Starting phenix.real_space_refine on Tue May 20 22:20:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sav_40281/05_2025/8sav_40281_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sav_40281/05_2025/8sav_40281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sav_40281/05_2025/8sav_40281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sav_40281/05_2025/8sav_40281.map" model { file = "/net/cci-nas-00/data/ceres_data/8sav_40281/05_2025/8sav_40281_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sav_40281/05_2025/8sav_40281_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 138 5.16 5 C 12771 2.51 5 N 3528 2.21 5 O 4014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20451 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "B" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "F" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "J" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "Z" 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: "A" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.86, per 1000 atoms: 0.63 Number of scatterers: 20451 At special positions: 0 Unit cell: (142.844, 149.24, 121.524, 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 138 16.00 O 4014 8.00 N 3528 7.00 C 12771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 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=2.03 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 G 32 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 601 " - " ASN A 138 " " NAG A 602 " - " ASN A 392 " " NAG E 601 " - " ASN E 138 " " NAG E 602 " - " ASN E 392 " " NAG I 601 " - " ASN I 138 " " NAG I 602 " - " ASN I 392 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 396 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 156 " " NAG U 1 " - " ASN E 262 " " NAG V 1 " - " ASN E 396 " " NAG W 1 " - " ASN I 386 " " NAG X 1 " - " ASN I 332 " " NAG Y 1 " - " ASN I 156 " " NAG Z 1 " - " ASN I 262 " " NAG a 1 " - " ASN I 396 " Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 2.6 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4638 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 20.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.500A pdb=" N THR A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.841A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 536 through 544 Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.882A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.106A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.506A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.974A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 461 through 464 removed outlier: 3.664A pdb=" N LYS E 463 " --> pdb=" O ASN E 461 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 464 " --> pdb=" O SER E 461l" (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 461 through 464' Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.508A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.833A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 4.333A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.512A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 4.026A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.725A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.616A pdb=" N PHE H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 353 removed outlier: 3.582A pdb=" N HIS I 352 " --> pdb=" O GLU I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 461 through 464 removed outlier: 3.532A pdb=" N LYS I 463 " --> pdb=" O ASN I 461 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR I 464 " --> pdb=" O SER I 461l" (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 461 through 464' Processing helix chain 'I' and resid 474 through 484 removed outlier: 3.542A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 544 Processing helix chain 'J' and resid 570 through 596 removed outlier: 3.889A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 625 removed outlier: 4.246A pdb=" N ASP J 624 " --> pdb=" O SER J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 removed outlier: 4.384A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 3.735A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU J 647 " --> pdb=" O TYR J 643 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.666A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.510A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.442A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.046A 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 46 removed outlier: 3.619A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.807A pdb=" N ARG A 192 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.516A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 360 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.064A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 421 removed outlier: 3.849A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 309 removed outlier: 6.125A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.536A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET C 18 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 82 " --> pdb=" O MET C 18 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 68 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.695A pdb=" N GLN C 10 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 109 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP C 36 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN C 58 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.803A pdb=" N THR D 5 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.551A pdb=" N VAL D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN D 89 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.548A pdb=" N GLN D 90 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.313A pdb=" N TRP E 35 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.616A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.804A pdb=" N ARG E 192 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.623A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 360 through 361 Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.065A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 421 removed outlier: 3.815A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 301 through 309 removed outlier: 6.237A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 423 through 425 Processing sheet with id=AC6, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.754A pdb=" N MET G 18 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.625A pdb=" N GLN G 10 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN G 58 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 4 through 7 removed outlier: 4.216A pdb=" N ASP H 70 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'H' and resid 53 through 54 removed outlier: 5.849A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN H 89 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 494 through 499 removed outlier: 3.570A pdb=" N THR I 499 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP I 35 " --> pdb=" O THR I 499 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.618A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD5, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AD6, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.844A pdb=" N ARG I 192 " --> pdb=" O VAL I 182 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.271A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 259 through 261 removed outlier: 10.239A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 298 current: chain 'I' and resid 360 through 361 Processing sheet with id=AD9, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.039A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 443 through 456 current: chain 'I' and resid 413 through 421 removed outlier: 3.842A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 301 through 309 removed outlier: 6.070A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.560A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET K 18 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU K 82 " --> pdb=" O MET K 18 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.718A pdb=" N GLN K 10 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP K 36 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.283A pdb=" N ASP L 70 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.622A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.549A pdb=" N GLN L 90 " --> pdb=" O PHE L 97 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1788 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: 7.71 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6597 1.34 - 1.46: 4987 1.46 - 1.58: 9086 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 20856 Sorted by residual: bond pdb=" C TRP C 100B" pdb=" N ASP C 100C" ideal model delta sigma weight residual 1.333 1.375 -0.042 1.38e-02 5.25e+03 9.44e+00 bond pdb=" C TRP K 100B" pdb=" N ASP K 100C" ideal model delta sigma weight residual 1.333 1.367 -0.034 1.38e-02 5.25e+03 6.12e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 20851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 27552 2.49 - 4.99: 653 4.99 - 7.48: 73 7.48 - 9.98: 12 9.98 - 12.47: 6 Bond angle restraints: 28296 Sorted by residual: angle pdb=" C ASP G 100C" pdb=" N PHE G 100D" pdb=" CA PHE G 100D" ideal model delta sigma weight residual 121.70 134.17 -12.47 1.80e+00 3.09e-01 4.80e+01 angle pdb=" C ASP C 100C" pdb=" N PHE C 100D" pdb=" CA PHE C 100D" ideal model delta sigma weight residual 121.70 133.88 -12.18 1.80e+00 3.09e-01 4.58e+01 angle pdb=" C ASP K 100C" pdb=" N PHE K 100D" pdb=" CA PHE K 100D" ideal model delta sigma weight residual 121.70 133.20 -11.50 1.80e+00 3.09e-01 4.08e+01 angle pdb=" C THR A 460 " pdb=" N ASN A 461 " pdb=" CA ASN A 461 " ideal model delta sigma weight residual 121.70 132.14 -10.44 1.80e+00 3.09e-01 3.37e+01 angle pdb=" C THR E 460 " pdb=" N ASN E 461 " pdb=" CA ASN E 461 " ideal model delta sigma weight residual 121.70 131.99 -10.29 1.80e+00 3.09e-01 3.27e+01 ... (remaining 