Starting phenix.real_space_refine on Sun Aug 24 12:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tq1_41498/08_2025/8tq1_41498.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tq1_41498/08_2025/8tq1_41498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tq1_41498/08_2025/8tq1_41498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tq1_41498/08_2025/8tq1_41498.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tq1_41498/08_2025/8tq1_41498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tq1_41498/08_2025/8tq1_41498.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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 132 5.16 5 C 12387 2.51 5 N 3316 2.21 5 O 3953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19788 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3414 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "J" Number of atoms: 3422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3422 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "K" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3421 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 966 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 304 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "L" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 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: 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: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: "J" 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: "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: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 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 Time building chain proxies: 4.46, per 1000 atoms: 0.23 Number of scatterers: 19788 At special positions: 0 Unit cell: (125.4, 120.175, 164.065, 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 132 16.00 O 3953 8.00 N 3316 7.00 C 12387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=1.48 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.06 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.20 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 109 " - pdb=" SG CYS H 119 " distance=2.03 Simple disulfide: pdb=" SG CYS H 115 " - pdb=" SG CYS H 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 120 " - pdb=" SG CYS H 131 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 5 " " BMA U 3 " - " MAN U 5 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 355 " " NAG A 609 " - " ASN A 363 " " NAG A 610 " - " ASN A 392 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 448 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 355 " " NAG E 609 " - " ASN E 363 " " NAG E 610 " - " ASN E 392 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 386 " " NAG E 613 " - " ASN E 448 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 133 " " NAG J 603 " - " ASN J 234 " " NAG J 604 " - " ASN J 276 " " NAG J 605 " - " ASN J 295 " " NAG J 606 " - " ASN J 301 " " NAG J 607 " - " ASN J 332 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 355 " " NAG J 610 " - " ASN J 392 " " NAG J 611 " - " ASN J 197 " " NAG J 612 " - " ASN J 386 " " NAG J 613 " - " ASN J 363 " " NAG J 614 " - " ASN J 448 " " NAG K 701 " - " ASN K 611 " " NAG K 702 " - " ASN K 637 " " NAG L 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 197 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN J 160 " " NAG T 1 " - " ASN J 156 " " NAG U 1 " - " ASN J 262 " " NAG V 1 " - " ASN E 160 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 262 " " NAG Y 1 " - " ASN E 332 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 792.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 45 sheets defined 21.6% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.919A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.850A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.559A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.433A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.562A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 95B removed outlier: 4.342A pdb=" N THR D 95A" --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 117 removed outlier: 4.027A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 126 Processing helix chain 'J' and resid 139 through 151 Processing helix chain 'J' and resid 195 through 198 Processing helix chain 'J' and resid 334 through 354 removed outlier: 3.906A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 387 through 390 Processing helix chain 'J' and resid 475 through 484 Processing helix chain 'K' and resid 523 through 528 removed outlier: 4.383A pdb=" N GLY K 527 " --> pdb=" O GLY K 524 " (cutoff:3.500A) Processing helix chain 'K' and resid 536 through 542 Processing helix chain 'K' and resid 569 through 596 Processing helix chain 'K' and resid 618 through 625 Processing helix chain 'K' and resid 627 through 635 Processing helix chain 'K' and resid 638 through 659 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.582A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.194A 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 