Starting phenix.real_space_refine on Wed Jun 18 00:21:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sav_40281/06_2025/8sav_40281_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sav_40281/06_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_40281/06_2025/8sav_40281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sav_40281/06_2025/8sav_40281.map" model { file = "/net/cci-nas-00/data/ceres_data/8sav_40281/06_2025/8sav_40281_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sav_40281/06_2025/8sav_40281_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 12771 2.51 5 N 3528 2.21 5 O 4014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20451 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "B" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "F" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "J" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.35, per 1000 atoms: 0.60 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: 6.36 Conformation dependent library (CDL) restraints added in 2.6 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4638 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 20.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 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: 6.80 Time building geometry restraints manager: 7.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6597 1.34 - 1.46: 4987 1.46 - 1.58: 9086 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 20856 Sorted by residual: bond pdb=" C TRP C 100B" pdb=" N ASP C 100C" ideal model delta sigma weight residual 1.333 1.375 -0.042 1.38e-02 5.25e+03 9.44e+00 bond pdb=" C TRP K 100B" pdb=" N ASP K 100C" ideal model delta sigma weight residual 1.333 1.367 -0.034 1.38e-02 5.25e+03 6.12e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 20851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 27552 2.49 - 4.99: 653 4.99 - 7.48: 73 7.48 - 9.98: 12 9.98 - 12.47: 6 Bond angle restraints: 28296 Sorted by residual: angle pdb=" C ASP G 100C" pdb=" N PHE G 100D" pdb=" CA PHE G 100D" ideal model delta sigma weight residual 121.70 134.17 -12.47 1.80e+00 3.09e-01 4.80e+01 angle pdb=" C ASP C 100C" pdb=" N PHE C 100D" pdb=" CA PHE C 100D" ideal model delta sigma weight residual 121.70 133.88 -12.18 1.80e+00 3.09e-01 4.58e+01 angle pdb=" C ASP K 100C" pdb=" N PHE K 100D" pdb=" CA PHE K 100D" ideal model delta sigma weight residual 121.70 133.20 -11.50 1.80e+00 3.09e-01 4.08e+01 angle pdb=" C THR A 460 " pdb=" N ASN A 461 " pdb=" CA ASN A 461 " ideal model delta sigma weight residual 121.70 132.14 -10.44 1.80e+00 3.09e-01 3.37e+01 angle pdb=" C THR E 460 " pdb=" N ASN E 461 " pdb=" CA ASN E 461 " ideal model delta sigma weight residual 121.70 131.99 -10.29 1.80e+00 3.09e-01 3.27e+01 ... (remaining 28291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 12304 21.99 - 43.98: 708 43.98 - 65.98: 105 65.98 - 87.97: 105 87.97 - 109.96: 50 Dihedral angle restraints: 13272 sinusoidal: 6048 harmonic: 7224 Sorted by residual: dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.62 -65.62 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.23 -65.23 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.99 -64.99 1 1.00e+01 1.00e-02 5.54e+01 ... (remaining 13269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2649 0.057 - 0.114: 491 0.114 - 0.172: 139 0.172 - 0.229: 8 0.229 - 0.286: 16 Chirality restraints: 3303 Sorted by residual: chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3300 not shown) Planarity restraints: 3591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 100D" -0.030 2.00e-02 2.50e+03 2.91e-02 1.48e+01 pdb=" CG PHE G 100D" 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE G 100D" -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE G 100D" -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE G 100D" 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 100D" -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE G 100D" -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 50 " 0.018 2.00e-02 2.50e+03 1.89e-02 8.89e+00 pdb=" CG TRP K 50 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP K 50 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP K 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP K 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 