28291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 12304 21.99 - 43.98: 708 43.98 - 65.98: 105 65.98 - 87.97: 105 87.97 - 109.96: 50 Dihedral angle restraints: 13272 sinusoidal: 6048 harmonic: 7224 Sorted by residual: dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.62 -65.62 1 1.00e+01 1.00e-02 5.64e+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 93.00 158.23 -65.23 1 1.00e+01 1.00e-02 5.58e+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 93.00 157.99 -64.99 1 1.00e+01 1.00e-02 5.54e+01 ... (remaining 13269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2649 0.057 - 0.114: 491 0.114 - 0.172: 139 0.172 - 0.229: 8 0.229 - 0.286: 16 Chirality restraints: 3303 Sorted by residual: 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 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3300 not shown) Planarity restraints: 3591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 100D" -0.030 2.00e-02 2.50e+03 2.91e-02 1.48e+01 pdb=" CG PHE G 100D" 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE G 100D" -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE G 100D" -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE G 100D" 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 100D" -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE G 100D" -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 50 " 0.018 2.00e-02 2.50e+03 1.89e-02 8.89e+00 pdb=" CG TRP K 50 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP K 50 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP K 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP K 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 50 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 50 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP K 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 58 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO D 59 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " -0.035 5.00e-02 4.00e+02 ... (remaining 3588 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 160 2.58 - 3.16: 17230 3.16 - 3.74: 29491 3.74 - 4.32: 41034 4.32 - 4.90: 69523 Nonbonded interactions: 157438 Sorted by model distance: nonbonded pdb=" O ASP G 100C" pdb=" OH TYR H 36 " model vdw 2.003 3.040 nonbonded pdb=" O ASP K 100C" pdb=" OH TYR L 36 " model vdw 2.042 3.040 nonbonded pdb=" O ASP C 100C" pdb=" OH TYR D 36 " model vdw 2.044 3.040 nonbonded pdb=" O ASN A 461 " pdb=" OG1 THR A 464 " model vdw 2.108 3.040 nonbonded pdb=" OD1 ASN A 461 " pdb=" OG1 THR A 464 " model vdw 2.192 3.040 ... (remaining 157433 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 48.450 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.150 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.005 0.047 20952 Z= 0.248 Angle : 0.967 18.118 28542 Z= 0.500 Chirality : 0.053 0.286 3303 Planarity : 0.005 0.064 3570 Dihedral : 17.297 109.962 8508 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.58 % Favored : 93.18 % Rotamer: Outliers : 0.14 % Allowed : 0.09 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2478 helix: 0.26 (0.25), residues: 411 sheet: -0.74 (0.18), residues: 759 loop : -1.63 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP K 50 HIS 0.004 0.001 HIS E 249 PHE 0.067 0.002 PHE G 100D TYR 0.025 0.002 TYR L 91 ARG 0.010 0.001 ARG E 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 21) link_NAG-ASN : angle 3.17126 ( 63) link_ALPHA1-6 : bond 0.00624 ( 3) link_ALPHA1-6 : angle 1.53177 ( 9) link_BETA1-4 : bond 0.01252 ( 27) link_BETA1-4 : angle 5.01465 ( 81) link_ALPHA1-3 : bond 0.01185 ( 3) link_ALPHA1-3 : angle 3.00139 ( 9) hydrogen bonds : bond 0.21827 ( 657) hydrogen bonds : angle 8.70581 ( 1788) SS BOND : bond 0.00263 ( 42) SS BOND : angle 0.81822 ( 84) covalent geometry : bond 0.00507 (20856) covalent geometry : angle 0.91778 (28296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 2.536 Fit side-chains revert: symmetry clash REVERT: C 48 MET cc_start: 0.8084 (mtm) cc_final: 0.7766 (mtt) REVERT: E 434 MET cc_start: 0.7848 (ttp) cc_final: 0.7394 (mtm) REVERT: F 586 TYR cc_start: 0.9354 (t80) cc_final: 0.9124 (t80) REVERT: G 72 ASP cc_start: 0.8365 (t0) cc_final: 0.7965 (t0) REVERT: H 82 ASP cc_start: 0.6924 (m-30) cc_final: 0.6379 (m-30) REVERT: K 32 CYS cc_start: 0.5703 (t) cc_final: 0.5426 (t) outliers start: 3 outliers final: 0 residues processed: 200 average time/residue: 0.2837 time to fit residues: 92.1754 Evaluate side-chains 133 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 145 optimal weight: 0.3980 chunk 226 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 105 HIS E 72 HIS F 540 GLN F 658 GLN G 102 HIS I 72 HIS J 540 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.089421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076785 restraints weight = 68728.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078424 restraints weight = 53069.