139 through 151 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.903A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 480 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 570 through 571 No H-bonds generated for 'chain 'F' and resid 570 through 571' Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.515A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 660 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.390A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.989A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR A 236 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N GLU A 92 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR A 90 " --> pdb=" O PRO A 238 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN A 88 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.644A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.602A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.903A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.955A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.985A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.934A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.326A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 13 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.363A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR J 40 " --> pdb=" O CYS K 604 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N CYS K 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.791A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 75 through 76 removed outlier: 6.557A pdb=" N CYS J 54 " --> pdb=" O VAL J 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'J' and resid 200 through 203 removed outlier: 6.627A pdb=" N ALA J 200 " --> pdb=" O ALA J 433 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N TYR J 435 " --> pdb=" O ALA J 200 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 259 through 261 removed outlier: 3.623A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY J 451 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N THR J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N ILE J 453 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 11.924A pdb=" N PHE J 288 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA J 329 " --> pdb=" O CYS J 418 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 271 through 274 removed outlier: 10.521A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 11.924A pdb=" N PHE J 288 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N ILE J 453 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N THR J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY J 451 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE J 358 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE J 468 " --> pdb=" O ILE J 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 304 through 312 removed outlier: 6.344A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 3 through 8 Processing sheet with id=AC7, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.723A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.723A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.583A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.583A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.205A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.870A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.913A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD8, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.573A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 259 through 261 removed outlier: 10.433A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.684A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 307 through 312 removed outlier: 6.410A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.578A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.578A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.330A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 9 through 13 removed outlier: 5.279A pdb=" N PHE I 95B" --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'H' and resid 113 through 115 808 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3613 1.33 - 1.46: 6925 1.46 - 1.59: 9461 1.59 - 1.72: 0 1.72 - 1.85: 180 Bond restraints: 20179 Sorted by residual: bond pdb=" C LYS E 502 " pdb=" O LYS E 502 " ideal model delta sigma weight residual 1.235 1.195 0.039 1.18e-02 7.18e+03 1.11e+01 bond pdb=" C3 BMA U 3 " pdb=" O3 BMA U 3 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.55e+00 bond pdb=" N CYS J 74 " pdb=" CA CYS J 74 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.31e-02 5.83e+03 7.84e+00 bond pdb=" N CYS A 74 " pdb=" CA CYS A 74 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.11e+00 bond pdb=" N LYS J 502 " pdb=" CA LYS J 502 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.83e+00 ... (remaining 20174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 25942 2.40 - 4.80: 1251 4.80 - 7.19: 160 7.19 - 9.59: 18 9.59 - 11.99: 5 Bond angle restraints: 27376 Sorted by residual: angle pdb=" N