50 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 50 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP K 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 58 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO D 59 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " -0.035 5.00e-02 4.00e+02 ... (remaining 3588 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 160 2.58 - 3.16: 17230 3.16 - 3.74: 29491 3.74 - 4.32: 41034 4.32 - 4.90: 69523 Nonbonded interactions: 157438 Sorted by model distance: nonbonded pdb=" O ASP G 100C" pdb=" OH TYR H 36 " model vdw 2.003 3.040 nonbonded pdb=" O ASP K 100C" pdb=" OH TYR L 36 " model vdw 2.042 3.040 nonbonded pdb=" O ASP C 100C" pdb=" OH TYR D 36 " model vdw 2.044 3.040 nonbonded pdb=" O ASN A 461 " pdb=" OG1 THR A 464 " model vdw 2.108 3.040 nonbonded pdb=" OD1 ASN A 461 " pdb=" OG1 THR A 464 " model vdw 2.192 3.040 ... (remaining 157433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 47.730 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20952 Z= 0.248 Angle : 0.967 18.118 28542 Z= 0.500 Chirality : 0.053 0.286 3303 Planarity : 0.005 0.064 3570 Dihedral : 17.297 109.962 8508 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.58 % Favored : 93.18 % Rotamer: Outliers : 0.14 % Allowed : 0.09 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2478 helix: 0.26 (0.25), residues: 411 sheet: -0.74 (0.18), residues: 759 loop : -1.63 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP K 50 HIS 0.004 0.001 HIS E 249 PHE 0.067 0.002 PHE G 100D TYR 0.025 0.002 TYR L 91 ARG 0.010 0.001 ARG E 508 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 21) link_NAG-ASN : angle 3.17126 ( 63) link_ALPHA1-6 : bond 0.00624 ( 3) link_ALPHA1-6 : angle 1.53177 ( 9) link_BETA1-4 : bond 0.01252 ( 27) link_BETA1-4 : angle 5.01465 ( 81) link_ALPHA1-3 : bond 0.01185 ( 3) link_ALPHA1-3 : angle 3.00139 ( 9) hydrogen bonds : bond 0.21827 ( 657) hydrogen bonds : angle 8.70581 ( 1788) SS BOND : bond 0.00263 ( 42) SS BOND : angle 0.81822 ( 84) covalent geometry : bond 0.00507 (20856) covalent geometry : angle 0.91778 (28296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 2.659 Fit side-chains revert: symmetry clash REVERT: C 48 MET cc_start: 0.8084 (mtm) cc_final: 0.7766 (mtt) REVERT: E 434 MET cc_start: 0.7848 (ttp) cc_final: 0.7394 (mtm) REVERT: F 586 TYR cc_start: 0.9354 (t80) cc_final: 0.9124 (t80) REVERT: G 72 ASP cc_start: 0.8365 (t0) cc_final: 0.7965 (t0) REVERT: H 82 ASP cc_start: 0.6924 (m-30) cc_final: 0.6379 (m-30) REVERT: K 32 CYS cc_start: 0.5703 (t) cc_final: 0.5426 (t) outliers start: 3 outliers final: 0 residues processed: 200 average time/residue: 0.2970 time to fit residues: 96.8598 Evaluate side-chains 133 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 145 optimal weight: 0.3980 chunk 226 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 105 HIS E 72 HIS F 540 GLN F 658 GLN G 102 HIS I 72 HIS J 540 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.089421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076785 restraints weight = 68728.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078424 restraints weight = 53069.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078996 restraints weight = 39077.084| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20952 Z= 0.230 Angle : 0.863 15.180 28542 Z= 0.434 Chirality : 0.052 0.368 3303 Planarity : 0.005 0.055 3570 Dihedral : 13.820 85.539 3837 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.26 % Favored : 92.41 % Rotamer: Outliers : 1.01 % Allowed : 6.48 % Favored : 92.51 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2478 helix: 0.37 (0.26), residues: 399 sheet: -0.64 (0.19), residues: 681 loop : -1.76 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 571 HIS 0.004 0.001 HIS A 374 PHE 0.056 0.003 PHE G 100D TYR 0.032 0.002 TYR H 91 ARG 0.004 0.001 ARG I 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00935 ( 21) link_NAG-ASN : angle 4.41113 ( 63) link_ALPHA1-6 : bond 0.00793 ( 3) link_ALPHA1-6 : angle 1.59517 ( 9) link_BETA1-4 : bond 0.00816 ( 27) link_BETA1-4 : angle 3.25284 ( 81) link_ALPHA1-3 : bond 0.00845 ( 3) link_ALPHA1-3 : angle 2.07146 ( 9) hydrogen bonds : bond 0.05072 ( 657) hydrogen bonds : angle 6.28375 ( 1788) SS BOND : bond 0.00487 ( 42) SS BOND : angle 1.15457 ( 84) covalent geometry : bond 0.00520 (20856) covalent geometry : angle 0.81943 (28296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.7769 (mtm) cc_final: 0.7566 (mtt) REVERT: C 69 MET cc_start: 0.7548 (mtm) cc_final: 0.7256 (mtp) REVERT: E 434 MET cc_start: 0.8115 (ttp) cc_final: 0.7714 (ttp) REVERT: F 535 MET cc_start: 0.6078 (mpp) cc_final: 0.5739 (tpp) REVERT: G 72 ASP cc_start: 0.8353 (t0) cc_final: 0.8116 (t0) REVERT: I 434 MET cc_start: 0.7988 (ttp) cc_final: 0.7762 (ttp) REVERT: K 32 CYS cc_start: 0.6161 (t) cc_final: 0.5835 (t) outliers start: 22 outliers final: 14 residues processed: 154 average time/residue: 0.2622 time to fit residues: 68.6808 Evaluate side-chains 136 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 234 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 147 ASN H 90 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.090583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077980 restraints weight = 67621.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079459 restraints weight = 50086.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080355 restraints weight = 39560.643| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20952 Z= 0.155 Angle : 0.782 14.213 28542 Z= 0.389 Chirality : 0.049 0.474 3303 Planarity : 0.004 0.047 3570 Dihedral : 11.974 88.364 3837 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.89 % Favored : 93.79 % Rotamer: Outliers : 1.20 % Allowed : 9.24 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2478 helix: 0.40 (0.26), residues: 411 sheet: -0.44 (0.19), residues: 684 loop : -1.71 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 100B HIS 0.004 0.001 HIS G 102 PHE 0.045 0.002 PHE G 100D TYR 0.024 0.002 TYR H 91 ARG 0.003 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00865 ( 21) link_NAG-ASN : angle 4.33695 ( 63) link_ALPHA1-6 : bond 0.00750 ( 3) link_ALPHA1-6 : angle 1.66983 ( 9) link_BETA1-4 : bond 0.00987 ( 27) link_BETA1-4 : angle 3.22813 ( 81) link_ALPHA1-3 : bond 0.01160 ( 3) link_ALPHA1-3 : angle 1.43552 ( 9) hydrogen bonds : bond 0.04256 ( 657) hydrogen bonds : angle 5.68401 ( 1788) SS BOND : bond 0.00301 ( 42) SS BOND : angle 0.85763 ( 84) covalent geometry : bond 0.00336 (20856) covalent geometry : angle 0.73531 (28296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 TRP cc_start: 0.5365 (m100) cc_final: 0.5145 (m100) REVERT: E 369 MET cc_start: 0.7702 (ttm) cc_final: 0.7091 (ttm) REVERT: E 434 MET cc_start: 0.8158 (ttp) cc_final: 0.7729 (ttp) REVERT: F 535 MET cc_start: 0.6022 (mpp) cc_final: 0.5742 (tpp) REVERT: G 72 ASP cc_start: 0.8308 (t0) cc_final: 0.8054 (t0) REVERT: J 535 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6712 (mmp) REVERT: K 32 CYS cc_start: 0.6036 (t) cc_final: 0.5692 (t) outliers start: 26 outliers final: 20 residues processed: 154 average time/residue: 0.2846 time to fit residues: 74.3345 Evaluate side-chains 141 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain 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 F residue 657 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN E 428 GLN I 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.088455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075650 restraints weight = 69052.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.076749 restraints weight = 55495.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077635 restraints weight = 42483.579| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20952 Z= 0.208 Angle : 0.803 14.367 28542 Z= 0.404 Chirality : 0.050 0.452 3303 Planarity : 0.005 0.049 3570 Dihedral : 10.543 87.750 3837 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.47 % Favored : 92.17 % Rotamer: Outliers : 2.11 % Allowed : 10.90 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2478 helix: 0.44 (0.26), residues: 393 sheet: -0.61 (0.19), residues: 693 loop : -1.86 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 100B HIS 0.006 0.001 HIS E 374 PHE 0.048 0.003 PHE G 100D TYR 0.033 0.002 TYR H 91 ARG 0.003 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00962 ( 21) link_NAG-ASN : angle 4.14078 ( 63) link_ALPHA1-6 : bond 0.00761 ( 3) link_ALPHA1-6 : angle 1.58225 ( 9) link_BETA1-4 : bond 0.00911 ( 27) link_BETA1-4 : angle 