Starting phenix.real_space_refine on Tue Jun 17 01:31:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tni_41417/06_2025/8tni_41417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tni_41417/06_2025/8tni_41417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tni_41417/06_2025/8tni_41417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tni_41417/06_2025/8tni_41417.map" model { file = "/net/cci-nas-00/data/ceres_data/8tni_41417/06_2025/8tni_41417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tni_41417/06_2025/8tni_41417.cif" } resolution = 3.61 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= 0.001 sd= 0.023 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 134 5.16 5 C 12095 2.51 5 N 3303 2.21 5 O 3867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19399 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "X" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1143 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1730 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" 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: "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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.95, per 1000 atoms: 0.72 Number of scatterers: 19399 At special positions: 0 Unit cell: (135.29, 136.95, 165.17, 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 134 16.00 O 3867 8.00 N 3303 7.00 C 12095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 50 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 100A" - pdb=" SG CYS X 100Q" distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 99 " distance=2.03 Simple disulfide: pdb=" SG CYS J1023 " - pdb=" SG CYS J1088 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 332 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 88 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 448 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 332 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 197 " " NAG C 610 " - " ASN C 88 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 448 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 332 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 88 " " NAG E 610 " - " ASN E 392 " " NAG E 611 " - " ASN E 339 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 160 " " NAG L 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN C 156 " " NAG Q 1 " - " ASN C 160 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 276 " " NAG T 1 " - " ASN C 363 " " NAG U 1 " - " ASN C 386 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 262 " " NAG Y 1 " - " ASN E 363 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 160 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.15 Conformation dependent library (CDL) restraints added in 2.6 seconds 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 42 sheets defined 18.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.557A pdb=" N GLU A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.511A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.762A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.935A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.010A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.919A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.904A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.897A pdb=" N GLY C 380 " --> pdb=" O ASN C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.987A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.814A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.579A pdb=" N ASN D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.513A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.718A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 removed outlier: 4.509A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 4.099A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.054A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.510A pdb=" N GLY E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.853A pdb=" N GLY E 354 " --> pdb=" O LYS E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'F' and resid 523 through 527 removed outlier: 4.488A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 541 removed outlier: 3.800A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.531A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.633A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 641 through 664 removed outlier: 4.212A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.840A pdb=" N THR X 87 " --> pdb=" O PRO X 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 1079 through 1083 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 4.641A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.989A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 176 removed outlier: 3.501A pdb=" N CYS A 131 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.827A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 removed outlier: 3.830A pdb=" N LEU A 454 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 417 removed outlier: 3.825A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 305 through 308 removed outlier: 3.643A pdb=" N ALA A 319 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.635A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.082A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 175 removed outlier: 3.679A pdb=" N CYS C 131 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.041A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.691A pdb=" N ARG C 273 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 413 through 417 removed outlier: 3.780A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 413 through 417 removed outlier: 3.780A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AB7, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.659A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 382 through 383 removed outlier: 4.423A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 495 through 499 Processing sheet with id=AC1, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.813A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 132 through 133 removed outlier: 3.543A pdb=" N THR E 132 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 168 through 169 removed outlier: 7.226A pdb=" N CYS X 100A" --> pdb=" O SER X 100T" (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER X 100T" --> pdb=" O CYS X 100A" (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU X 100C" --> pdb=" O ALA X 100R" (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.629A pdb=" N ARG E 273 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 454 " --> pdb=" O ILE E 284 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 413 through 417 removed outlier: 4.031A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR E 297 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.982A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'H' and resid 47 through 51 removed outlier: 4.566A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE H 34 " --> pdb=" O LEU H 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.841A pdb=" N GLY I 10 " --> pdb=" O GLN I 108 