Starting phenix.real_space_refine on Sun Aug 24 14:31:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sav_40281/08_2025/8sav_40281_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sav_40281/08_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_40281/08_2025/8sav_40281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sav_40281/08_2025/8sav_40281.map" model { file = "/net/cci-nas-00/data/ceres_data/8sav_40281/08_2025/8sav_40281_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sav_40281/08_2025/8sav_40281_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.70, per 1000 atoms: 0.23 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: 2.07 Conformation dependent library (CDL) restraints added in 802.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.92 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: 3.58 Time building geometry restraints manager: 2.68 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: 0.02 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: 0.010 Normalize map: mean=0, sd=1: 2.000 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.160 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.590 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.010 0.001 ARG E 508 TYR 0.025 0.002 TYR L 91 PHE 0.067 0.002 PHE G 100D TRP 0.049 0.002 TRP K 50 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00507 (20856) covalent geometry : angle 0.91778 (28296) SS BOND : bond 0.00263 ( 42) SS BOND : angle 0.81822 ( 84) hydrogen bonds : bond 0.21827 ( 657) hydrogen bonds : angle 8.70581 ( 1788) link_ALPHA1-3 : bond 0.01185 ( 3) link_ALPHA1-3 : angle 3.00139 ( 9) 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_NAG-ASN : bond 0.00742 ( 21) link_NAG-ASN : angle 3.17126 ( 63) *********************** 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 : 0.810 Fit side-chains revert: symmetry clash REVERT: C 48 MET cc_start: 0.8084 (mtm) cc_final: 0.7768 (mtt) REVERT: E 434 MET cc_start: 0.7848 (ttp) cc_final: 0.7326 (mtm) REVERT: F 586 TYR cc_start: 0.9354 (t80) cc_final: 0.9120 (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: 0.6378 (m-30) REVERT: K 32 CYS cc_start: 0.5703 (t) cc_final: 0.5422 (t) outliers start: 3 outliers final: 0 residues processed: 200 average time/residue: 0.1368 time to fit residues: 44.7138 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 : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS F 540 GLN G 102 HIS I 72 HIS J 540 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.091488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078926 restraints weight = 67854.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080304 restraints weight = 49889.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.081325 restraints weight = 39265.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.082036 restraints weight = 31560.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082211 restraints weight = 29348.376| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20952 Z= 0.172 Angle : 0.819 13.611 28542 Z= 0.410 Chirality : 0.051 0.421 3303 Planarity : 0.005 0.053 3570 Dihedral : 13.700 87.965 3837 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.50 % Favored : 93.26 % Rotamer: Outliers : 0.97 % Allowed : 5.79 % Favored : 93.24 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.16), residues: 2478 helix: 0.66 (0.26), residues: 381 sheet: -0.51 (0.19), residues: 681 loop : -1.69 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 273 TYR 0.028 0.002 TYR H 91 PHE 0.052 0.002 PHE G 100D TRP 0.031 0.002 TRP F 571 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00379 (20856) covalent geometry : angle 0.77517 (28296) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.05949 ( 84) hydrogen bonds : bond 0.04566 ( 657) hydrogen bonds : angle 6.16069 ( 1788) link_ALPHA1-3 : bond 0.00798 ( 3) link_ALPHA1-3 : angle 1.97400 ( 9) link_ALPHA1-6 : bond 0.00844 ( 3) link_ALPHA1-6 : angle 1.67385 ( 9) link_BETA1-4 : bond 0.00801 ( 27) link_BETA1-4 : angle 3.31322 ( 81) link_NAG-ASN : bond 0.00677 ( 21) link_NAG-ASN : angle 4.14171 ( 63) *********************** 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 167 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.7774 (mtm) cc_final: 0.7546 (mtt) REVERT: E 434 MET cc_start: 0.7924 (ttp) cc_final: 0.7216 (mtm) REVERT: G 72 ASP cc_start: 0.8302 (t0) cc_final: 0.8036 (t0) REVERT: I 188 THR cc_start: 0.8169 (p) cc_final: 0.7812 (t) REVERT: K 32 CYS cc_start: 0.6128 (t) cc_final: 0.5785 (t) outliers start: 21 outliers final: 12 residues processed: 160 average time/residue: 0.1342 time to fit residues: 36.0251 Evaluate side-chains 138 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 210 PHE Chi-restraints excluded: chain I residue 373 THR 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 78 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 157 optimal weight: 0.0020 chunk 75 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 147 ASN F 658 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 = 0.3751 r_free = 0.3751 target = 0.090123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077456 restraints weight = 68707.