE cc_start: 0.8185 (t80) cc_final: 0.7784 (t80) REVERT: E 426 MET cc_start: 0.6936 (ttm) cc_final: 0.6277 (ttt) REVERT: E 435 TYR cc_start: 0.8919 (t80) cc_final: 0.8550 (t80) REVERT: E 494 LEU cc_start: 0.9296 (tp) cc_final: 0.8885 (tp) REVERT: F 574 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8585 (ttpt) REVERT: F 658 GLN cc_start: 0.9112 (tp40) cc_final: 0.8864 (tp40) outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.2801 time to fit residues: 128.9805 Evaluate side-chains 236 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 34 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 552 GLN D 651 ASN A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081009 restraints weight = 44830.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083067 restraints weight = 27835.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084449 restraints weight = 20099.051| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4779 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= 0.143 Angle : 0.635 13.246 22311 Z= 0.309 Chirality : 0.046 0.291 2774 Planarity : 0.004 0.040 2718 Dihedral : 6.705 60.415 3716 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1709 helix: 1.58 (0.25), residues: 451 sheet: 0.51 (0.24), residues: 454 loop : -0.13 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 610 HIS 0.005 0.001 HIS C 72 PHE 0.024 0.002 PHE A 53 TYR 0.023 0.002 TYR B 643 ARG 0.005 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 58) link_NAG-ASN : angle 2.56161 ( 174) link_ALPHA1-6 : bond 0.00790 ( 3) link_ALPHA1-6 : angle 1.84557 ( 9) link_BETA1-4 : bond 0.00354 ( 16) link_BETA1-4 : angle 1.58873 ( 48) link_ALPHA1-3 : bond 0.01266 ( 3) link_ALPHA1-3 : angle 1.68683 ( 9) hydrogen bonds : bond 0.04434 ( 627) hydrogen bonds : angle 4.87176 ( 1845) SS BOND : bond 0.00502 ( 35) SS BOND : angle 1.18097 ( 70) covalent geometry : bond 0.00315 (16174) covalent geometry : angle 0.58661 (22001) *********************** 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 295 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 1.691 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: 0.8892 (ttm) cc_final: 0.8226 (tpp) REVERT: C 112 TRP cc_start: 0.8896 (t-100) cc_final: 0.8482 (t-100) REVERT: C 180 ASP cc_start: 0.8431 (m-30) cc_final: 0.7875 (m-30) REVERT: C 252 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8424 (mtmt) REVERT: D 548 ILE cc_start: 0.8979 (mm) cc_final: 0.8536 (mm) REVERT: D 574 LYS cc_start: 0.9398 (mmtp) cc_final: 0.9109 (mmtm) REVERT: D 626 MET cc_start: 0.7101 (tpp) cc_final: 0.6712 (mtt) REVERT: A 35 TRP cc_start: 0.8148 (m100) cc_final: 0.7435 (m100) REVERT: A 85 HIS cc_start: 0.8422 (t70) cc_final: 0.8217 (t-90) REVERT: A 173 TYR cc_start: 0.8580 (p90) cc_final: 0.7935 (p90) REVERT: A 180 ASP cc_start: 0.8825 (m-30) cc_final: 0.8615 (m-30) REVERT: A 195 ASN cc_start: 0.8795 (p0) cc_final: 0.8525 (p0) REVERT: A 217 TYR cc_start: 0.8938 (m-80) cc_final: 0.7861 (m-80) REVERT: A 315 GLN cc_start: 0.8640 (mp10) cc_final: 0.8411 (mp10) REVERT: A 484 TYR cc_start: 0.9313 (p90) cc_final: 0.9112 (p90) REVERT: B 530 MET cc_start: 0.8336 (mtp) cc_final: 0.8026 (mtp) REVERT: B 565 LEU cc_start: 0.8565 (mt) cc_final: 