GLY G 8 " pdb=" CA GLY G 8 " pdb=" C GLY G 8 " ideal model delta sigma weight residual 112.73 120.42 -7.69 1.20e+00 6.94e-01 4.11e+01 angle pdb=" CA PRO E 206 " pdb=" N PRO E 206 " pdb=" CD PRO E 206 " ideal model delta sigma weight residual 112.00 103.90 8.10 1.40e+00 5.10e-01 3.35e+01 angle pdb=" CA PHE A 53 " pdb=" CB PHE A 53 " pdb=" CG PHE A 53 " ideal model delta sigma weight residual 113.80 119.36 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" C LEU A 52 " pdb=" N PHE A 53 " pdb=" CA PHE A 53 " ideal model delta sigma weight residual 122.73 113.52 9.21 1.92e+00 2.71e-01 2.30e+01 angle pdb=" CA THR J 499 " pdb=" C THR J 499 " pdb=" O THR J 499 " ideal model delta sigma weight residual 121.33 116.25 5.08 1.08e+00 8.57e-01 2.21e+01 ... (remaining 27371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 12453 21.58 - 43.16: 431 43.16 - 64.74: 116 64.74 - 86.32: 45 86.32 - 107.91: 26 Dihedral angle restraints: 13071 sinusoidal: 6199 harmonic: 6872 Sorted by residual: dihedral pdb=" CB CYS J 126 " pdb=" SG CYS J 126 " pdb=" SG CYS J 196 " pdb=" CB CYS J 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.31 -67.31 1 1.00e+01 1.00e-02 5.90e+01 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 93.00 153.76 -60.76 1 1.00e+01 1.00e-02 4.91e+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 93.00 149.48 -56.48 1 1.00e+01 1.00e-02 4.30e+01 ... (remaining 13068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2525 0.071 - 0.141: 639 0.141 - 0.212: 109 0.212 - 0.282: 8 0.282 - 0.353: 8 Chirality restraints: 3289 Sorted by residual: chirality pdb=" C1 NAG E 613 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG E 613 " pdb=" O5 NAG E 613 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB ILE H 117 " pdb=" CA ILE H 117 " pdb=" CG1 ILE H 117 " pdb=" CG2 ILE H 117 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 3286 not shown) Planarity restraints: 3441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 504 " 0.597 9.50e-02 1.11e+02 2.68e-01 4.37e+01 pdb=" NE ARG J 504 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG J 504 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG J 504 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 504 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS E 205 " -0.087 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO E 206 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO E 206 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 206 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 582 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ALA F 582 " 0.075 2.00e-02 2.50e+03 pdb=" O ALA F 582 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL F 583 " -0.025 2.00e-02 2.50e+03 ... (remaining 3438 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 363 2.67 - 3.22: 17872 3.22 - 3.78: 29998 3.78 - 4.34: 42522 4.34 - 4.90: 69363 Nonbonded interactions: 160118 Sorted by model distance: nonbonded pdb=" O GLY C 96 " pdb=" OH TYR D 96 " model vdw 2.108 3.040 nonbonded pdb=" NE2 GLN D 17 " pdb=" O SER D 18 " model vdw 2.139 3.120 nonbonded pdb=" NH1 ARG A 178 " pdb=" O VAL A 181 " model vdw 2.244 3.120 nonbonded pdb=" O PHE C 29 " pdb=" NH2 ARG C 71 " model vdw 2.256 3.120 nonbonded pdb=" O PHE G 29 " pdb=" NH2 ARG G 71 " model vdw 2.279 3.120 ... (remaining 160113 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 185 or resid 189 through 612)) selection = (chain 'E' and (resid 33 through 457 or resid 464 through 503 or resid 602 throu \ gh 613)) selection = (chain 'J' and (resid 33 through 503 or resid 603 through 614)) } ncs_group { reference = (chain 'B' and (resid 520 through 545 or resid 570 through 702)) selection = chain 'F' selection = (chain 'K' and (resid 520 through 545 or resid 570 through 702)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.540 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.008 0.547 20299 Z= 0.390 Angle : 1.220 30.833 27695 Z= 0.673 Chirality : 0.065 0.353 3289 Planarity : 0.009 0.268 3384 Dihedral : 13.271 107.905 8538 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.24 % Allowed : 4.95 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.17), residues: 2344 helix: 0.66 (0.25), residues: 386 sheet: 0.72 (0.19), residues: 677 loop : 0.65 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG A 500 TYR 0.027 0.003 TYR I 49 PHE 0.031 0.003 PHE A 53 TRP 0.033 0.003 TRP A 479 HIS 0.009 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00716 (20179) covalent geometry : angle 1.17210 (27376) SS BOND : bond 0.08953 ( 41) SS BOND : angle 4.38661 ( 82) hydrogen bonds : bond 0.14654 ( 750) hydrogen bonds : angle 7.53961 ( 2082) link_ALPHA1-3 : bond 0.00642 ( 4) link_ALPHA1-3 : angle 2.71976 ( 12) link_ALPHA1-6 : bond 0.00944 ( 2) link_ALPHA1-6 : angle 0.84569 ( 6) link_BETA1-4 : bond 0.00678 ( 16) link_BETA1-4 : angle 3.66502 ( 48) link_NAG-ASN : bond 0.00359 ( 57) link_NAG-ASN : angle 2.77283 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 365 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8317 (m-80) cc_final: 0.8032 (m-80) REVERT: B 588 