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.078965 restraints weight = 50564.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079777 restraints weight = 40408.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.080301 restraints weight = 32553.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.080559 restraints weight = 30434.976| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20952 Z= 0.182 Angle : 0.798 14.656 28542 Z= 0.398 Chirality : 0.050 0.473 3303 Planarity : 0.004 0.047 3570 Dihedral : 11.930 89.680 3837 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.78 % Favored : 92.86 % Rotamer: Outliers : 1.29 % Allowed : 8.87 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.16), residues: 2478 helix: 0.25 (0.25), residues: 429 sheet: -0.48 (0.19), residues: 693 loop : -1.65 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 273 TYR 0.028 0.002 TYR H 91 PHE 0.043 0.002 PHE G 100D TRP 0.036 0.002 TRP C 100B HIS 0.004 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00407 (20856) covalent geometry : angle 0.75315 (28296) SS BOND : bond 0.00339 ( 42) SS BOND : angle 0.92598 ( 84) hydrogen bonds : bond 0.04436 ( 657) hydrogen bonds : angle 5.69328 ( 1788) link_ALPHA1-3 : bond 0.01157 ( 3) link_ALPHA1-3 : angle 1.37068 ( 9) link_ALPHA1-6 : bond 0.00683 ( 3) link_ALPHA1-6 : angle 1.60647 ( 9) link_BETA1-4 : bond 0.01009 ( 27) link_BETA1-4 : angle 3.17955 ( 81) link_NAG-ASN : bond 0.00877 ( 21) link_NAG-ASN : angle 4.38303 ( 63) *********************** 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 163 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8062 (ttp) cc_final: 0.7716 (ttp) REVERT: B 586 TYR cc_start: 0.9220 (t80) cc_final: 0.9014 (t80) REVERT: E 369 MET cc_start: 0.7721 (ttm) cc_final: 0.7138 (ttm) REVERT: E 434 MET cc_start: 0.8195 (ttp) cc_final: 0.7690 (ttp) REVERT: F 535 MET cc_start: 0.6736 (mmt) cc_final: 0.6535 (mmp) REVERT: G 72 ASP cc_start: 0.8346 (t0) cc_final: 0.8136 (t0) REVERT: I 188 THR cc_start: 0.8128 (p) cc_final: 0.7833 (t) REVERT: K 32 CYS cc_start: 0.5969 (t) cc_final: 0.5644 (t) outliers start: 28 outliers final: 20 residues processed: 153 average time/residue: 0.1326 time to fit residues: 34.2335 Evaluate side-chains 138 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 PHE 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 C residue 10 GLN Chi-restraints excluded: chain E residue 122 LEU 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 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 122 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain K residue 100 TRP 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 51 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 123 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 H 90 GLN I 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.090183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.077404 restraints weight = 68281.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.078647 restraints weight = 52421.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.079605 restraints weight = 40192.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080269 restraints weight = 33549.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080398 restraints weight = 31510.809| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20952 Z= 0.167 Angle : 0.757 13.636 28542 Z= 0.379 Chirality : 0.049 0.478 3303 Planarity : 0.004 0.048 3570 Dihedral : 10.397 83.876 3837 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.30 % Favored : 93.34 % Rotamer: Outliers : 1.84 % Allowed : 10.34 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.16), residues: 2478 helix: 0.57 (0.26), residues: 393 sheet: -0.44 (0.19), residues: 693 loop : -1.75 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.022 0.002 TYR H 91 PHE 0.038 0.002 PHE C 100D TRP 0.035 0.002 TRP C 100B HIS 0.005 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00371 (20856) covalent geometry : angle 0.71492 (28296) SS BOND : bond 0.00318 ( 42) SS BOND : angle 0.81195 ( 84) hydrogen bonds : bond 0.03936 ( 657) hydrogen bonds : angle 5.43021 ( 1788) link_ALPHA1-3 : bond 0.01072 ( 3) link_ALPHA1-3 : angle 1.91509 ( 9) link_ALPHA1-6 : bond 0.00766 ( 