0.8000 (tt) REVERT: B 631 TRP cc_start: 0.8956 (t-100) cc_final: 0.8636 (t60) REVERT: B 648 GLU cc_start: 0.8215 (tp30) cc_final: 0.7917 (tp30) REVERT: B 655 LYS cc_start: 0.8505 (tptp) cc_final: 0.8133 (tptm) REVERT: E 103 GLN cc_start: 0.8659 (tp40) cc_final: 0.8409 (tp40) REVERT: E 426 MET cc_start: 0.6978 (ttm) cc_final: 0.6337 (ttt) REVERT: E 435 TYR cc_start: 0.8952 (t80) cc_final: 0.8475 (t80) REVERT: F 551 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7838 (pp30) REVERT: F 574 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8546 (ttpt) REVERT: F 631 TRP cc_start: 0.8277 (t-100) cc_final: 0.7981 (t-100) REVERT: F 656 ASN cc_start: 0.8722 (m-40) cc_final: 0.8108 (t0) REVERT: F 658 GLN cc_start: 0.9135 (tp40) cc_final: 0.8930 (tp40) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.3126 time to fit residues: 138.3513 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 : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN D 651 ASN A 72 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 552 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.079898 restraints weight = 44865.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.081792 restraints weight = 28659.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083109 restraints weight = 21037.316| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16289 Z= 0.187 Angle : 0.655 13.061 22311 Z= 0.321 Chirality : 0.046 0.292 2774 Planarity : 0.004 0.046 2718 Dihedral : 6.680 57.574 3716 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.06 % Allowed : 1.10 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1709 helix: 1.56 (0.25), residues: 457 sheet: 0.42 (0.24), residues: 452 loop : -0.19 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP F 610 HIS 0.007 0.001 HIS A 85 PHE 0.021 0.002 PHE A 53 TYR 0.026 0.002 TYR F 643 ARG 0.008 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 58) link_NAG-ASN : angle 2.47450 ( 174) link_ALPHA1-6 : bond 0.00765 ( 3) link_ALPHA1-6 : angle 1.89445 ( 9) link_BETA1-4 : bond 0.00285 ( 16) link_BETA1-4 : angle 1.64771 ( 48) link_ALPHA1-3 : bond 0.01170 ( 3) link_ALPHA1-3 : angle 1.81653 ( 9) hydrogen bonds : bond 0.04463 ( 627) hydrogen bonds : angle 4.87399 ( 1845) SS BOND : bond 0.00392 ( 35) SS BOND : angle 1.09112 ( 70) covalent geometry : bond 0.00423 (16174) covalent geometry : angle 0.61205 (22001) *********************** 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 283 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 1.770 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: 0.8903 (ttm) cc_final: 0.8703 (ttm) REVERT: C 112 TRP cc_start: 0.8862 (t-100) cc_final: 0.8651 (t-100) REVERT: C 180 ASP cc_start: 0.8472 (m-30) cc_final: 0.7905 (m-30) REVERT: D 574 LYS cc_start: 0.9369 (mmtp) cc_final: 0.9128 (mmtm) REVERT: D 626 MET cc_start: 0.7145 (tpp) cc_final: 0.6830 (mtt) REVERT: A 35 TRP cc_start: 0.8081 (m100) cc_final: 0.6015 (m100) REVERT: A 85 HIS cc_start: 0.8459 (t70) cc_final: 0.8188 (t-170) REVERT: A 173 TYR cc_start: 0.8575 (p90) cc_final: 0.7940 (p90) REVERT: A 195 ASN cc_start: 0.8878 (p0) cc_final: 0.8610 (p0) REVERT: A 217 TYR cc_start: 0.8869 (m-80) cc_final: 0.7861 (m-80) REVERT: A 502 LYS