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078993 restraints weight = 39077.237| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20952 Z= 0.230 Angle : 0.863 15.180 28542 Z= 0.434 Chirality : 0.052 0.368 3303 Planarity : 0.005 0.055 3570 Dihedral : 13.820 85.539 3837 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.26 % Favored : 92.41 % Rotamer: Outliers : 1.01 % Allowed : 6.48 % Favored : 92.51 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2478 helix: 0.37 (0.26), residues: 399 sheet: -0.64 (0.19), residues: 681 loop : -1.76 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 571 HIS 0.004 0.001 HIS A 374 PHE 0.056 0.003 PHE G 100D TYR 0.032 0.002 TYR H 91 ARG 0.004 0.001 ARG I 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00935 ( 21) link_NAG-ASN : angle 4.41113 ( 63) link_ALPHA1-6 : bond 0.00793 ( 3) link_ALPHA1-6 : angle 1.59517 ( 9) link_BETA1-4 : bond 0.00816 ( 27) link_BETA1-4 : angle 3.25284 ( 81) link_ALPHA1-3 : bond 0.00845 ( 3) link_ALPHA1-3 : angle 2.07146 ( 9) hydrogen bonds : bond 0.05072 ( 657) hydrogen bonds : angle 6.28375 ( 1788) SS BOND : bond 0.00487 ( 42) SS BOND : angle 1.15457 ( 84) covalent geometry : bond 0.00520 (20856) covalent geometry : angle 0.81943 (28296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.7768 (mtm) cc_final: 0.7566 (mtt) REVERT: C 69 MET cc_start: 0.7548 (mtm) cc_final: 0.7256 (mtp) REVERT: E 434 MET cc_start: 0.8115 (ttp) cc_final: 0.7714 (ttp) REVERT: F 535 MET cc_start: 0.6079 (mpp) cc_final: 0.5739 (tpp) REVERT: G 72 ASP cc_start: 0.8354 (t0) cc_final: 0.8116 (t0) REVERT: I 434 MET cc_start: 0.7988 (ttp) cc_final: 0.7762 (ttp) REVERT: K 32 CYS cc_start: 0.6162 (t) cc_final: 0.5835 (t) outliers start: 22 outliers final: 14 residues processed: 154 average time/residue: 0.2595 time to fit residues: 68.1042 Evaluate side-chains 136 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 234 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 147 ASN H 90 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.090402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.077773 restraints weight = 67393.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.079231 restraints weight = 49747.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080267 restraints weight = 39442.645| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20952 Z= 0.162 Angle : 0.783 13.910 28542 Z= 0.390 Chirality : 0.050 0.469 3303 Planarity : 0.004 0.048 3570 Dihedral : 11.838 88.248 3837 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.01 % Favored : 93.66 % Rotamer: Outliers : 1.20 % Allowed : 9.24 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.16), residues: 2478 helix: 0.28 (0.25), residues: 429 sheet: -0.44 (0.19), residues: 684 loop : -1.71 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 100B HIS 0.005 0.001 HIS G 102 PHE 0.044 0.002 PHE G 100D TYR 0.025 0.002 TYR H 91 ARG 0.003 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00864 ( 21) link_NAG-ASN : angle 4.25028 ( 63) link_ALPHA1-6 : bond 0.00689 ( 3) link_ALPHA1-6 : angle 1.60247 ( 9) link_BETA1-4 : bond 0.00909 ( 27) link_BETA1-4 : angle 3.16408 ( 81) link_ALPHA1-3 : bond 0.01203 ( 3) link_ALPHA1-3 : angle 1.38405 ( 9) hydrogen bonds : bond 0.04292 ( 657) hydrogen bonds : angle 5.64881 ( 1788) SS BOND : bond 0.00308 ( 42) SS BOND : angle 0.86890 ( 84) covalent geometry : bond 0.00355 (20856) covalent geometry : angle 0.73902 (28296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 11 MET cc_start: 0.7016 (tpp) cc_final: 0.6738 (tpt) REVERT: C 50 TRP cc_start: 0.5415 (m100) cc_final: 0.5194 (m100) REVERT: C 110 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8376 (tt) REVERT: E 369 MET cc_start: 0.7649 (ttm) cc_final: 0.7059 (ttm) REVERT: E 434 MET cc_start: 0.8188 (ttp) cc_final: 0.7762 (ttp) REVERT: F 530 MET cc_start: 0.6417 (mtm) cc_final: 0.5738 (mtm) REVERT: F 535 MET cc_start: 0.6053 (mpp) cc_final: 0.5770 (tpp) REVERT: G 72 ASP cc_start: 0.8322 (t0) cc_final: 0.8068 (t0) REVERT: J 535 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6632 (mmp) REVERT: K 32 CYS cc_start: 0.6019 (t) cc_final: 0.5683 (t) outliers start: 26 outliers final: 19 residues processed: 154 average time/residue: 0.2862 time to fit residues: 75.0687 Evaluate side-chains 141 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN I 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.089862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077075 restraints weight = 68667.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.078093 restraints weight = 52452.