3) link_ALPHA1-6 : angle 1.65381 ( 9) link_BETA1-4 : bond 0.00845 ( 27) link_BETA1-4 : angle 3.05147 ( 81) link_NAG-ASN : bond 0.00848 ( 21) link_NAG-ASN : angle 4.07030 ( 63) *********************** 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 173 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8241 (p) cc_final: 0.7962 (t) REVERT: B 535 MET cc_start: 0.6608 (mpp) cc_final: 0.6361 (mmp) REVERT: E 369 MET cc_start: 0.7726 (ttm) cc_final: 0.7157 (ttm) REVERT: E 434 MET cc_start: 0.8353 (ttp) cc_final: 0.7760 (ttp) REVERT: F 530 MET cc_start: 0.5669 (OUTLIER) cc_final: 0.5227 (mtt) REVERT: F 535 MET cc_start: 0.6805 (mmt) cc_final: 0.6600 (mmp) REVERT: G 72 ASP cc_start: 0.8293 (t0) cc_final: 0.8075 (t0) REVERT: I 188 THR cc_start: 0.8132 (p) cc_final: 0.7845 (t) REVERT: J 535 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6560 (mmp) REVERT: K 32 CYS cc_start: 0.5951 (t) cc_final: 0.5653 (t) outliers start: 40 outliers final: 26 residues processed: 164 average time/residue: 0.1189 time to fit residues: 33.2161 Evaluate side-chains 148 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 570 VAL 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 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 515 ILE Chi-restraints excluded: chain F residue 530 MET 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 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 K residue 5 VAL Chi-restraints excluded: chain K residue 100 TRP 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 135 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 107 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 247 optimal weight: 8.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS J 611 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.087587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075099 restraints weight = 68782.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075905 restraints weight = 58673.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.076585 restraints weight = 46554.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077546 restraints weight = 37221.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077604 restraints weight = 32546.950| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 20952 Z= 0.230 Angle : 0.816 14.135 28542 Z= 0.412 Chirality : 0.050 0.406 3303 Planarity : 0.005 0.048 3570 Dihedral : 9.903 80.579 3837 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.83 % Favored : 91.81 % Rotamer: Outliers : 2.34 % Allowed : 11.59 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.16), residues: 2478 helix: 0.20 (0.25), residues: 429 sheet: -0.54 (0.19), residues: 726 loop : -1.96 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.026 0.002 TYR H 91 PHE 0.038 0.003 PHE C 100D TRP 0.035 0.002 TRP F 571 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00525 (20856) covalent geometry : angle 0.77778 (28296) SS BOND : bond 0.00411 ( 42) SS BOND : angle 0.97361 ( 84) hydrogen bonds : bond 0.04355 ( 657) hydrogen bonds : angle 5.45284 ( 1788) link_ALPHA1-3 : bond 0.01111 ( 3) link_ALPHA1-3 : angle 2.12713 ( 9) link_ALPHA1-6 : bond 0.00826 ( 3) link_ALPHA1-6 : angle 1.53281 ( 9) link_BETA1-4 : bond 0.00984 ( 27) link_BETA1-4 : angle 2.97267 ( 81) link_NAG-ASN : bond 0.00883 ( 21) link_NAG-ASN : angle 4.02511 ( 63) *********************** 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 178 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8859 (tp) REVERT: B 530 MET cc_start: 0.6669 (mtm) cc_final: 0.6405 (mtm) REVERT: C 16 GLU cc_start: 0.7414 (tt0) cc_final: 0.7014 (tt0) REVERT: C 50 TRP cc_start: 0.5753 (m100) cc_final: 0.5399 (m100) REVERT: F 535 MET cc_start: 0.7000 (mmt) cc_final: 0.6670 (mmp) REVERT: I 188 THR cc_start: 0.8196 (p) cc_final: 0.7904 (t) REVERT: I 443 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8813 (tp) REVERT: J 535 MET cc_start: 0.7125 (mmp) cc_final: 0.6515 (mmp) REVERT: K 32 CYS cc_start: 0.5945 (t) cc_final: 0.5710 (t) outliers start: 51 outliers final: 37 residues processed: 170 average time/residue: 0.1231 time to fit residues: 35.6588 Evaluate side-chains 161 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 369 MET 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 584 GLU 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 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 373 THR Chi-restraints excluded: chain E residue 452 LEU 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 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 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 373 THR Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 484 TYR 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 6 GLN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 100 TRP 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 97 optimal weight: 5.9990 chunk 219 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 148 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 246 optimal weight: 8.