cc_start: 0.8363 (tmmt) cc_final: 0.8143 (tttt) REVERT: B 542 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8091 (ttt90) REVERT: B 565 LEU cc_start: 0.8610 (mt) cc_final: 0.8026 (tt) REVERT: B 648 GLU cc_start: 0.8239 (tp30) cc_final: 0.7907 (tp30) REVERT: B 655 LYS cc_start: 0.8500 (tptp) cc_final: 0.8145 (tptm) REVERT: E 264 SER cc_start: 0.8653 (m) cc_final: 0.8208 (p) REVERT: E 426 MET cc_start: 0.6675 (ttm) cc_final: 0.6120 (ttt) REVERT: E 435 TYR cc_start: 0.9005 (t80) cc_final: 0.8805 (t80) REVERT: E 494 LEU cc_start: 0.9306 (tp) cc_final: 0.9018 (tp) REVERT: F 577 GLN cc_start: 0.8304 (tp40) cc_final: 0.7879 (tm-30) REVERT: F 603 ILE cc_start: 0.8349 (pt) cc_final: 0.7683 (tt) REVERT: F 626 MET cc_start: 0.6604 (ttm) cc_final: 0.6185 (ttm) REVERT: F 631 TRP cc_start: 0.8240 (t-100) cc_final: 0.7912 (t-100) REVERT: F 642 ILE cc_start: 0.9494 (pt) cc_final: 0.9229 (pt) REVERT: F 653 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8587 (tm-30) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.2663 time to fit residues: 112.7048 Evaluate side-chains 220 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN E 72 HIS E 302 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.076509 restraints weight = 46035.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.078358 restraints weight = 29189.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079643 restraints weight = 21449.013| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 16289 Z= 0.293 Angle : 0.798 12.374 22311 Z= 0.387 Chirality : 0.050 0.298 2774 Planarity : 0.005 0.051 2718 Dihedral : 7.417 58.453 3716 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1709 helix: 1.25 (0.24), residues: 454 sheet: 0.15 (0.23), residues: 473 loop : -0.48 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP F 610 HIS 0.007 0.002 HIS A 85 PHE 0.026 0.003 PHE E 361 TYR 0.028 0.002 TYR F 586 ARG 0.009 0.001 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 58) link_NAG-ASN : angle 2.76380 ( 174) link_ALPHA1-6 : bond 0.00701 ( 3) link_ALPHA1-6 : angle 2.08838 ( 9) link_BETA1-4 : bond 0.00313 ( 16) link_BETA1-4 : angle 1.87238 ( 48) link_ALPHA1-3 : bond 0.00913 ( 3) link_ALPHA1-3 : angle 2.12896 ( 9) hydrogen bonds : bond 0.05074 ( 627) hydrogen bonds : angle 5.21624 ( 1845) SS BOND : bond 0.00785 ( 35) SS BOND : angle 1.37906 ( 70) covalent geometry : bond 0.00667 (16174) covalent geometry : angle 0.75395 (22001) *********************** 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 254 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.770 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 180 ASP cc_start: 0.8616 (m-30) cc_final: 0.8057 (m-30) REVERT: C 252 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8385 (mtmt) REVERT: D 574 LYS cc_start: 0.9431 (mmtp) cc_final: 0.9147 (mmtm) REVERT: D 626 MET cc_start: 0.7349 (tpp) cc_final: 0.7012 (mtt) REVERT: D 656 ASN cc_start: 0.8477 (m-40) cc_final: 0.8242 (m110) REVERT: A 104 MET cc_start: 0.8479 (tpp) cc_final: 0.7285 (tpp) REVERT: A 173 TYR cc_start: 0.8515 (p90) cc_final: 0.8067 (p90) REVERT: A 195 ASN cc_start: 0.9029 (p0) cc_final: 0.8777 (p0) REVERT: A 217 TYR cc_start: 0.8956 (m-80) cc_final: 0.7737 (m-80) REVERT: A 484 TYR cc_start: 0.9308 (p90) cc_final: 0.8989 (p90) REVERT: A 494 LEU cc_start: 0.9286 (mm) cc_final: 0.8975 (mm) REVERT: B 530 MET cc_start: 0.8389 (mtp) cc_final: 0.8039 (mtp) REVERT: B 542 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8146 (ttt90) REVERT: B 565 LEU cc_start: 0.8670 (mt) cc_final: 0.8045 (tt) REVERT: B 648 GLU cc_start: 0.8287 (tp30) cc_final: 0.7999 (tp30) REVERT: B 655 LYS cc_start: 0.8498 (tptp) cc_final: 0.8180 (tptp) REVERT: E 426 MET cc_start: 0.7206 (ttm) cc_final: 0.6674 (ttt) REVERT: F 579 ARG cc_start: 0.8828 (mtp180) cc_final: 0.8320 (mtp180) REVERT: F 603 ILE cc_start: 0.8419 (pt) cc_final: 0.7771 (tt) REVERT: F 626 MET cc_start: 0.6908 (ttm) cc_final: 0.6485 (ttm) REVERT: F 642 ILE cc_start: 0.9486 (pt) cc_final: 0.9241 (pt) REVERT: F 647 GLU cc_start: 0.8589 (pp20) cc_final: 0.8388 (tm-30) REVERT: F 648 GLU cc_start: 0.8430 (tp30) cc_final: 0.8189 (tp30) REVERT: F 653 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8654 (tm-30) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2833 time to fit residues: 105.9803 Evaluate side-chains 200 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 187 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN D 651 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.079465 restraints weight = 44441.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.081382 restraints weight = 27807.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.082707 restraints weight = 20185.900| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16289 Z= 0.145 Angle : 0.658 12.279 22311 Z= 0.319 Chirality : 0.046 0.302 2774 Planarity : 0.004 0.051 2718 Dihedral : 6.810 59.319 3716 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1709 helix: 1.58 (0.25), residues: 447 sheet: 0.24 (0.24), residues: 459 loop : -0.43 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP F 610 HIS 0.004 0.001 HIS C 249 PHE 0.022 0.002 PHE A 53 TYR 0.025 0.002 TYR D 638 ARG 0.009 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 58) link_NAG-ASN : angle 2.66048 ( 174) link_ALPHA1-6 : bond 0.00722 ( 3) link_ALPHA1-6 : angle 1.76948 ( 9) link_BETA1-4 : bond 0.00258 ( 16) link_BETA1-4 : angle 1.58087 ( 48) link_ALPHA1-3 : bond 0.01173 ( 3) link_ALPHA1-3 : angle 1.57609 ( 9) hydrogen bonds : bond 0.04432 ( 627) hydrogen bonds : angle 4.92554 ( 1845) SS BOND : bond 0.00416 ( 35) SS BOND : angle 1.34380 ( 70) covalent geometry : bond 0.00325 (16174) covalent geometry : angle 0.60751 (22001) *********************** 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 266 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 TRP cc_start: 0.8821 (t-100) cc_final: 0.8366 (t-100) REVERT: C 180 ASP cc_start: 0.8556 (m-30) cc_final: 0.8034 (m-30) REVERT: C 210 PHE cc_start: 0.7791 (m-80) cc_final: 0.7579 (m-80) REVERT: C 252 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8380 (mtmt) REVERT: D 542 ARG cc_start: 0.8871 (ttp-110) cc_final: 0.8665 (ttp80) REVERT: D 574 LYS cc_start: 0.9386 (mmtp) cc_final: 0.9142 (mmtm) REVERT: D 591 GLN cc_start: 0.8888 (tt0) cc_final: 0.8325 (tp40) REVERT: D 626 MET cc_start: 0.7011 (tpp) cc_final: 0.6745 (mtt) REVERT: D 656 ASN cc_start: 0.8476 (m-40) cc_final: 0.8250 (m110) REVERT: A 104 MET cc_start: 0.8296 (tpp) cc_final: 0.6962 (tpp) REVERT: A 173 TYR cc_start: 0.8479 (p90) cc_final: 0.8070 (p90) REVERT: A 217 TYR cc_start: 0.8898 (m-80) cc_final: 0.7600 (m-80) REVERT: A 426 MET cc_start: 0.7244 (ttm) cc_final: 0.6978 (ttp) REVERT: A 484 TYR cc_start: 0.9193 (p90) cc_final: 0.8879 (p90) REVERT: B 542 ARG cc_start: 0.8329 (ttp80) cc_final: 0.8028 (ttt90) REVERT: B 565 LEU cc_start: 0.8656 (mt) cc_final: 0.7944 (tt) REVERT: B 648 GLU cc_start: 0.8250 (tp30) cc_final: 0.8004 (tp30) REVERT: B 655 LYS cc_start: 0.8446 (tptp) cc_final: 0.8093 (tptm) REVERT: E 340 GLU cc_start: 0.8607 (tt0) cc_final: 0.8378 (tt0) REVERT: E 414 ILE cc_start: 0.9494 (mm) cc_final: 0.9038 (tp) REVERT: E 426 MET cc_start: 0.6944 (ttm) cc_final: 0.6398 (ttt) REVERT: F 603 ILE cc_start: 0.8407 (pt) cc_final: 0.7758 (tt) REVERT: F 642 ILE cc_start: 0.9466 (pt) cc_final: 0.9207 (pt) REVERT: F 653 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8607 (tm-30) REVERT: F 654 GLU cc_start: 0.8970 (tp30) cc_final: 0.8598 (tp30) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2833 time to fit residues: 111.4561 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 : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 70 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN D 651 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.078574 restraints weight = 44953.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.080472 restraints weight = 28026.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.081773 restraints weight = 20348.272| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16289 Z= 0.188 Angle : 0.685 11.858 22311 Z= 0.335 Chirality : 0.047 0.305 2774 Planarity : 0.004 0.048 2718 Dihedral : 6.693 58.388 3716 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1709 helix: 1.58 (0.25), residues: 443 sheet: 0.14 (0.23), residues: 464 loop : -0.46 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP F 610 HIS 0.016 0.002 HIS C 72 PHE 0.020 0.002 PHE A 53 TYR 0.023 0.002 TYR D 638 ARG 0.008 0.001 ARG D 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 58) link_NAG-ASN : angle 2.51311 ( 174) link_ALPHA1-6 : bond 0.00800 ( 3) link_ALPHA1-6 : angle 1.80075 ( 9) link_BETA1-4 : bond 0.00245 ( 16) link_BETA1-4 : angle 1.63409 ( 48) link_ALPHA1-3 : bond 0.01038 ( 3) link_ALPHA1-3 : angle 1.72669 ( 9) hydrogen bonds : bond 0.04472 ( 627) hydrogen bonds : angle 4.96415 ( 1845) SS BOND : bond 0.00378 ( 35) SS BOND : angle 1.64517 ( 70) covalent geometry : bond 0.00430 (16174) covalent geometry : angle 0.63904 (22001) *********************** 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 257 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9080 (ttm) cc_final: 0.8110 (tpp) REVERT: C 180 ASP cc_start: 0.8587 (m-30) cc_final: 0.8046 (m-30) REVERT: C 252 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8410 (mtmt) REVERT: D 542 ARG cc_start: 0.8864 (ttp-110) cc_final: 0.8425 (ttp80) REVERT: D 574 LYS cc_start: 0.9418 (mmtp) cc_final: 0.9140 (mmtm) REVERT: D 591 GLN cc_start: 0.8885 (tt0) cc_final: 0.8367 (tp40) REVERT: D 614 TRP cc_start: 0.6855 (m-10) cc_final: 0.6416 (m-10) REVERT: D 626 MET