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079248 restraints weight = 41299.570| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20952 Z= 0.167 Angle : 0.755 13.941 28542 Z= 0.378 Chirality : 0.049 0.467 3303 Planarity : 0.004 0.048 3570 Dihedral : 10.320 85.922 3837 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.62 % Favored : 93.06 % Rotamer: Outliers : 1.93 % Allowed : 10.80 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2478 helix: 0.59 (0.26), residues: 393 sheet: -0.50 (0.19), residues: 693 loop : -1.77 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 100B HIS 0.005 0.001 HIS G 102 PHE 0.045 0.002 PHE G 100D TYR 0.027 0.002 TYR H 91 ARG 0.003 0.000 ARG D 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00882 ( 21) link_NAG-ASN : angle 4.02894 ( 63) link_ALPHA1-6 : bond 0.00802 ( 3) link_ALPHA1-6 : angle 1.63458 ( 9) link_BETA1-4 : bond 0.00869 ( 27) link_BETA1-4 : angle 3.02821 ( 81) link_ALPHA1-3 : bond 0.01079 ( 3) link_ALPHA1-3 : angle 1.96537 ( 9) hydrogen bonds : bond 0.03910 ( 657) hydrogen bonds : angle 5.37547 ( 1788) SS BOND : bond 0.00347 ( 42) SS BOND : angle 0.82808 ( 84) covalent geometry : bond 0.00371 (20856) covalent geometry : angle 0.71348 (28296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8284 (p) cc_final: 0.8021 (t) REVERT: B 535 MET cc_start: 0.6738 (mpp) cc_final: 0.6494 (mmp) REVERT: B 586 TYR cc_start: 0.9207 (t80) cc_final: 0.8962 (t80) REVERT: C 11 MET cc_start: 0.6974 (tpp) cc_final: 0.6539 (tpt) REVERT: E 188 THR cc_start: 0.8178 (p) cc_final: 0.7955 (t) REVERT: E 369 MET cc_start: 0.7731 (ttm) cc_final: 0.7119 (ttm) REVERT: E 434 MET cc_start: 0.8382 (ttp) cc_final: 0.7807 (ttp) REVERT: F 535 MET cc_start: 0.6435 (mpp) cc_final: 0.6142 (mpp) REVERT: G 72 ASP cc_start: 0.8263 (t0) cc_final: 0.8043 (t0) REVERT: I 188 THR cc_start: 0.8150 (p) cc_final: 0.7876 (t) REVERT: J 535 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6760 (mmp) REVERT: K 32 CYS cc_start: 0.5980 (t) cc_final: 0.5686 (t) outliers start: 42 outliers final: 29 residues processed: 169 average time/residue: 0.2604 time to fit residues: 74.4213 Evaluate side-chains 153 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 chunk 189 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN E 287 HIS ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.091933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079483 restraints weight = 67712.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.080698 restraints weight = 50128.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.081781 restraints weight = 38337.987| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20952 Z= 0.124 Angle : 0.705 13.008 28542 Z= 0.351 Chirality : 0.047 0.394 3303 Planarity : 0.004 0.047 3570 Dihedral : 9.412 78.129 3837 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.45 % Favored : 94.31 % Rotamer: Outliers : 1.52 % Allowed : 11.63 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2478 helix: 0.47 (0.25), residues: 429 sheet: -0.30 (0.19), residues: 681 loop : -1.60 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 50 HIS 0.004 0.001 HIS G 102 PHE 0.039 0.002 PHE G 100D TYR 0.019 0.001 TYR E 142 ARG 0.004 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00747 ( 21) link_NAG-ASN : angle 3.70124 ( 63) link_ALPHA1-6 : bond 0.00872 ( 3) link_ALPHA1-6 : angle 1.66170 ( 9) link_BETA1-4 : bond 0.00824 ( 27) link_BETA1-4 : angle 2.79795 ( 81) link_ALPHA1-3 : bond 0.01145 ( 3) link_ALPHA1-3 : angle 1.81509 ( 9) hydrogen bonds : bond 0.03402 ( 657) hydrogen bonds : angle 5.15235 ( 1788) SS BOND : bond 0.00257 ( 42) SS BOND : angle 0.65602 ( 84) covalent geometry : bond 0.00260 (20856) covalent geometry : angle 0.66676 (28296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 2.546 Fit side-chains REVERT: A 188 THR cc_start: 0.8215 (p) cc_final: 0.7989 (t) REVERT: A 426 MET cc_start: 0.7248 (tpt) cc_final: 0.6755 (tpt) REVERT: B 530 MET cc_start: 0.5966 (mtm) cc_final: 0.5475 (mtm) REVERT: B 535 MET cc_start: 0.6657 (mpp) cc_final: 0.6361 (mmp) REVERT: B 586 TYR cc_start: 0.9200 (t80) cc_final: 0.8991 (t80) REVERT: C 11 MET cc_start: 0.6964 (tpp) cc_final: 0.6576 (tpt) REVERT: C 16 GLU cc_start: 0.7197 (tt0) cc_final: 0.6833 (tt0) REVERT: E 369 MET cc_start: 0.7599 (ttm) cc_final: 0.7001 (ttm) REVERT: E 434 MET cc_start: 0.8361 (ttp) cc_final: 0.7921 (ttp) REVERT: F 535 MET cc_start: 0.6278 (mpp) cc_final: 0.5898 (mpp) REVERT: I 188 THR cc_start: 0.8029 (p) cc_final: 0.7785 (t) REVERT: J 530 MET cc_start: 0.5950 (mtm) cc_final: 0.5612 (mtm) REVERT: J 535 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6655 (mmp) REVERT: K 32 CYS cc_start: 0.5858 (t) cc_final: 0.5589 (t) outliers start: 33 outliers final: 27 residues processed: 161 average time/residue: 0.2772 time to fit residues: 74.5410 Evaluate side-chains 153 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 170 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 189 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 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 = 0.3763 r_free = 0.3763 target = 0.090538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.077867 restraints weight = 67871.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078876 restraints weight = 52164.