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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** ** K 6 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 = 0.3757 r_free = 0.3757 target = 0.089407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076854 restraints weight = 66409.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078324 restraints weight = 46861.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079324 restraints weight = 36799.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.080030 restraints weight = 31091.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.080528 restraints weight = 27498.200| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20952 Z= 0.148 Angle : 0.734 13.319 28542 Z= 0.369 Chirality : 0.048 0.410 3303 Planarity : 0.004 0.049 3570 Dihedral : 9.429 74.845 3837 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.93 % Favored : 93.70 % Rotamer: Outliers : 2.25 % Allowed : 12.23 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.16), residues: 2478 helix: 0.53 (0.25), residues: 411 sheet: -0.53 (0.19), residues: 690 loop : -1.79 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 617 TYR 0.020 0.001 TYR H 91 PHE 0.033 0.002 PHE G 100D TRP 0.041 0.002 TRP G 50 HIS 0.006 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00325 (20856) covalent geometry : angle 0.69713 (28296) SS BOND : bond 0.00281 ( 42) SS BOND : angle 0.75041 ( 84) hydrogen bonds : bond 0.03731 ( 657) hydrogen bonds : angle 5.21313 ( 1788) link_ALPHA1-3 : bond 0.01111 ( 3) link_ALPHA1-3 : angle 2.00338 ( 9) link_ALPHA1-6 : bond 0.00885 ( 3) link_ALPHA1-6 : angle 1.54497 ( 9) link_BETA1-4 : bond 0.00855 ( 27) link_BETA1-4 : angle 2.77881 ( 81) link_NAG-ASN : bond 0.00781 ( 21) link_NAG-ASN : angle 3.74895 ( 63) *********************** 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 184 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.7950 (mmt) cc_final: 0.7699 (mmp) REVERT: A 188 THR cc_start: 0.8217 (p) cc_final: 0.7957 (t) REVERT: B 530 MET cc_start: 0.6541 (mtm) cc_final: 0.5962 (mtm) REVERT: B 586 TYR cc_start: 0.9205 (t80) cc_final: 0.8961 (t80) REVERT: C 16 GLU cc_start: 0.7158 (tt0) cc_final: 0.6796 (tt0) REVERT: C 50 TRP cc_start: 0.5481 (m100) cc_final: 0.5132 (m100) REVERT: E 188 THR cc_start: 0.7970 (p) cc_final: 0.7716 (t) REVERT: E 434 MET cc_start: 0.8530 (ttp) cc_final: 0.8039 (ttp) REVERT: I 188 THR cc_start: 0.8093 (p) cc_final: 0.7828 (t) REVERT: I 290 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8993 (t) REVERT: J 535 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6575 (mmp) REVERT: K 32 CYS cc_start: 0.5784 (t) cc_final: 0.5535 (t) outliers start: 49 outliers final: 36 residues processed: 176 average time/residue: 0.1286 time to fit residues: 37.9618 Evaluate side-chains 161 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 373 THR 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 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 452 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 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 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 J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 610 TRP 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 98 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 6 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 = 0.3690 r_free = 0.3690 target = 0.086947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.074147 restraints weight = 68805.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075053 restraints weight = 56943.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.075910 restraints weight = 44367.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077047 restraints weight = 36047.