3.08425 ( 81) link_ALPHA1-3 : bond 0.01067 ( 3) link_ALPHA1-3 : angle 2.01037 ( 9) hydrogen bonds : bond 0.04293 ( 657) hydrogen bonds : angle 5.48736 ( 1788) SS BOND : bond 0.00384 ( 42) SS BOND : angle 0.95290 ( 84) covalent geometry : bond 0.00476 (20856) covalent geometry : angle 0.76127 (28296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8358 (p) cc_final: 0.8084 (t) REVERT: A 434 MET cc_start: 0.8124 (ttp) cc_final: 0.7828 (ttp) REVERT: B 535 MET cc_start: 0.6794 (mpp) cc_final: 0.6301 (mmp) REVERT: B 586 TYR cc_start: 0.9249 (t80) cc_final: 0.8989 (t80) REVERT: E 188 THR cc_start: 0.8149 (p) cc_final: 0.7944 (t) REVERT: E 369 MET cc_start: 0.7793 (ttm) cc_final: 0.7155 (ttm) REVERT: E 434 MET cc_start: 0.8458 (ttp) cc_final: 0.7881 (ttp) REVERT: F 535 MET cc_start: 0.6582 (mpp) cc_final: 0.6270 (mpp) REVERT: G 72 ASP cc_start: 0.8308 (t0) cc_final: 0.8090 (t0) REVERT: J 535 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7213 (mmp) REVERT: K 32 CYS cc_start: 0.5965 (t) cc_final: 0.5723 (t) outliers start: 46 outliers final: 32 residues processed: 173 average time/residue: 0.2551 time to fit residues: 74.8896 Evaluate side-chains 154 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU 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 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 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 E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 189 optimal weight: 0.0670 chunk 166 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.090974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078630 restraints weight = 67931.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080230 restraints weight = 50690.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.080912 restraints weight = 36765.154| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20952 Z= 0.131 Angle : 0.719 13.213 28542 Z= 0.360 Chirality : 0.047 0.404 3303 Planarity : 0.004 0.048 3570 Dihedral : 9.662 81.557 3837 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.37 % Favored : 94.31 % Rotamer: Outliers : 1.56 % Allowed : 12.09 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2478 helix: 0.76 (0.26), residues: 393 sheet: -0.40 (0.19), residues: 684 loop : -1.70 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP G 50 HIS 0.007 0.001 HIS C 102 PHE 0.040 0.002 PHE G 100D TYR 0.019 0.001 TYR E 142 ARG 0.004 0.000 ARG G 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 21) link_NAG-ASN : angle 3.76496 ( 63) link_ALPHA1-6 : bond 0.00862 ( 3) link_ALPHA1-6 : angle 1.67261 ( 9) link_BETA1-4 : bond 0.00823 ( 27) link_BETA1-4 : angle 2.86443 ( 81) link_ALPHA1-3 : bond 0.01142 ( 3) link_ALPHA1-3 : angle 1.81804 ( 9) hydrogen bonds : bond 0.03569 ( 657) hydrogen bonds : angle 5.23519 ( 1788) SS BOND : bond 0.00258 ( 42) SS BOND : angle 0.71955 ( 84) covalent geometry : bond 0.00276 (20856) covalent geometry : angle 0.68020 (28296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 2.466 Fit side-chains revert: symmetry clash REVERT: A 188 THR cc_start: 0.8245 (p) cc_final: 0.8023 (t) REVERT: B 530 MET cc_start: 0.6069 (mtm) cc_final: 0.5626 (mtm) REVERT: B 586 TYR cc_start: 0.9235 (t80) cc_final: 0.9003 (t80) REVERT: C 16 GLU cc_start: 0.7150 (tt0) cc_final: 0.6656 (tt0) REVERT: E 369 MET cc_start: 0.7583 (ttm) cc_final: 0.6961 (ttm) REVERT: F 535 MET cc_start: 0.6395 (mpp) cc_final: 0.6009 (mpp) REVERT: I 188 THR cc_start: 0.8089 (p) cc_final: 0.7827 (t) REVERT: J 535 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6716 (mmp) REVERT: K 32 CYS cc_start: 0.5953 (t) cc_final: 0.5671 (t) outliers start: 34 outliers final: 21 residues processed: 159 average time/residue: 0.2857 time to fit residues: 76.1242 Evaluate side-chains 144 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 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 L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 170 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 189 optimal weight: 0.0070 chunk 32 optimal weight: 6.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.088295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075555 restraints weight = 68412.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076495 restraints weight = 55331.