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.079849 restraints weight = 40918.194| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20952 Z= 0.156 Angle : 0.717 13.320 28542 Z= 0.361 Chirality : 0.047 0.399 3303 Planarity : 0.004 0.047 3570 Dihedral : 9.121 71.294 3837 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.42 % Favored : 93.34 % Rotamer: Outliers : 2.16 % Allowed : 12.00 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2478 helix: 0.72 (0.26), residues: 411 sheet: -0.40 (0.19), residues: 693 loop : -1.59 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP K 50 HIS 0.004 0.001 HIS G 102 PHE 0.035 0.002 PHE G 100D TYR 0.019 0.001 TYR D 91 ARG 0.003 0.000 ARG E 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 21) link_NAG-ASN : angle 3.70763 ( 63) link_ALPHA1-6 : bond 0.00897 ( 3) link_ALPHA1-6 : angle 1.52519 ( 9) link_BETA1-4 : bond 0.00861 ( 27) link_BETA1-4 : angle 2.75504 ( 81) link_ALPHA1-3 : bond 0.01084 ( 3) link_ALPHA1-3 : angle 2.10691 ( 9) hydrogen bonds : bond 0.03567 ( 657) hydrogen bonds : angle 5.10022 ( 1788) SS BOND : bond 0.00295 ( 42) SS BOND : angle 0.71869 ( 84) covalent geometry : bond 0.00347 (20856) covalent geometry : angle 0.67973 (28296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 2.303 Fit side-chains REVERT: A 188 THR cc_start: 0.8207 (p) cc_final: 0.7980 (t) REVERT: A 443 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8821 (tp) REVERT: B 530 MET cc_start: 0.6422 (mtm) cc_final: 0.5923 (mtm) REVERT: C 11 MET cc_start: 0.6993 (tpp) cc_final: 0.6572 (tpt) REVERT: C 16 GLU cc_start: 0.7203 (tt0) cc_final: 0.6818 (tt0) REVERT: C 50 TRP cc_start: 0.5477 (m100) cc_final: 0.5130 (m100) REVERT: E 188 THR cc_start: 0.8148 (p) cc_final: 0.7928 (t) REVERT: E 369 MET cc_start: 0.7603 (ttm) cc_final: 0.7016 (ttm) REVERT: F 535 MET cc_start: 0.6627 (mpp) cc_final: 0.6301 (mpp) REVERT: I 188 THR cc_start: 0.8184 (p) cc_final: 0.7917 (t) REVERT: I 443 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8791 (tp) REVERT: J 535 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6902 (mmp) REVERT: K 32 CYS cc_start: 0.5821 (t) cc_final: 0.5563 (t) outliers start: 47 outliers final: 36 residues processed: 162 average time/residue: 0.2609 time to fit residues: 71.8782 Evaluate side-chains 159 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 95 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 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 = 0.3728 r_free = 0.3728 target = 0.088807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076421 restraints weight = 68267.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077284 restraints weight = 56284.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078035 restraints weight = 44412.133| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20952 Z= 0.200 Angle : 0.762 13.003 28542 Z= 0.385 Chirality : 0.049 0.400 3303 Planarity : 0.005 0.061 3570 Dihedral : 9.104 64.395 3837 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.98 % Favored : 92.70 % Rotamer: Outliers : 2.48 % Allowed : 12.32 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2478 helix: 0.60 (0.26), residues: 411 sheet: -0.50 (0.19), residues: 696 loop : -1.73 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 100B HIS 0.008 0.001 HIS K 102 PHE 0.036 0.002 PHE G 100D TYR 0.023 0.002 TYR H 91 ARG 0.003 0.000 ARG E 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00831 ( 21) link_NAG-ASN : angle 3.78290 ( 63) link_ALPHA1-6 : bond 0.00987 ( 3) link_ALPHA1-6 : angle 1.29894 ( 9) link_BETA1-4 : bond 0.00901 ( 27) link_BETA1-4 : angle 2.76240 ( 81) link_ALPHA1-3 : bond 0.01088 ( 3) link_ALPHA1-3 : angle 2.22225 ( 9) hydrogen bonds : bond 0.03934 ( 657) hydrogen bonds : angle 5.19386 ( 1788) SS BOND : bond 0.00335 ( 42) SS BOND : angle 0.84096 ( 84) covalent geometry : bond 0.00455 (20856) covalent geometry : angle 0.72602 (28296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 2.555 Fit side-chains REVERT: A 188 THR cc_start: 0.8332 (p) cc_final: 0.8106 (t) REVERT: A 443 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8824 (tp) REVERT: B 535 MET cc_start: 0.7440 (mmp) cc_final: 0.7234 (mmp) REVERT: C 11 MET cc_start: 0.7061 (tpp) cc_final: 0.6812 (tpt) REVERT: C 16 GLU cc_start: 0.7323 (tt0) cc_final: 0.6919 (tt0) REVERT: C 50 TRP cc_start: 0.5720 (m100) cc_final: 0.5346 (m100) REVERT: E 188 THR cc_start: 0.8021 (p) cc_final: 0.7808 (t) REVERT: E 369 MET cc_start: 0.7631 (ttm) cc_final: 0.7027 (ttm) REVERT: F 530 MET cc_start: 0.6766 (mtm) cc_final: 0.6053 (mtm) REVERT: F 535 MET cc_start: 0.7002 (mpp) cc_final: 0.6692 (mpp) REVERT: I 188 THR cc_start: 0.8268 (p) cc_final: 0.8014 (t) REVERT: I 290 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9036 (t) REVERT: J 535 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7296 (mmp) outliers start: 54 outliers final: 44 residues processed: 172 average time/residue: 0.2685 time to fit residues: 79.7065 Evaluate side-chains 165 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 610 TRP Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 143 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 227 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 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 = 0.3771 r_free = 0.3771 target = 0.090976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.078846 restraints weight = 67950.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080078 restraints weight = 50365.