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8357 (mtt-85) REVERT: J 114 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7988 (mm-40) REVERT: J 320 THR cc_start: 0.9422 (m) cc_final: 0.9032 (p) REVERT: J 426 MET cc_start: 0.8512 (tpp) cc_final: 0.8212 (mmm) REVERT: K 581 LEU cc_start: 0.8980 (tp) cc_final: 0.8727 (tp) REVERT: K 601 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8650 (mtpt) REVERT: K 636 SER cc_start: 0.9126 (t) cc_final: 0.8808 (p) REVERT: E 217 TYR cc_start: 0.8743 (m-80) cc_final: 0.8364 (m-80) REVERT: E 371 VAL cc_start: 0.9345 (t) cc_final: 0.9107 (p) REVERT: F 601 LYS cc_start: 0.8988 (mttp) cc_final: 0.8783 (mtmm) REVERT: G 66 ARG cc_start: 0.7305 (ptp-170) cc_final: 0.5589 (mtm180) REVERT: G 68 THR cc_start: 0.9139 (m) cc_final: 0.8896 (p) REVERT: I 30 TYR cc_start: 0.8959 (m-80) cc_final: 0.8748 (m-80) REVERT: I 45 LYS cc_start: 0.8720 (tttt) cc_final: 0.8500 (tttt) outliers start: 5 outliers final: 2 residues processed: 367 average time/residue: 0.1333 time to fit residues: 71.7653 Evaluate side-chains 269 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 267 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain E residue 502 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82AHIS J 130 GLN K 607 ASN K 630 GLN ** M 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN F 625 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075619 restraints weight = 39237.187| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.54 r_work: 0.2910 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20299 Z= 0.200 Angle : 0.693 10.905 27695 Z= 0.356 Chirality : 0.048 0.288 3289 Planarity : 0.004 0.052 3384 Dihedral : 8.701 83.836 4215 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.44 % Allowed : 7.21 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.17), residues: 2344 helix: 1.54 (0.26), residues: 405 sheet: 0.50 (0.19), residues: 741 loop : 0.34 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 66 TYR 0.019 0.002 TYR E 318 PHE 0.015 0.002 PHE D 98 TRP 0.026 0.002 TRP A 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00456 (20179) covalent geometry : angle 0.65900 (27376) SS BOND : bond 0.00349 ( 41) SS BOND : angle 1.32421 ( 82) hydrogen bonds : bond 0.04993 ( 750) hydrogen bonds : angle 5.71565 ( 2082) link_ALPHA1-3 : bond 0.00510 ( 4) link_ALPHA1-3 : angle 4.04169 ( 12) link_ALPHA1-6 : bond 0.01060 ( 2) link_ALPHA1-6 : angle 1.53971 ( 6) link_BETA1-4 : bond 0.00635 ( 16) link_BETA1-4 : angle 2.48667 ( 48) link_NAG-ASN : bond 0.00272 ( 57) link_NAG-ASN : angle 2.09909 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 588 ARG cc_start: 0.8858 (mtm110) cc_final: 0.8374 (mtt-85) REVERT: J 141 ASP cc_start: 0.8138 (m-30) cc_final: 0.7891 (t0) REVERT: K 542 ARG cc_start: 0.8669 (mtm110) cc_final: 0.8412 (mtm110) REVERT: K 636 SER cc_start: 0.9231 (t) cc_final: 0.8895 (p) REVERT: M 3 GLN cc_start: 0.8348 (mm-40) cc_final: 0.8124 (mm110) REVERT: M 72 ASP cc_start: 0.8247 (t0) cc_final: 0.8005 (t0) REVERT: M 91 TYR cc_start: 0.8994 (m-80) cc_final: 0.8785 (m-80) REVERT: N 79 GLN cc_start: 0.8085 (mt0) cc_final: 0.7782 (mp10) REVERT: F 632 ASP cc_start: 0.9115 (t0) cc_final: 0.8837 (t0) REVERT: F 648 GLU cc_start: 0.8430 (tp30) cc_final: 0.8002 (tp30) REVERT: G 75 LYS cc_start: 0.9183 (mptt) cc_final: 0.8947 (mmtm) outliers start: 30 outliers final: 19 residues processed: 316 average time/residue: 0.1565 time to fit residues: 72.9423 Evaluate side-chains 282 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain I residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 212 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075658 restraints weight = 39741.975| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.51 r_work: 0.2904 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20299 Z= 0.163 Angle : 0.615 10.213 27695 Z= 0.312 Chirality : 0.046 0.295 3289 Planarity : 0.004 0.045 3384 Dihedral : 7.587 72.587 4208 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.68 % Allowed : 7.98 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.17), residues: 2344 helix: 1.62 (0.27), residues: 412 sheet: 0.47 (0.19), residues: 751 loop : 0.16 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 166 TYR 0.019 0.001 TYR G 27 PHE 0.014 0.002 PHE A 53 TRP 0.019 0.001 TRP A 479 HIS 0.005 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00374 (20179) covalent geometry : angle 0.58465 (27376) SS BOND : bond 0.00428 ( 41) SS BOND : angle 1.23949 ( 82) hydrogen bonds : bond 0.04210 ( 750) hydrogen bonds : angle 5.26762 ( 2082) link_ALPHA1-3 : bond 0.00533 ( 4) link_ALPHA1-3 : angle 3.67693 ( 12) link_ALPHA1-6 : bond 0.01122 ( 2) link_ALPHA1-6 : angle 1.23544 ( 6) link_BETA1-4 : bond 0.00515 ( 16) link_BETA1-4 : angle 2.24835 ( 48) link_NAG-ASN : bond 0.00213 ( 57) link_NAG-ASN : angle 1.85958 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 292 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.9274 (tpp) cc_final: 0.8236 (tpt) REVERT: A 381 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 588 ARG cc_start: 0.8845 (mtm110) cc_final: 