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077163 restraints weight = 31516.481| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20952 Z= 0.255 Angle : 0.827 13.556 28542 Z= 0.418 Chirality : 0.050 0.406 3303 Planarity : 0.005 0.060 3570 Dihedral : 9.532 70.772 3837 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.84 % Favored : 90.84 % Rotamer: Outliers : 2.80 % Allowed : 12.18 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.16), residues: 2478 helix: 0.19 (0.25), residues: 429 sheet: -0.56 (0.19), residues: 726 loop : -2.04 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 617 TYR 0.024 0.002 TYR H 91 PHE 0.037 0.003 PHE K 100D TRP 0.039 0.003 TRP K 50 HIS 0.008 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00590 (20856) covalent geometry : angle 0.79163 (28296) SS BOND : bond 0.00410 ( 42) SS BOND : angle 0.99315 ( 84) hydrogen bonds : bond 0.04344 ( 657) hydrogen bonds : angle 5.37877 ( 1788) link_ALPHA1-3 : bond 0.01064 ( 3) link_ALPHA1-3 : angle 2.41093 ( 9) link_ALPHA1-6 : bond 0.00926 ( 3) link_ALPHA1-6 : angle 1.33523 ( 9) link_BETA1-4 : bond 0.00976 ( 27) link_BETA1-4 : angle 2.85332 ( 81) link_NAG-ASN : bond 0.00895 ( 21) link_NAG-ASN : angle 3.89359 ( 63) *********************** 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 187 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8850 (tp) REVERT: B 535 MET cc_start: 0.6826 (mmp) cc_final: 0.6514 (mmp) REVERT: C 16 GLU cc_start: 0.7375 (tt0) cc_final: 0.7023 (tt0) REVERT: C 50 TRP cc_start: 0.5698 (m100) cc_final: 0.5325 (m100) REVERT: E 434 MET cc_start: 0.8627 (ttp) cc_final: 0.8358 (ttp) REVERT: E 443 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8866 (tp) REVERT: I 188 THR cc_start: 0.8239 (p) cc_final: 0.7942 (t) REVERT: I 290 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9080 (t) REVERT: I 434 MET cc_start: 0.7918 (ttp) cc_final: 0.7709 (mtm) REVERT: J 530 MET cc_start: 0.6269 (mtm) cc_final: 0.6052 (mtm) REVERT: J 535 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7032 (mmp) outliers start: 61 outliers final: 49 residues processed: 174 average time/residue: 0.1211 time to fit residues: 36.4054 Evaluate side-chains 169 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 443 ILE Chi-restraints excluded: chain E residue 452 LEU 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 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 G residue 111 VAL Chi-restraints excluded: chain H residue 18 THR 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 270 ILE Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 475 MET 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 610 TRP Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 70 THR 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 190 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 177 optimal weight: 0.0040 chunk 148 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.089598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.077120 restraints weight = 68331.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.078525 restraints weight = 51753.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.079289 restraints weight = 38586.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.079985 restraints weight = 32037.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080203 restraints weight = 29825.628| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20952 Z= 0.142 Angle : 0.732 12.793 28542 Z= 0.367 Chirality : 0.047 0.404 3303 Planarity : 0.004 0.048 3570 Dihedral : 9.010 62.459 3837 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.05 % Favored : 93.62 % Rotamer: Outliers : 1.79 % Allowed : 14.07 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.16), residues: 2478 helix: 0.62 (0.26), residues: 411 sheet: -0.49 (0.19), residues: 690 loop : -1.80 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 542 TYR 0.018 0.001 TYR H 91 PHE 0.030 0.002 PHE K 100D TRP 0.056 0.002 TRP G 50 HIS 0.007 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00309 (20856) covalent geometry : angle 0.69757 (28296) SS BOND : bond 0.00264 ( 42) SS BOND : angle 0.71930 ( 84) hydrogen bonds : bond 0.03589 ( 657) hydrogen bonds : angle 5.11431 ( 1788) link_ALPHA1-3 : bond 0.01086 ( 3) link_ALPHA1-3 : angle 1.93356 ( 9) link_ALPHA1-6 : bond 0.01049 ( 3) link_ALPHA1-6 : angle 1.28529 ( 9) link_BETA1-4 : bond 0.00884 ( 27) link_BETA1-4 : angle 2.68860 ( 81) link_NAG-ASN : bond 0.00742 ( 21) link_NAG-ASN : angle 3.62776 ( 63) *********************** 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 164 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.820 Fit side-chains REVERT: A 100 MET cc_start: 0.7407 (mtm) cc_final: 0.7000 (mtm) REVERT: A 188 THR cc_start: 0.8251 (p) cc_final: 0.8018 (t) REVERT: B 530 MET cc_start: 0.6568 (mtm) cc_final: 0.6063 (mtm) REVERT: B 535 MET cc_start: 0.6808 (mmp) cc_final: 0.5911 (mmp) REVERT: C 50 TRP cc_start: 0.5570 (m100) cc_final: 0.5218 (m100) REVERT: D 71 TYR cc_start: 0.5740 (t80) cc_final: 0.5027 (t80) REVERT: E 434 MET cc_start: 0.8581 (ttp) cc_final: 0.8300 (ttp) REVERT: G 10 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.5772 (mp10) REVERT: I 290 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.9040 (t) REVERT: I 484 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6757 (t80) REVERT: J 530 MET cc_start: 0.6223 (mtm) cc_final: 0.5922 (mtm) REVERT: J 535 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6720 (mmp) outliers start: 39 outliers final: 31 residues processed: 156 average time/residue: 0.1236 time to fit residues: 32.9136 Evaluate side-chains 151 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 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 70 THR Chi-restraints excluded: chain C residue 89 VAL 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 416 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain I residue 34 LEU 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 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 18 MET Chi-restraints excluded: chain K residue 100 TRP 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 241 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 196 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 238 optimal weight: 0.0870 chunk 145 optimal weight: 0.0170 chunk 30 optimal weight: 0.0020 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 478 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS G 100AASN I 147 ASN I 287 HIS J 611 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.092274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.079634 restraints weight = 67763.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081167 restraints weight = 48906.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082338 restraints weight = 35947.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.082893 restraints weight = 29340.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.083065 restraints weight = 26940.385| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20952 Z= 0.119 Angle : 0.692 12.997 28542 Z= 0.346 Chirality : 0.046 0.390 3303 Planarity : 0.004 0.047 3570 Dihedral : 8.362 58.209 3837 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 1.33 % Allowed : 14.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.17), residues: 2478 helix: 0.73 (0.25), residues: 432 sheet: -0.22 (0.20), residues: 684 loop : -1.55 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 508 TYR 0.018 0.001 TYR E 142 PHE 0.023 0.001 PHE G 100D TRP 0.064 0.002 TRP G 50 HIS 0.004 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00239 (20856) covalent geometry : angle 0.65932 (28296) SS BOND : bond 0.00264 ( 42) SS BOND : angle 0.64856 ( 84) hydrogen bonds : bond 0.03058 ( 657) hydrogen bonds : angle 4.90297 ( 1788) link_ALPHA1-3 : bond 0.01051 ( 3) link_ALPHA1-3 : angle 1.80032 ( 9) link_ALPHA1-6 : bond 0.01109 ( 3) link_ALPHA1-6 : angle 1.07855 ( 9) link_BETA1-4 : bond 0.00768 ( 27) link_BETA1-4 : angle 2.54511 ( 81) link_NAG-ASN : bond 0.00733 ( 21) link_NAG-ASN : angle 3.46977 ( 63) *********************** 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 161 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.7322 (mtm) cc_final: 0.6921 (mtm) REVERT: A 188 THR cc_start: 0.8046 (p) cc_final: 0.7808 (t) REVERT: B 530 MET cc_start: 0.6458 (mtm) cc_final: 0.5970 (mtm) REVERT: B 535 MET cc_start: 0.7058 (mmp) cc_final: 0.6143 (mmp) REVERT: B 586 TYR cc_start: 0.9174 (t80) cc_final: 0.8928 (t80) REVERT: C 50 TRP cc_start: 0.5272 (m100) cc_final: 0.4983 (m100) REVERT: D 71 TYR cc_start: 0.5573 (t80) cc_final: 0.4963 (t80) REVERT: E 369 MET cc_start: 0.7497 (ttm) cc_final: 0.6970 (ttm) REVERT: E 434 MET cc_start: 0.8536 (ttp) cc_final: 0.8278 (ttp) REVERT: F 586 TYR cc_start: 0.9170 (t80) cc_final: 0.8888 (t80) REVERT: I 290 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8986 (t) REVERT: J 535 MET cc_start: 0.6860 (mmp) cc_final: 0.6457 (mmp) outliers start: 29 outliers final: 23 residues processed: 151 average time/residue: 0.1228 time to fit residues: 31.8209 Evaluate side-chains 141 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL 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 290 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 460 THR 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 100 ASN Chi-restraints excluded: chain K residue 100 TRP 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 20 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 206 optimal weight: 0.3980 chunk 165 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** 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 = 0.3809 r_free = 0.3809 target = 0.092005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.079974 restraints weight = 66790.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081452 restraints weight = 47089.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.082448 restraints weight = 36717.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083161 restraints weight = 30878.