cc_start: 0.7118 (tpp) cc_final: 0.6773 (mtt) REVERT: D 647 GLU cc_start: 0.8413 (mp0) cc_final: 0.7929 (mp0) REVERT: A 104 MET cc_start: 0.8465 (tpp) cc_final: 0.7144 (tpp) REVERT: A 173 TYR cc_start: 0.8491 (p90) cc_final: 0.8107 (p90) REVERT: A 195 ASN cc_start: 0.8934 (p0) cc_final: 0.8664 (p0) REVERT: A 217 TYR cc_start: 0.8854 (m-80) cc_final: 0.7714 (m-80) REVERT: A 426 MET cc_start: 0.7049 (ttm) cc_final: 0.6734 (ttp) REVERT: A 484 TYR cc_start: 0.9222 (p90) cc_final: 0.8912 (p90) REVERT: B 542 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8037 (ttt90) REVERT: B 565 LEU cc_start: 0.8505 (mt) cc_final: 0.7988 (tt) REVERT: B 648 GLU cc_start: 0.8290 (tp30) cc_final: 0.8078 (tp30) REVERT: B 655 LYS cc_start: 0.8383 (tptp) cc_final: 0.8075 (tptm) REVERT: E 414 ILE cc_start: 0.9490 (mm) cc_final: 0.9036 (tp) REVERT: E 426 MET cc_start: 0.6942 (ttm) cc_final: 0.6404 (ttt) REVERT: F 603 ILE cc_start: 0.8390 (pt) cc_final: 0.7743 (tt) REVERT: F 626 MET cc_start: 0.6505 (ttm) cc_final: 0.6016 (ttm) REVERT: F 642 ILE cc_start: 0.9459 (pt) cc_final: 0.9201 (pt) REVERT: F 653 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8690 (tm-30) REVERT: F 654 GLU cc_start: 0.8967 (tp30) cc_final: 0.8600 (tp30) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2969 time to fit residues: 112.7632 Evaluate side-chains 199 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.097116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081156 restraints weight = 44793.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.083061 restraints weight = 28119.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.084378 restraints weight = 20437.930| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5716 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= 0.129 Angle : 0.627 11.391 22311 Z= 0.308 Chirality : 0.045 0.309 2774 Planarity : 0.004 0.050 2718 Dihedral : 6.181 59.081 3716 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1709 helix: 1.56 (0.25), residues: 453 sheet: 0.32 (0.24), residues: 443 loop : -0.43 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 610 HIS 0.009 0.001 HIS C 72 PHE 0.015 0.001 PHE C 383 TYR 0.024 0.001 TYR D 638 ARG 0.009 0.001 ARG D 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 58) link_NAG-ASN : angle 2.36766 ( 174) link_ALPHA1-6 : bond 0.00806 ( 3) link_ALPHA1-6 : angle 1.62333 ( 9) link_BETA1-4 : bond 0.00284 ( 16) link_BETA1-4 : angle 1.47148 ( 48) link_ALPHA1-3 : bond 0.01217 ( 3) link_ALPHA1-3 : angle 1.44136 ( 9) hydrogen bonds : bond 0.04112 ( 627) hydrogen bonds : angle 4.78978 ( 1845) SS BOND : bond 0.00256 ( 35) SS BOND : angle 1.40170 ( 70) covalent geometry : bond 0.00289 (16174) covalent geometry : angle 0.58385 (22001) ********************** 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 263 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.628 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: 0.9036 (ttm) cc_final: 0.8038 (tpp) REVERT: C 180 ASP cc_start: 0.8467 (m-30) cc_final: 0.7975 (m-30) REVERT: C 252 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8384 (mtmt) REVERT: C 500 ARG cc_start: 0.2465 (ptt-90) cc_final: 0.1971 (ptt-90) REVERT: D 542 ARG cc_start: 0.8828 (ttp-110) cc_final: 0.8377 (ttp80) REVERT: D 574 LYS cc_start: 0.9371 (mmtp) cc_final: 0.9120 (mmtm) REVERT: D 591 GLN cc_start: 0.8871 (tt0) cc_final: 0.8149 (tp40) REVERT: D 631 TRP cc_start: 0.8920 (t-100) cc_final: 0.8677 (t-100) REVERT: A 104 MET cc_start: 0.8383 (tpp) cc_final: 0.6952 (tpp) REVERT: A 173 TYR cc_start: 0.8434 (p90) cc_final: 0.8131 (p90) REVERT: A 195 ASN cc_start: 0.8866 (p0) cc_final: 0.8568 (p0) REVERT: A 217 TYR cc_start: 0.8832 (m-80) cc_final: 0.7381 (m-80) REVERT: A 484 TYR cc_start: 0.9186 (p90) cc_final: 0.8842 (p90) REVERT: B 538 THR cc_start: 0.9459 (p) cc_final: 0.9217 (p) REVERT: B 542 ARG cc_start: 0.8350 (ttp80) cc_final: 0.7912 (ttt180) REVERT: B 565 LEU cc_start: 0.8459 (mt) cc_final: 0.7969 (tt) REVERT: B 647 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7384 (mt-10) REVERT: B 655 LYS cc_start: 0.8254 (tptp) cc_final: 0.7966 (tptm) REVERT: E 162 THR cc_start: 0.8990 (p) cc_final: 0.8722 (p) REVERT: E 414 ILE cc_start: 0.9477 (mm) cc_final: 0.9028 (tp) REVERT: E 426 MET cc_start: 0.6765 (ttm) cc_final: 0.6315 (ttt) REVERT: F 577 GLN cc_start: 0.8325 (tp40) cc_final: 0.7904 (tm-30) REVERT: F 603 ILE cc_start: 0.8369 (pt) cc_final: 0.7716 (tt) REVERT: F 626 MET cc_start: 0.6427 (ttm) cc_final: 0.6037 (ttm) REVERT: F 642 ILE cc_start: 0.9446 (pt) cc_final: 0.9188 (pt) REVERT: F 648 GLU cc_start: 0.7980 (tp30) cc_final: 0.7764 (tp30) REVERT: F 653 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8659 (tm-30) REVERT: F 654 GLU cc_start: 0.8954 (tp30) cc_final: 0.8585 (tp30) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2746 time to fit residues: 107.4674 Evaluate side-chains 212 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 8.9990 chunk 141 optimal weight: 0.0170 chunk 130 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN A 85 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.079619 restraints weight = 45255.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081449 restraints weight = 28921.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082699 restraints weight = 21307.741| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16289 Z= 0.191 Angle : 0.679 12.265 22311 Z= 0.332 Chirality : 0.046 0.347 2774 Planarity : 0.004 0.051 2718 Dihedral : 6.371 57.502 3716 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1709 helix: 1.72 (0.25), residues: 440 sheet: 0.19 (0.24), residues: 459 loop : -0.46 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP D 614 HIS 0.010 0.001 HIS C 72 PHE 0.021 0.002 PHE A 53 TYR 0.022 0.002 TYR D 638 ARG 0.006 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 58) link_NAG-ASN : angle 2.51627 ( 174) link_ALPHA1-6 : bond 0.00823 ( 3) link_ALPHA1-6 : angle 1.75360 ( 9) link_BETA1-4 : bond 0.00240 ( 16) link_BETA1-4 : angle 1.59388 ( 48) link_ALPHA1-3 : bond 0.01026 ( 3) link_ALPHA1-3 : angle 1.68514 ( 9) hydrogen bonds : bond 0.04292 ( 627) hydrogen bonds : angle 4.83185 ( 1845) SS BOND : bond 0.00390 ( 35) SS BOND : angle 1.39527 ( 70) covalent geometry : bond 0.00436 (16174) covalent geometry : angle 0.63460 (22001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4942.35 seconds wall clock time: 87 minutes 23.89 seconds (5243.89 seconds total)