0.8363 (mtt-85) REVERT: J 114 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8075 (mm-40) REVERT: J 141 ASP cc_start: 0.8046 (m-30) cc_final: 0.7818 (t0) REVERT: K 636 SER cc_start: 0.9221 (t) cc_final: 0.8898 (p) REVERT: N 32 TYR cc_start: 0.9133 (m-80) cc_final: 0.8789 (m-80) REVERT: N 42 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8569 (tptp) REVERT: E 217 TYR cc_start: 0.8962 (m-80) cc_final: 0.8267 (m-80) REVERT: F 648 GLU cc_start: 0.8519 (tp30) cc_final: 0.8097 (tp30) REVERT: G 83 ARG cc_start: 0.7406 (ptp-170) cc_final: 0.7101 (ptp-170) REVERT: H 129 TYR cc_start: 0.7954 (m-80) cc_final: 0.7663 (m-80) outliers start: 35 outliers final: 28 residues processed: 315 average time/residue: 0.1541 time to fit residues: 71.6487 Evaluate side-chains 293 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 111 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN D 31 ASN ** M 81 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 = 0.3396 r_free = 0.3396 target = 0.095605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074447 restraints weight = 39687.306| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.55 r_work: 0.2882 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20299 Z= 0.159 Angle : 0.590 9.448 27695 Z= 0.296 Chirality : 0.045 0.319 3289 Planarity : 0.004 0.035 3384 Dihedral : 6.727 59.087 4208 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.12 % Allowed : 8.89 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.17), residues: 2344 helix: 1.67 (0.27), residues: 412 sheet: 0.50 (0.19), residues: 725 loop : 0.02 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 542 TYR 0.018 0.001 TYR J 173 PHE 0.013 0.002 PHE A 383 TRP 0.014 0.001 TRP A 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00369 (20179) covalent geometry : angle 0.56111 (27376) SS BOND : bond 0.00356 ( 41) SS BOND : angle 1.16969 ( 82) hydrogen bonds : bond 0.03856 ( 750) hydrogen bonds : angle 5.00703 ( 2082) link_ALPHA1-3 : bond 0.00574 ( 4) link_ALPHA1-3 : angle 3.81752 ( 12) link_ALPHA1-6 : bond 0.01497 ( 2) link_ALPHA1-6 : angle 1.18428 ( 6) link_BETA1-4 : bond 0.00447 ( 16) link_BETA1-4 : angle 2.08755 ( 48) link_NAG-ASN : bond 0.00201 ( 57) link_NAG-ASN : angle 1.74142 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: B 588 ARG cc_start: 0.8882 (mtm110) cc_final: 0.8366 (mtt-85) REVERT: D 79 GLN cc_start: 0.7760 (mp10) cc_final: 0.7032 (mp10) REVERT: J 78 ASP cc_start: 0.6750 (t0) cc_final: 0.6538 (p0) REVERT: J 114 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8061 (mm-40) REVERT: J 141 ASP cc_start: 0.8010 (m-30) cc_final: 0.7761 (t0) REVERT: J 150 MET cc_start: 0.8745 (mmm) cc_final: 0.8315 (tpp) REVERT: K 581 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8607 (tp) REVERT: K 621 GLU cc_start: 0.8271 (tt0) cc_final: 0.7914 (mt-10) REVERT: K 636 SER cc_start: 0.9252 (t) cc_final: 0.8921 (p) REVERT: N 32 TYR cc_start: 0.9138 (m-80) cc_final: 0.8752 (m-80) REVERT: N 42 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8666 (tptp) REVERT: E 217 TYR cc_start: 0.9024 (m-80) cc_final: 0.8280 (m-80) REVERT: G 52 ASN cc_start: 0.8311 (t0) cc_final: 0.7979 (t0) REVERT: G 89 VAL cc_start: 0.8864 (t) cc_final: 0.8576 (p) REVERT: I 95 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7839 (mp10) outliers start: 44 outliers final: 31 residues processed: 312 average time/residue: 0.1530 time to fit residues: 71.0616 Evaluate side-chains 300 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 221 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074187 restraints weight = 39415.899| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.54 r_work: 0.2883 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20299 Z= 0.136 Angle : 0.564 9.491 27695 Z= 0.282 Chirality : 0.045 0.329 3289 Planarity : 0.004 0.036 3384 Dihedral : 6.192 56.433 4208 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.12 % Allowed : 9.57 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2344 helix: 1.64 (0.27), residues: 416 sheet: 0.63 (0.20), residues: 698 loop : -0.08 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 542 TYR 0.019 0.001 TYR G 27 PHE 0.013 0.001 PHE A 383 TRP 0.016 0.001 TRP E 479 HIS 0.004 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00311 (20179) covalent geometry : angle 0.53734 (27376) SS BOND : bond 0.00333 ( 41) SS BOND : angle 0.94577 ( 82) hydrogen bonds : bond 0.03670 ( 750) hydrogen bonds : angle 4.88980 ( 2082) link_ALPHA1-3 : bond 0.00635 ( 4) link_ALPHA1-3 : angle 3.77671 ( 12) link_ALPHA1-6 : bond 0.01597 ( 2) link_ALPHA1-6 : angle 1.60338 ( 6) link_BETA1-4 : bond 0.00442 ( 16) link_BETA1-4 : angle 2.00225 ( 48) link_NAG-ASN : bond 0.00189 ( 57) link_NAG-ASN : angle 1.65305 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: B 588 ARG cc_start: 0.8895 (mtm110) cc_final: 0.8372 (mtt-85) REVERT: D 79 GLN cc_start: 0.7726 (mp10) cc_final: 0.7078 (mp10) REVERT: J 114 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8098 (mm-40) REVERT: J 150 MET cc_start: 0.8716 (mmm) cc_final: 0.8300 (tpp) REVERT: K 581 LEU cc_start: 0.8968 (tp) cc_final: 0.8606 (tp) REVERT: K 621 GLU cc_start: 0.8297 (tt0) cc_final: 0.7953 (mt-10) REVERT: K 636 SER cc_start: 0.9235 (t) cc_final: 0.8915 (p) REVERT: N 32 TYR cc_start: 0.9136 (m-80) cc_final: 0.8789 (m-80) REVERT: N 42 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8666 (tptp) REVERT: N 83 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: E 217 TYR cc_start: 0.9022 (m-80) cc_final: 0.8294 (m-80) REVERT: F 648 GLU cc_start: 0.8412 (tp30) cc_final: 0.8028 (tp30) REVERT: G 75 LYS cc_start: 0.9103 (mmtp) cc_final: 0.8888 (mttm) REVERT: H 113 GLU cc_start: 0.7841 (tt0) cc_final: 0.7452 (tt0) outliers start: 44 outliers final: 36 residues processed: 314 average time/residue: 0.1557 time to fit residues: 72.0512 Evaluate side-chains 308 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 61 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 37 optimal weight: 0.0030 chunk 177 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82AHIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.075490 restraints weight = 39337.318| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.46 r_work: 0.2892 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20299 Z= 0.114 Angle : 0.547 9.510 27695 Z= 0.273 Chirality : 0.044 0.330 3289 Planarity : 0.003 0.046 3384 Dihedral : 5.813 56.432 4208 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.97 % Allowed : 10.10 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.17), residues: 2344 helix: 1.75 (0.27), residues: 416 sheet: 0.64 (0.20), residues: 706 loop : -0.07 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 542 TYR 0.017 0.001 TYR G 27 PHE 0.012 0.001 PHE A 383 TRP 0.014 0.001 TRP E 479 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00258 (20179) covalent geometry : angle 0.52037 (27376) SS BOND : bond 0.00299 ( 41) SS BOND : angle 0.87102 ( 82) hydrogen bonds : bond 0.03462 ( 750) hydrogen bonds : angle 4.76912 ( 2082) link_ALPHA1-3 : bond 0.00660 ( 4) link_ALPHA1-3 : angle 3.69709 ( 12) link_ALPHA1-6 : bond 0.01558 ( 2) link_ALPHA1-6 : angle 1.89603 ( 6) link_BETA1-4 : bond 0.00438 ( 16) link_BETA1-4 : angle 1.95521 ( 48) link_NAG-ASN : bond 0.00192 ( 57) link_NAG-ASN : angle 1.59642 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.8860 (m) cc_final: 0.8513 (p) REVERT: B 571 TRP cc_start: 0.7433 (m100) cc_final: 0.7206 (m-10) REVERT: B 588 ARG cc_start: 0.8857 (mtm110) cc_final: 0.8344 (mtt-85) REVERT: D 79 GLN cc_start: 0.7694 (mp10) cc_final: 0.7079 (mp10) REVERT: J 114 GLN cc_start: 0.8280 (mm-40) cc_final: 0.8055 (mm-40) REVERT: J 150 MET cc_start: 0.8710 (mmm) cc_final: 0.8334 (tpp) REVERT: K 581 LEU cc_start: 0.8948 (tp) cc_final: 0.8618 (tp) REVERT: K 617 ARG cc_start: 0.8805 (mtp85) cc_final: 0.8594 (mtp85) REVERT: K 636 SER cc_start: 0.9239 (t) cc_final: 0.8919 (p) REVERT: N 32 TYR cc_start: 0.9114 (m-80) cc_final: 0.8730 (m-80) REVERT: N 42 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8703 (tptp) REVERT: N 83 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6909 (mm-30) REVERT: N 94 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7318 (mtp180) REVERT: E 217 TYR cc_start: 0.9005 (m-80) cc_final: 0.8331 (m-80) REVERT: F 648 GLU cc_start: 0.8434 (tp30) cc_final: 0.7969 (tp30) REVERT: H 113 GLU cc_start: 0.7838 (tt0) cc_final: 0.7365 (tt0) outliers start: 41 outliers final: 32 residues processed: 311 average time/residue: 0.1483 time to fit residues: 68.3815 Evaluate side-chains 300 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 267 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 416 LEU Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 88 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 174 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.070693 restraints weight = 39838.938| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.51 r_work: 0.2813 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20299 Z= 0.269 Angle : 0.655 9.455 27695 Z= 0.327 Chirality : 0.047 0.312 3289 Planarity : 0.004 0.050 3384 Dihedral : 6.116 57.447 4208 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.31 % Allowed : 10.05 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.17), residues: 2344 helix: 1.37 (0.27), residues: 418 sheet: 0.51 (0.20), residues: 681 loop : -0.22 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 542 TYR 0.019 0.002 TYR D 49 PHE 0.018 0.002 PHE J 383 TRP 0.018 0.002 TRP E 479 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00634 (20179) covalent geometry : angle 0.62954 (27376) SS BOND : bond 0.00445 ( 41) SS BOND : angle 1.10194 ( 82) hydrogen bonds : bond 0.04344 ( 750) hydrogen bonds : angle 5.03665 ( 2082) link_ALPHA1-3 : bond 0.00594 ( 4) link_ALPHA1-3 : angle 3.55588 ( 12) link_ALPHA1-6 : bond 0.01340 ( 2) link_ALPHA1-6 : angle 1.88181 ( 6) link_BETA1-4 : bond 0.00401 ( 16) link_BETA1-4 : angle 2.08109 ( 48) link_NAG-ASN : bond 0.00302 ( 57) link_NAG-ASN : angle 1.77969 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: B 571 TRP cc_start: 0.7625 (m100) cc_final: 0.7395 (m-10) REVERT: B 588 ARG cc_start: 0.8922 (mtm110) cc_final: 