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.083682 restraints weight = 27159.677| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 20952 Z= 0.172 Angle : 0.830 59.163 28542 Z= 0.453 Chirality : 0.048 0.761 3303 Planarity : 0.004 0.051 3570 Dihedral : 8.368 58.190 3837 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.69 % Favored : 94.11 % Rotamer: Outliers : 1.24 % Allowed : 15.40 % Favored : 83.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.17), residues: 2478 helix: 0.75 (0.25), residues: 432 sheet: -0.20 (0.20), residues: 684 loop : -1.54 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 469 TYR 0.017 0.001 TYR E 142 PHE 0.021 0.001 PHE G 100D TRP 0.087 0.003 TRP G 100B HIS 0.004 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00355 (20856) covalent geometry : angle 0.80445 (28296) SS BOND : bond 0.00237 ( 42) SS BOND : angle 0.65251 ( 84) hydrogen bonds : bond 0.03057 ( 657) hydrogen bonds : angle 4.89922 ( 1788) link_ALPHA1-3 : bond 0.01049 ( 3) link_ALPHA1-3 : angle 1.80408 ( 9) link_ALPHA1-6 : bond 0.01110 ( 3) link_ALPHA1-6 : angle 1.07534 ( 9) link_BETA1-4 : bond 0.00813 ( 27) link_BETA1-4 : angle 2.58043 ( 81) link_NAG-ASN : bond 0.00748 ( 21) link_NAG-ASN : angle 3.46807 ( 63) ********************** 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 144 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.7340 (mtm) cc_final: 0.6951 (mtm) REVERT: A 188 THR cc_start: 0.8052 (p) cc_final: 0.7790 (t) REVERT: B 530 MET cc_start: 0.6439 (mtm) cc_final: 0.5962 (mtm) REVERT: B 535 MET cc_start: 0.7035 (mmp) cc_final: 0.6101 (mmp) REVERT: B 586 TYR cc_start: 0.9166 (t80) cc_final: 0.8926 (t80) REVERT: C 50 TRP cc_start: 0.5250 (m100) cc_final: 0.4966 (m100) REVERT: D 71 TYR cc_start: 0.5573 (t80) cc_final: 0.4956 (t80) REVERT: E 369 MET cc_start: 0.7487 (ttm) cc_final: 0.6960 (ttm) REVERT: E 434 MET cc_start: 0.8552 (ttp) cc_final: 0.8275 (ttp) REVERT: F 515 ILE cc_start: 0.5068 (OUTLIER) cc_final: 0.4155 (pt) REVERT: F 535 MET cc_start: 0.6329 (mmp) cc_final: 0.5901 (mmp) REVERT: F 586 TYR cc_start: 0.9161 (t80) cc_final: 0.8886 (t80) REVERT: I 290 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8985 (t) REVERT: J 535 MET cc_start: 0.6804 (mmp) cc_final: 0.6404 (mmp) outliers start: 27 outliers final: 24 residues processed: 135 average time/residue: 0.1201 time to fit residues: 28.3714 Evaluate side-chains 141 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL 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 290 THR Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 460 THR 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 100 ASN Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain K residue 111 VAL 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 178 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 166 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** 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 = 0.3810 r_free = 0.3810 target = 0.092075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.080094 restraints weight = 67197.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081514 restraints weight = 47781.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082521 restraints weight = 37623.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.083210 restraints weight = 31619.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.083690 restraints weight = 27979.793| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.564 20952 Z= 0.333 Angle : 0.767 33.701 28542 Z= 0.432 Chirality : 0.052 1.325 3303 Planarity : 0.005 0.171 3570 Dihedral : 8.368 58.190 3837 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.69 % Favored : 94.11 % Rotamer: Outliers : 1.24 % Allowed : 15.40 % Favored : 83.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.17), residues: 2478 helix: 0.75 (0.25), residues: 432 sheet: -0.20 (0.20), residues: 684 loop : -1.55 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 469 TYR 0.017 0.001 TYR E 142 PHE 0.021 0.001 PHE G 100D TRP 0.087 0.003 TRP G 100B HIS 0.004 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00674 (20856) covalent geometry : angle 0.73814 (28296) SS BOND : bond 0.00259 ( 42) SS BOND : angle 0.65366 ( 84) hydrogen bonds : bond 0.03057 ( 657) hydrogen bonds : angle 4.89919 ( 1788) link_ALPHA1-3 : bond 0.01048 ( 3) link_ALPHA1-3 : angle 1.80366 ( 9) link_ALPHA1-6 : bond 0.01111 ( 3) link_ALPHA1-6 : angle 1.07533 ( 9) link_BETA1-4 : bond 0.00807 ( 27) link_BETA1-4 : angle 2.57879 ( 81) link_NAG-ASN : bond 0.00748 ( 21) link_NAG-ASN : angle 3.46815 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.85 seconds wall clock time: 45 minutes 35.84 seconds (2735.84 seconds total)