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077371 restraints weight = 43187.672| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20952 Z= 0.208 Angle : 0.774 13.776 28542 Z= 0.390 Chirality : 0.049 0.404 3303 Planarity : 0.005 0.049 3570 Dihedral : 9.488 76.870 3837 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.38 % Favored : 92.25 % Rotamer: Outliers : 2.57 % Allowed : 11.95 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2478 helix: 0.47 (0.26), residues: 411 sheet: -0.51 (0.19), residues: 690 loop : -1.81 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP K 50 HIS 0.007 0.001 HIS C 102 PHE 0.039 0.002 PHE G 100D TYR 0.022 0.002 TYR H 91 ARG 0.003 0.000 ARG C 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00862 ( 21) link_NAG-ASN : angle 3.84082 ( 63) link_ALPHA1-6 : bond 0.00858 ( 3) link_ALPHA1-6 : angle 1.49105 ( 9) link_BETA1-4 : bond 0.00921 ( 27) link_BETA1-4 : angle 2.85612 ( 81) link_ALPHA1-3 : bond 0.01081 ( 3) link_ALPHA1-3 : angle 2.23793 ( 9) hydrogen bonds : bond 0.04052 ( 657) hydrogen bonds : angle 5.27206 ( 1788) SS BOND : bond 0.00401 ( 42) SS BOND : angle 0.88472 ( 84) covalent geometry : bond 0.00477 (20856) covalent geometry : angle 0.73719 (28296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 127 time to evaluate : 2.315 Fit side-chains revert: symmetry clash REVERT: A 188 THR cc_start: 0.8318 (p) cc_final: 0.8064 (t) REVERT: A 443 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8824 (tp) REVERT: B 535 MET cc_start: 0.7538 (mmp) cc_final: 0.7058 (mmp) REVERT: C 16 GLU cc_start: 0.7289 (tt0) cc_final: 0.6794 (tt0) REVERT: C 50 TRP cc_start: 0.5673 (m100) cc_final: 0.5346 (m100) REVERT: E 148 ASN cc_start: 0.7953 (p0) cc_final: 0.7752 (p0) REVERT: E 369 MET cc_start: 0.7643 (ttm) cc_final: 0.7035 (ttm) REVERT: E 434 MET cc_start: 0.8507 (ttp) cc_final: 0.7991 (ttp) REVERT: F 530 MET cc_start: 0.6737 (mtm) cc_final: 0.5992 (mtm) REVERT: F 535 MET cc_start: 0.6886 (mpp) cc_final: 0.6505 (mpp) REVERT: I 188 THR cc_start: 0.8193 (p) cc_final: 0.7931 (t) REVERT: I 290 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8989 (t) REVERT: I 443 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8800 (tp) REVERT: J 535 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7337 (mmp) REVERT: K 32 CYS cc_start: 0.5957 (t) cc_final: 0.5720 (t) outliers start: 56 outliers final: 38 residues processed: 173 average time/residue: 0.2582 time to fit residues: 76.0599 Evaluate side-chains 160 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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 369 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 LEU 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 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 F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU 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 373 THR Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 95 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 157 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.088695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076111 restraints weight = 68351.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076869 restraints weight = 55515.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077641 restraints weight = 44486.526| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20952 Z= 0.193 Angle : 0.760 13.458 28542 Z= 0.384 Chirality : 0.048 0.402 3303 Planarity : 0.004 0.049 3570 Dihedral : 9.272 70.694 3837 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.42 % Favored : 93.26 % Rotamer: Outliers : 2.30 % Allowed : 12.92 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2478 helix: 0.37 (0.25), residues: 429 sheet: -0.49 (0.19), residues: 690 loop : -1.83 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 50 HIS 0.007 0.001 HIS C 102 PHE 0.038 0.002 PHE G 100D TYR 0.021 0.002 TYR H 91 ARG 0.003 0.000 ARG E 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00797 ( 21) link_NAG-ASN : angle 3.78697 ( 63) link_ALPHA1-6 : bond 0.00986 ( 3) link_ALPHA1-6 : angle 1.34586 ( 9) link_BETA1-4 : bond 0.00891 ( 27) link_BETA1-4 : angle 2.75480 ( 81) link_ALPHA1-3 : bond 0.01091 ( 3) link_ALPHA1-3 : angle 2.14845 ( 9) hydrogen bonds : bond 0.03922 ( 657) hydrogen bonds : angle 5.21835 ( 1788) SS