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.080981 restraints weight = 37983.080| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20952 Z= 0.127 Angle : 0.699 12.908 28542 Z= 0.351 Chirality : 0.046 0.396 3303 Planarity : 0.004 0.047 3570 Dihedral : 8.661 59.919 3837 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.61 % Favored : 94.19 % Rotamer: Outliers : 1.89 % Allowed : 13.38 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2478 helix: 0.61 (0.25), residues: 429 sheet: -0.23 (0.19), residues: 681 loop : -1.63 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP G 50 HIS 0.005 0.001 HIS K 102 PHE 0.033 0.002 PHE G 100D TYR 0.018 0.001 TYR E 142 ARG 0.004 0.000 ARG J 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 21) link_NAG-ASN : angle 3.55904 ( 63) link_ALPHA1-6 : bond 0.01075 ( 3) link_ALPHA1-6 : angle 1.21638 ( 9) link_BETA1-4 : bond 0.00822 ( 27) link_BETA1-4 : angle 2.61572 ( 81) link_ALPHA1-3 : bond 0.01085 ( 3) link_ALPHA1-3 : angle 1.88754 ( 9) hydrogen bonds : bond 0.03341 ( 657) hydrogen bonds : angle 5.02119 ( 1788) SS BOND : bond 0.00271 ( 42) SS BOND : angle 0.64470 ( 84) covalent geometry : bond 0.00271 (20856) covalent geometry : angle 0.66514 (28296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 2.385 Fit side-chains REVERT: A 100 MET cc_start: 0.7481 (mtm) cc_final: 0.7071 (mtm) REVERT: A 188 THR cc_start: 0.8200 (p) cc_final: 0.7970 (t) REVERT: A 434 MET cc_start: 0.7275 (ttp) cc_final: 0.7007 (mtp) REVERT: B 530 MET cc_start: 0.6338 (mtm) cc_final: 0.5889 (mtm) REVERT: C 11 MET cc_start: 0.6981 (tpp) cc_final: 0.6642 (tpt) REVERT: C 16 GLU cc_start: 0.7178 (tt0) cc_final: 0.6745 (tt0) REVERT: C 50 TRP cc_start: 0.5416 (m100) cc_final: 0.5013 (m100) REVERT: C 110 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7576 (tt) REVERT: E 369 MET cc_start: 0.7602 (ttm) cc_final: 0.7038 (ttm) REVERT: E 434 MET cc_start: 0.8357 (ttp) cc_final: 0.8099 (mtm) REVERT: F 530 MET cc_start: 0.6611 (mtm) cc_final: 0.5870 (mtm) REVERT: F 535 MET cc_start: 0.6722 (mpp) cc_final: 0.6411 (mpp) REVERT: I 188 THR cc_start: 0.8158 (p) cc_final: 0.7934 (t) REVERT: I 290 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.9012 (t) REVERT: I 508 ARG cc_start: 0.4117 (OUTLIER) cc_final: 0.3894 (ttm-80) REVERT: J 535 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6810 (mmp) outliers start: 41 outliers final: 27 residues processed: 160 average time/residue: 0.2613 time to fit residues: 71.5171 Evaluate side-chains 150 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 128 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 200 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 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 = 0.3702 r_free = 0.3702 target = 0.087457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074846 restraints weight = 69142.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075662 restraints weight = 57004.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076457 restraints weight = 45723.676| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20952 Z= 0.254 Angle : 0.821 13.336 28542 Z= 0.416 Chirality : 0.050 0.403 3303 Planarity : 0.005 0.050 3570 Dihedral : 9.071 59.638 3837 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.64 % Favored : 91.04 % Rotamer: Outliers : 2.48 % Allowed : 13.56 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.16), residues: 2478 helix: 0.42 (0.25), residues: 411 sheet: -0.44 (0.19), residues: 732 loop : -1.91 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 50 HIS 0.007 0.002 HIS E 374 PHE 0.037 0.003 PHE G 100D TYR 0.024 0.002 TYR H 91 ARG 0.004 0.001 ARG K 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 21) link_NAG-ASN : angle 3.85014 ( 63) link_ALPHA1-6 : bond 0.01063 ( 3) link_ALPHA1-6 : angle 1.09502 ( 9) link_BETA1-4 : bond 0.01018 ( 27) link_BETA1-4 : angle 2.79794 ( 81) link_ALPHA1-3 : bond 0.00997 ( 3) link_ALPHA1-3 : angle 2.40175 ( 9) hydrogen bonds : bond 0.04280 ( 657) hydrogen bonds : angle 5.28208 ( 1788) SS BOND : bond 0.00402 ( 42) SS BOND : angle 1.01554 ( 84) covalent geometry : bond 0.00585 (20856) covalent geometry : angle 0.78658 (28296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 2.383 Fit side-chains REVERT: A 188 THR cc_start: 0.8379 (p) cc_final: 0.8176 (t) REVERT: A 443 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8808 (tp) REVERT: B 530 MET cc_start: 0.6723 (mtm) cc_final: 0.6304 (mtm) REVERT: C 10 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7196 (pt0) REVERT: C 11 MET cc_start: 0.7199 (tpp) cc_final: 0.6889 (tpt) REVERT: C 16 GLU cc_start: 0.7524 (tt0) cc_final: 0.7148 (tt0) REVERT: C 50 TRP cc_start: 0.5828 (m100) cc_final: 0.5569 (m100) REVERT: D 71 TYR cc_start: 0.5572 (t80) cc_final: 0.4883 (t80) REVERT: E 434 MET cc_start: 0.8620 (ttp) cc_final: 0.8342 (ttp) REVERT: F 530 MET cc_start: 0.6921 (mtm) cc_final: 0.6183 (mtm) REVERT: F 535 MET cc_start: 0.7268 (mpp) cc_final: 0.7009 (mpp) REVERT: I 188 THR cc_start: 0.8325 (p) cc_final: 0.8054 (t) REVERT: I 290 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9073 (t) REVERT: J 530 MET cc_start: 0.6480 (mtm) cc_final: 0.6021 (mtm) REVERT: J 535 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7486 (mmp) outliers start: 54 outliers final: 39 residues processed: 159 average time/residue: 0.2675 time to fit residues: 72.8883 Evaluate side-chains 157 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 610 TRP Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 222 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 117 optimal weight: 0.0070 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.090874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078471 restraints weight = 67578.