0.8408 (mtt-85) REVERT: D 42 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8415 (mmmm) REVERT: J 320 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.9000 (p) REVERT: K 581 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8667 (tp) REVERT: K 636 SER cc_start: 0.9314 (t) cc_final: 0.8954 (p) REVERT: N 32 TYR cc_start: 0.9226 (m-80) cc_final: 0.8859 (m-80) REVERT: N 42 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8644 (tptp) REVERT: N 83 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: H 113 GLU cc_start: 0.7829 (tt0) cc_final: 0.7352 (tt0) outliers start: 48 outliers final: 39 residues processed: 282 average time/residue: 0.1497 time to fit residues: 63.1683 Evaluate side-chains 283 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 183 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.070738 restraints weight = 39532.131| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.52 r_work: 0.2812 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20299 Z= 0.240 Angle : 0.634 9.479 27695 Z= 0.316 Chirality : 0.046 0.309 3289 Planarity : 0.004 0.058 3384 Dihedral : 6.052 57.337 4208 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.36 % Allowed : 10.29 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.18), residues: 2344 helix: 1.40 (0.27), residues: 416 sheet: 0.42 (0.20), residues: 681 loop : -0.31 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 542 TYR 0.018 0.002 TYR D 49 PHE 0.015 0.002 PHE J 383 TRP 0.014 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00564 (20179) covalent geometry : angle 0.60839 (27376) SS BOND : bond 0.00461 ( 41) SS BOND : angle 1.05600 ( 82) hydrogen bonds : bond 0.04146 ( 750) hydrogen bonds : angle 5.01911 ( 2082) link_ALPHA1-3 : bond 0.00612 ( 4) link_ALPHA1-3 : angle 3.49509 ( 12) link_ALPHA1-6 : bond 0.01461 ( 2) link_ALPHA1-6 : angle 1.88151 ( 6) link_BETA1-4 : bond 0.00378 ( 16) link_BETA1-4 : angle 2.01683 ( 48) link_NAG-ASN : bond 0.00253 ( 57) link_NAG-ASN : angle 1.79132 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 0.590 Fit side-chains REVERT: A 426 MET cc_start: 0.9064 (mmm) cc_final: 0.8813 (mmm) REVERT: B 571 TRP cc_start: 0.7586 (m100) cc_final: 0.7363 (m-10) REVERT: B 588 ARG cc_start: 0.8942 (mtm110) cc_final: 0.8411 (mtt-85) REVERT: D 79 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: J 320 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.8991 (p) REVERT: K 581 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8682 (tp) REVERT: K 636 SER cc_start: 0.9282 (t) cc_final: 0.8896 (p) REVERT: N 32 TYR cc_start: 0.9233 (m-80) cc_final: 0.8855 (m-80) REVERT: N 42 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8659 (tptp) REVERT: N 83 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: F 648 GLU cc_start: 0.8369 (tp30) cc_final: 0.8022 (tp30) REVERT: G 83 ARG cc_start: 0.7260 (ptp-170) cc_final: 0.6952 (ptp-170) REVERT: H 113 GLU cc_start: 0.7863 (tt0) cc_final: 0.7434 (tt0) outliers start: 49 outliers final: 37 residues processed: 283 average time/residue: 0.1424 time to fit residues: 60.3380 Evaluate side-chains 280 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 123 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 78 optimal weight: 0.0970 chunk 137 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 422 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074272 restraints weight = 39298.058| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.45 r_work: 0.2868 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20299 Z= 0.116 Angle : 0.572 9.963 27695 Z= 0.284 Chirality : 0.044 0.293 3289 Planarity : 0.004 0.058 3384 Dihedral : 5.564 56.768 4208 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.78 % Allowed : 11.20 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.18), residues: 2344 helix: 1.76 (0.27), residues: 415 sheet: 0.54 (0.21), residues: 682 loop : -0.26 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 542 TYR 0.017 0.001 TYR G 27 PHE 0.011 0.001 PHE A 383 TRP 0.012 0.001 TRP A 479 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00261 (20179) covalent geometry : angle 0.54811 (27376) SS BOND : bond 0.00325 ( 41) SS BOND : angle 0.86864 ( 82) hydrogen bonds : bond 0.03511 ( 750) hydrogen bonds : angle 4.75341 ( 2082) link_ALPHA1-3 : bond 0.00732 ( 4) link_ALPHA1-3 : angle 3.40955 ( 12) link_ALPHA1-6 : bond 0.01449 ( 2) link_ALPHA1-6 : angle 1.75348 ( 6) link_BETA1-4 : bond 0.00399 ( 16) link_BETA1-4 : angle 1.88184 ( 48) link_NAG-ASN : bond 0.00199 ( 57) link_NAG-ASN : angle 1.63747 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 0.536 Fit side-chains REVERT: A 110 SER cc_start: 0.8913 (m) cc_final: 0.8554 (p) REVERT: A 166 ARG cc_start: 0.8561 (mtm180) cc_final: 0.8286 (mtm180) REVERT: B 588 ARG cc_start: 0.8890 (mtm110) cc_final: 0.8398 (mtt-85) REVERT: D 42 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8388 (mmmm) REVERT: D 79 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: J 114 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7677 (mm-40) REVERT: J 150 MET cc_start: 0.8000 (tpp) cc_final: 0.7745 (tpp) REVERT: K 581 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8622 (tp) REVERT: K 636 SER cc_start: 0.9309 (t) cc_final: 0.8957 (p) REVERT: M 68 THR cc_start: 0.9410 (m) cc_final: 0.9036 (p) REVERT: N 32 TYR cc_start: 0.9167 (m-80) cc_final: 0.8741 (m-80) REVERT: N 42 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8633 (tptp) REVERT: N 83 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: N 94 ARG cc_start: 0.7857 (ttm110) cc_final: 0.7594 (mtp180) REVERT: E 217 TYR cc_start: 0.9026 (m-80) cc_final: 0.8276 (m-80) REVERT: G 72 ASP cc_start: 0.8468 (t0) cc_final: 0.8263 (t0) REVERT: I 95 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7928 (mp10) REVERT: H 113 GLU cc_start: 0.7822 (tt0) cc_final: 0.7346 (tt0) outliers start: 37 outliers final: 31 residues processed: 291 average time/residue: 0.1515 time to fit residues: 65.7285 Evaluate side-chains 289 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 83 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 143 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN I 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071464 restraints weight = 39883.740| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.47 r_work: 0.2822 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20299 Z= 0.240 Angle : 0.646 10.268 27695 Z= 0.321 Chirality : 0.046 0.294 3289 Planarity : 0.004 0.069 3384 Dihedral : 5.838 57.471 4208 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.73 % Allowed : 11.44 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.18), residues: 2344 helix: 1.50 (0.27), residues: 418 sheet: 0.46 (0.21), residues: 676 loop : -0.35 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 542 TYR 0.017 0.002 TYR I 49 PHE 0.018 0.002 PHE J 383 TRP 0.022 0.001 TRP A 479 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00566 (20179) covalent geometry : angle 0.62253 (27376) SS BOND : bond 0.00441 ( 41) SS BOND : angle 1.03253 ( 82) hydrogen bonds : bond 0.04135 ( 750) hydrogen bonds : angle 4.94900 ( 2082) link_ALPHA1-3 : bond 0.00652 ( 4) link_ALPHA1-3 : angle 3.29245 ( 12) link_ALPHA1-6 : bond 0.01317 ( 2) link_ALPHA1-6 : angle 1.86311 ( 6) link_BETA1-4 : bond 0.00347 ( 16) link_BETA1-4 : angle 1.98930 ( 48) link_NAG-ASN : bond 0.00268 ( 57) link_NAG-ASN : angle 1.73640 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.631 Fit side-chains REVERT: A 426 MET cc_start: 0.9072 (mmm) cc_final: 0.8813 (mmm) REVERT: B 588 ARG cc_start: 0.8934 (mtm110) cc_final: 0.8398 (mtt-85) REVERT: C 75 LYS cc_start: 0.9091 (mttp) cc_final: 0.8887 (ptpp) REVERT: D 42 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8428 (mmmm) REVERT: J 320 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.8966 (p) REVERT: K 581 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8730 (tp) REVERT: K 636 SER cc_start: 0.9310 (t) cc_final: 0.8927 (p) REVERT: N 32 TYR cc_start: 0.9251 (m-80) cc_final: 0.8857 (m-80) REVERT: N 42 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8614 (tptp) REVERT: G 83 ARG cc_start: 0.7153 (ptp-170) cc_final: 0.6913 (ptp-170) REVERT: I 95 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7911 (mp10) REVERT: H 113 GLU cc_start: 0.7883 (tt0) cc_final: 0.7437 (tt0) outliers start: 36 outliers final: 31 residues processed: 264 average time/residue: 0.1486 time to fit residues: 59.0595 Evaluate side-chains 270 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 320 THR Chi-restraints excluded: chain J residue 505 VAL Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 599 SER Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain H residue 115 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 22 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.094191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.073366 restraints weight = 39608.177| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.45 r_work: 0.2864 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20299 Z= 0.141 Angle : 0.587 10.069 27695 Z= 0.292 Chirality : 0.044 0.292 3289 Planarity : 0.004 0.064 3384 Dihedral : 5.565 56.969 4208 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.68 % Allowed : 11.59 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.18), residues: 2344 helix: 1.72 (0.27), residues: 416 sheet: 0.50 (0.21), residues: 674 loop : -0.32 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 542 TYR 0.017 0.001 TYR G 27 PHE 0.012 0.001 PHE M 102 TRP 0.017 0.001 TRP A 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00327 (20179) covalent geometry : angle 0.56308 (27376) SS BOND : bond 0.00353 ( 41) SS BOND : angle 0.89723 ( 82) hydrogen bonds : bond 0.03653 ( 750) hydrogen bonds : angle 4.79355 ( 2082) link_ALPHA1-3 : bond 0.00747 ( 4) link_ALPHA1-3 : angle 3.29039 ( 12) link_ALPHA1-6 : bond 0.01478 ( 2) link_ALPHA1-6 : angle 1.71959 ( 6) link_BETA1-4 : bond 0.00382 ( 16) link_BETA1-4 : angle 1.87457 ( 48) link_NAG-ASN : bond 0.00183 ( 57) link_NAG-ASN : angle 1.66274 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4831.97 seconds wall clock time: 83 minutes 40.58 seconds (5020.58 seconds total)