BOND : bond 0.00339 ( 42) SS BOND : angle 0.82279 ( 84) covalent geometry : bond 0.00440 (20856) covalent geometry : angle 0.72501 (28296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 2.527 Fit side-chains REVERT: A 443 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8802 (tp) REVERT: B 530 MET cc_start: 0.6453 (mtm) cc_final: 0.6091 (mtm) REVERT: B 535 MET cc_start: 0.7578 (mmp) cc_final: 0.6996 (mmp) REVERT: C 16 GLU cc_start: 0.7200 (tt0) cc_final: 0.6850 (tt0) REVERT: C 50 TRP cc_start: 0.5852 (m100) cc_final: 0.5427 (m100) REVERT: E 148 ASN cc_start: 0.7800 (p0) cc_final: 0.7579 (p0) REVERT: E 434 MET cc_start: 0.8600 (ttp) cc_final: 0.8370 (ttp) REVERT: F 530 MET cc_start: 0.6678 (mtm) cc_final: 0.5906 (mtm) REVERT: F 535 MET cc_start: 0.6954 (mpp) cc_final: 0.6600 (mpp) REVERT: I 188 THR cc_start: 0.8290 (p) cc_final: 0.8072 (t) REVERT: I 290 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.9014 (t) REVERT: J 535 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7266 (mmp) REVERT: K 32 CYS cc_start: 0.5855 (t) cc_final: 0.5627 (t) outliers start: 50 outliers final: 40 residues processed: 165 average time/residue: 0.2626 time to fit residues: 73.8966 Evaluate side-chains 158 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 2.563 ------------------------------------------------------------------------------- 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 443 ILE Chi-restraints excluded: chain A residue 452 LEU 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 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 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 F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 610 TRP Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 143 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.0670 chunk 118 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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** ** G 100AASN ** 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 = 0.3744 r_free = 0.3744 target = 0.089563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.077135 restraints weight = 68431.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.078439 restraints weight = 53027.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079266 restraints weight = 40011.678| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20952 Z= 0.148 Angle : 0.723 13.291 28542 Z= 0.364 Chirality : 0.047 0.396 3303 Planarity : 0.004 0.049 3570 Dihedral : 8.919 62.693 3837 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.30 % Favored : 93.38 % Rotamer: Outliers : 2.21 % Allowed : 13.56 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.16), residues: 2478 helix: 0.63 (0.26), residues: 411 sheet: -0.39 (0.20), residues: 690 loop : -1.75 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP G 50 HIS 0.005 0.001 HIS G 102 PHE 0.035 0.002 PHE G 100D TYR 0.018 0.001 TYR D 91 ARG 0.004 0.000 ARG J 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 21) link_NAG-ASN : angle 3.61880 ( 63) link_ALPHA1-6 : bond 0.01042 ( 3) link_ALPHA1-6 : angle 1.23505 ( 9) link_BETA1-4 : bond 0.00848 ( 27) link_BETA1-4 : angle 2.67251 ( 81) link_ALPHA1-3 : bond 0.01077 ( 3) link_ALPHA1-3 : angle 2.03983 ( 9) hydrogen bonds : bond 0.03563 ( 657) hydrogen bonds : angle 5.08642 ( 1788) SS BOND : bond 0.00277 ( 42) SS BOND : angle 0.72923 ( 84) covalent geometry : bond 0.00324 (20856) covalent geometry : angle 0.68840 (28296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 2.417 Fit side-chains REVERT: A 443 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8823 (tp) REVERT: B 530 MET cc_start: 0.6509 (mtm) cc_final: 0.6086 (mtm) REVERT: B 535 MET cc_start: 0.7461 (mmp) cc_final: 0.6950 (mmp) REVERT: C 16 GLU cc_start: 0.7423 (tt0) cc_final: 0.7042 (tt0) REVERT: C 50 TRP cc_start: 0.5658 (m100) cc_final: 0.5248 (m100) REVERT: E 148 ASN cc_start: 0.7830 (p0) cc_final: 0.7622 (p0) REVERT: E 434 MET cc_start: 0.8546 (ttp) cc_final: 0.8281 (ttp) REVERT: F 530 MET cc_start: 0.6654 (mtm) cc_final: 0.5984 (mtm) REVERT: F 535 MET cc_start: 0.6970 (mpp) cc_final: 0.6628 (mpp) REVERT: G 10 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.5905 (mp10) REVERT: I 188 THR cc_start: 0.8260 (p) cc_final: 0.7971 (t) REVERT: I 484 