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.079577 restraints weight = 51573.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.080490 restraints weight = 40227.817| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20952 Z= 0.126 Angle : 0.707 12.788 28542 Z= 0.354 Chirality : 0.047 0.394 3303 Planarity : 0.004 0.048 3570 Dihedral : 8.522 58.970 3837 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.57 % Favored : 94.23 % Rotamer: Outliers : 1.56 % Allowed : 14.44 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 2478 helix: 0.58 (0.25), residues: 429 sheet: -0.21 (0.20), residues: 681 loop : -1.67 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP G 50 HIS 0.005 0.001 HIS G 102 PHE 0.035 0.001 PHE G 100D TYR 0.018 0.001 TYR E 142 ARG 0.004 0.000 ARG A 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 21) link_NAG-ASN : angle 3.53612 ( 63) link_ALPHA1-6 : bond 0.01140 ( 3) link_ALPHA1-6 : angle 1.01333 ( 9) link_BETA1-4 : bond 0.00842 ( 27) link_BETA1-4 : angle 2.59505 ( 81) link_ALPHA1-3 : bond 0.00996 ( 3) link_ALPHA1-3 : angle 1.72674 ( 9) hydrogen bonds : bond 0.03331 ( 657) hydrogen bonds : angle 5.01664 ( 1788) SS BOND : bond 0.00255 ( 42) SS BOND : angle 0.74332 ( 84) covalent geometry : bond 0.00261 (20856) covalent geometry : angle 0.67389 (28296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 2.536 Fit side-chains REVERT: A 100 MET cc_start: 0.7393 (mtm) cc_final: 0.6991 (mtm) REVERT: A 434 MET cc_start: 0.7418 (ttp) cc_final: 0.7052 (mtp) REVERT: B 530 MET cc_start: 0.6689 (mtm) cc_final: 0.6264 (mtm) REVERT: C 11 MET cc_start: 0.6930 (tpp) cc_final: 0.6669 (tpt) REVERT: C 16 GLU cc_start: 0.7440 (tt0) cc_final: 0.7013 (tt0) REVERT: C 50 TRP cc_start: 0.5482 (m100) cc_final: 0.5197 (m100) REVERT: C 110 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7663 (tt) REVERT: D 71 TYR cc_start: 0.5673 (t80) cc_final: 0.5180 (t80) REVERT: E 369 MET cc_start: 0.7542 (ttm) cc_final: 0.6986 (ttm) REVERT: F 530 MET cc_start: 0.6727 (mtm) cc_final: 0.6032 (mtm) REVERT: F 535 MET cc_start: 0.6971 (mpp) cc_final: 0.6747 (mpp) REVERT: I 188 THR cc_start: 0.8254 (p) cc_final: 0.8040 (t) REVERT: I 290 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.9015 (t) REVERT: J 530 MET cc_start: 0.6284 (mtm) cc_final: 0.5712 (mtm) REVERT: J 535 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6813 (mmp) outliers start: 34 outliers final: 28 residues processed: 148 average time/residue: 0.2666 time to fit residues: 67.1922 Evaluate side-chains 147 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 231 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 216 optimal weight: 0.5980 chunk 188 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 196 optimal weight: 0.1980 chunk 186 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 229 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.092265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.080701 restraints weight = 67719.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.081681 restraints weight = 53658.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081994 restraints weight = 44039.657| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20952 Z= 0.119 Angle : 0.679 13.118 28542 Z= 0.340 Chirality : 0.045 0.388 3303 Planarity : 0.004 0.046 3570 Dihedral : 8.076 59.337 3837 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.73 % Favored : 94.11 % Rotamer: Outliers : 1.24 % Allowed : 14.94 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2478 helix: 0.81 (0.26), residues: 429 sheet: -0.12 (0.19), residues: 690 loop : -1.52 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP G 50 HIS 0.004 0.001 HIS A 72 PHE 0.027 0.001 PHE G 100D TYR 0.016 0.001 TYR E 142 ARG 0.004 0.000 ARG A 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00749 ( 21) link_NAG-ASN : angle 3.48026 ( 63) link_ALPHA1-6 : bond 0.01116 ( 3) link_ALPHA1-6 : angle 1.05243 ( 9) link_BETA1-4 : bond 0.00836 ( 27) link_BETA1-4 : angle 2.54574 ( 81) link_ALPHA1-3 : bond 0.00918 ( 3) link_ALPHA1-3 : angle 1.64449 ( 9) hydrogen bonds : bond 0.02972 ( 657) hydrogen bonds : angle 4.84622 ( 1788) SS BOND : bond 0.00241 ( 42) SS BOND : angle 0.65217 ( 84) covalent geometry : bond 0.00244 (20856) covalent geometry : angle 0.64592 (28296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4681.41 seconds wall clock time: 84 minutes 7.75 seconds (5047.75 seconds total)