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6744 (t80) REVERT: J 535 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7138 (mmp) outliers start: 48 outliers final: 41 residues processed: 167 average time/residue: 0.3004 time to fit residues: 84.5044 Evaluate side-chains 163 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 351 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 LEU 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 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 F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 443 ILE 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 18 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 128 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.086834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074202 restraints weight = 69352.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.074832 restraints weight = 56853.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.075633 restraints weight = 46168.356| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 20952 Z= 0.269 Angle : 0.833 13.189 28542 Z= 0.422 Chirality : 0.051 0.408 3303 Planarity : 0.005 0.051 3570 Dihedral : 9.226 58.668 3837 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.04 % Favored : 90.64 % Rotamer: Outliers : 2.80 % Allowed : 13.70 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2478 helix: 0.19 (0.25), residues: 429 sheet: -0.70 (0.19), residues: 714 loop : -2.00 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP G 50 HIS 0.007 0.002 HIS E 374 PHE 0.038 0.003 PHE G 100D TYR 0.024 0.002 TYR D 91 ARG 0.004 0.001 ARG L 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00918 ( 21) link_NAG-ASN : angle 3.86997 ( 63) link_ALPHA1-6 : bond 0.01055 ( 3) link_ALPHA1-6 : angle 1.09071 ( 9) link_BETA1-4 : bond 0.00964 ( 27) link_BETA1-4 : angle 2.79696 ( 81) link_ALPHA1-3 : bond 0.01026 ( 3) link_ALPHA1-3 : angle 2.37016 ( 9) hydrogen bonds : bond 0.04356 ( 657) hydrogen bonds : angle 5.35030 ( 1788) SS BOND : bond 0.00426 ( 42) SS BOND : angle 1.05824 ( 84) covalent geometry : bond 0.00621 (20856) covalent geometry : angle 0.79940 (28296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 115 time to evaluate : 3.314 Fit side-chains REVERT: A 443 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8804 (tp) REVERT: B 530 MET cc_start: 0.6946 (mtm) cc_final: 0.6498 (mtm) REVERT: B 535 MET cc_start: 0.7713 (mmp) cc_final: 0.6982 (mmp) REVERT: C 16 GLU cc_start: 0.7403 (tt0) cc_final: 0.7043 (tt0) REVERT: C 50 TRP cc_start: 0.6043 (m100) cc_final: 0.5737 (m100) REVERT: D 71 TYR cc_start: 0.5607 (t80) cc_final: 0.4945 (t80) REVERT: E 434 MET cc_start: 0.8697 (ttp) cc_final: 0.8463 (ttp) REVERT: F 530 MET cc_start: 0.7044 (mtm) cc_final: 0.6316 (mtm) REVERT: F 535 MET cc_start: 0.7260 (mpp) cc_final: 0.6955 (mpp) REVERT: G 10 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6030 (mp10) REVERT: I 290 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9053 (t) REVERT: J 535 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7488 (mmp) outliers start: 61 outliers final: 46 residues processed: 164 average time/residue: 0.3098 time to fit residues: 86.3551 Evaluate side-chains 161 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 351 LYS 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 452 LEU 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 452 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 GLN 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 36 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain 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 18 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 222 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** G 100AASN ** 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 = 0.3758 r_free = 0.3758 target = 0.090303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.078124 restraints weight = 67813.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079228 restraints weight = 50764.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080001 restraints weight = 39520.048| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20952 Z= 0.130 Angle : 0.718 12.806 28542 Z= 0.360 Chirality : 0.047 0.396 3303 Planarity : 0.004 0.049 3570 Dihedral : 8.643 59.845 3837 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.65 % Favored : 94.07 % Rotamer: Outliers : 1.56 % Allowed : 14.99 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2478 helix: 0.48 (0.25), residues: 429 sheet: -0.36 (0.20), residues: 690 loop : -1.76 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP G 50 HIS 0.005 0.001 HIS G 102 PHE 0.033 0.001 PHE G 100D TYR 0.020 0.001 TYR E 142 ARG 0.003 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 21) link_NAG-ASN : angle 3.53488 ( 63) link_ALPHA1-6 : bond 0.01108 ( 3) link_ALPHA1-6 : angle 0.98520 ( 9) link_BETA1-4 : bond 0.00835 ( 27) link_BETA1-4 : angle 2.60718 ( 81) link_ALPHA1-3 : bond 0.01044 ( 3) link_ALPHA1-3 : angle 1.72556 ( 9) hydrogen bonds : bond 0.03375 ( 657) hydrogen bonds : angle 5.05984 ( 1788) SS BOND : bond 0.00276 ( 42) SS BOND : angle 0.77218 ( 84) covalent geometry : bond 0.00275 (20856) covalent geometry : angle 0.68524 (28296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 2.321 Fit side-chains REVERT: B 530 MET cc_start: 0.6851 (mtm) cc_final: 0.6373 (mtm) REVERT: B 535 MET cc_start: 0.7564 (mmp) cc_final: 0.7025 (mmp) REVERT: C 16 GLU cc_start: 0.7489 (tt0) cc_final: 0.7072 (tt0) REVERT: C 50 TRP cc_start: 0.5530 (m100) cc_final: 0.5199 (m100) REVERT: D 71 TYR cc_start: 0.5677 (t80) cc_final: 0.5178 (t80) REVERT: E 434 MET cc_start: 0.8593 (ttp) cc_final: 0.8262 (ttp) REVERT: F 530 MET cc_start: 0.6836 (mtm) cc_final: 0.6035 (mtm) REVERT: F 535 MET cc_start: 0.7067 (mpp) cc_final: 0.6815 (mpp) REVERT: G 10 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.5839 (mp10) REVERT: I 188 THR cc_start: 0.8349 (p) cc_final: 0.8115 (t) REVERT: I 290 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.9003 (t) REVERT: I 484 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6813 (t80) REVERT: J 535 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6769 (mmp) outliers start: 34 outliers final: 28 residues processed: 153 average time/residue: 0.2924 time to fit residues: 74.4805 Evaluate side-chains 149 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 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 E residue 416 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 290 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 J residue 635 ILE Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 231 optimal weight: 0.0870 chunk 168 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 188 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.1764 ------------------------------------------------------------------------------- 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** ** G 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN K 100AASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.090073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.077696 restraints weight = 68322.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.078661 restraints weight = 53922.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079384 restraints weight = 43264.692| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20952 Z= 0.136 Angle : 0.707 12.972 28542 Z= 0.355 Chirality : 0.046 0.392 3303 Planarity : 0.004 0.048 3570 Dihedral : 8.436 59.746 3837 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.38 % Favored : 93.42 % Rotamer: Outliers : 1.66 % Allowed : 15.13 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2478 helix: 0.58 (0.25), residues: 429 sheet: -0.26 (0.20), residues: 687 loop : -1.69 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP G 50 HIS 0.004 0.001 HIS G 102 PHE 0.030 0.001 PHE G 100D TYR 0.017 0.001 TYR D 91 ARG 0.006 0.000 ARG A 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00771 ( 21) link_NAG-ASN : angle 3.56403 ( 63) link_ALPHA1-6 : bond 0.01100 ( 3) link_ALPHA1-6 : angle 1.05079 ( 9) link_BETA1-4 : bond 0.00864 ( 27) link_BETA1-4 : angle 2.61684 ( 81) link_ALPHA1-3 : bond 0.00924 ( 3) link_ALPHA1-3 : angle 1.82328 ( 9) hydrogen bonds : bond 0.03285 ( 657) hydrogen bonds : angle 4.97195 ( 1788) SS BOND : bond 0.00268 ( 42) SS BOND : angle 0.74030 ( 84) covalent geometry : bond 0.00294 (20856) covalent geometry : angle 0.67341 (28296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5932.34 seconds wall clock time: 107 minutes 59.35 seconds (6479.35 seconds total)