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR I 110 " --> pdb=" O GLY I 10 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 47 through 51 removed outlier: 4.790A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE I 34 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.764A pdb=" N VAL X 5 " --> pdb=" O ALA X 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 11 through 12 removed outlier: 3.934A pdb=" N ALA X 93 " --> pdb=" O HIS X 35 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS X 35 " --> pdb=" O ALA X 93 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET X 34 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.596A pdb=" N MET J 82 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AE3, first strand: chain 'J' and resid 45 through 51 removed outlier: 5.245A pdb=" N GLY J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG J 38 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE J 34 " --> pdb=" O LEU J 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1009 through 1013 removed outlier: 3.661A pdb=" N ALA J1013 " --> pdb=" O ILE J1105 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP J1035 " --> pdb=" O LEU J1047 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1009 through 1013 removed outlier: 3.661A pdb=" N ALA J1013 " --> pdb=" O ILE J1105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL J1097 " --> pdb=" O THR J1090 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1019 through 1024 546 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.46 Time building geometry restraints manager: 7.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6243 1.35 - 1.48: 5039 1.48 - 1.61: 8317 1.61 - 1.74: 2 1.74 - 1.87: 174 Bond restraints: 19775 Sorted by residual: bond pdb=" O3 TYS X 100I" pdb=" S TYS X 100I" ideal model delta sigma weight residual 1.458 1.636 -0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" O2 TYS X 100H" pdb=" S TYS X 100H" ideal model delta sigma weight residual 1.461 1.632 -0.171 2.00e-02 2.50e+03 7.30e+01 bond pdb=" OH TYS X 100I" pdb=" S TYS X 100I" ideal model delta sigma weight residual 1.679 1.536 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" OH TYS X 100H" pdb=" S TYS X 100H" ideal model delta sigma weight residual 1.679 1.554 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C1 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.399 1.480 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 19770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.07: 26792 6.07 - 12.13: 35 12.13 - 18.20: 1 18.20 - 24.26: 2 24.26 - 30.33: 2 Bond angle restraints: 26832 Sorted by residual: angle pdb=" O1 TYS X 100H" pdb=" S TYS X 100H" pdb=" O2 TYS X 100H" ideal model delta sigma weight residual 114.11 83.78 30.33 3.00e+00 1.11e-01 1.02e+02 angle pdb=" O2 TYS X 100H" pdb=" S TYS X 100H" pdb=" O3 TYS X 100H" ideal model delta sigma weight residual 115.38 88.75 26.63 3.00e+00 1.11e-01 7.88e+01 angle pdb=" OH TYS X 100H" pdb=" S TYS X 100H" pdb=" O2 TYS X 100H" ideal model delta sigma weight residual 104.74 85.59 19.15 3.00e+00 1.11e-01 4.07e+01 angle pdb=" OH TYS X 100H" pdb=" S TYS X 100H" pdb=" O1 TYS X 100H" ideal model delta sigma weight residual 104.92 123.18 -18.26 3.00e+00 1.11e-01 3.71e+01 angle pdb=" OH TYS X 100H" pdb=" S TYS X 100H" pdb=" O3 TYS X 100H" ideal model delta sigma weight residual 100.21 117.11 -16.90 3.00e+00 1.11e-01 3.17e+01 ... (remaining 26827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 11460 24.83 - 49.65: 1072 49.65 - 74.48: 174 74.48 - 99.30: 48 99.30 - 124.13: 20 Dihedral angle restraints: 12774 sinusoidal: 6034 harmonic: 6740 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual 93.00 -178.41 -88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 10.99 82.01 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 13.71 79.29 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 12771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 3167 0.181 - 0.362: 21 0.362 - 0.542: 3 0.542 - 0.723: 0 0.723 - 0.904: 1 Chirality restraints: 3192 Sorted by residual: chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB VAL J 100C" pdb=" CA VAL J 100C" pdb=" CG1 VAL J 100C" pdb=" CG2 VAL J 100C" both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 3189 not shown) Planarity restraints: 3406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 166 " -0.493 9.50e-02 1.11e+02 2.22e-01 3.29e+01 pdb=" NE ARG E 166 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG E 166 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG E 166 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG E 166 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 276 " 0.054 2.00e-02 2.50e+03 5.03e-02 3.16e+01 pdb=" CG ASN A 276 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN A 276 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 276 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " -0.007 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" CG ASN E 133 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " -0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " -0.044 2.00e-02 2.50e+03 ... (remaining 3403 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 866 2.70 - 3.25: 19216 3.25 - 3.80: 29741 3.80 - 4.35: 36650 4.35 - 4.90: 62845 Nonbonded interactions: 149318 Sorted by model distance: nonbonded pdb=" OG1 THR A 303 " pdb=" O GLY A 321 " model vdw 2.151 3.040 nonbonded pdb=" OG SER D 612 " pdb=" OD1 ASN D 616 " model vdw 2.169 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" O CYS D 604 " model vdw 2.195 3.040 nonbonded pdb=" O ALA A 55 " pdb=" ND1 HIS A 216 " model vdw 2.215 3.120 nonbonded pdb=" OG1 THR J1090 " pdb=" O ALA J1095C" model vdw 2.217 3.040 ... (remaining 149313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = (chain 'E' and (resid 31 through 505 or resid 601 through 610)) } ncs_group { reference = (chain 'B' and resid 519 through 664) selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'W' selection = chain 'Y' } 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: 9.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 49.970 Find NCS groups from input model: 0.950 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 0.178 19890 Z= 0.253 Angle : 0.978 30.326 27130 Z= 0.451 Chirality : 0.054 0.904 3192 Planarity : 0.006 0.222 3357 Dihedral : 18.761 124.130 8313 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.86 % Favored : 89.71 % Rotamer: Outliers : 0.54 % Allowed : 31.87 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.94 (0.17), residues: 2312 helix: 0.62 (0.29), residues: 371 sheet: -0.76 (0.23), residues: 536 loop : -2.15 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 69 HIS 0.006 0.001 HIS C 374 PHE 0.014 0.002 PHE B 522 TYR 0.019 0.001 TYR H 100B ARG 0.030 0.001 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00880 ( 49) link_NAG-ASN : angle 5.63134 ( 147) link_BETA1-4 : bond 0.00716 ( 22) link_BETA1-4 : angle 2.40316 ( 66) link_ALPHA1-3 : bond 0.02166 ( 1) link_ALPHA1-3 : angle 3.48526 ( 3) hydrogen bonds : bond 0.13625 ( 536) hydrogen bonds : angle 6.16684 ( 1449) SS BOND : bond 0.00438 ( 41) SS BOND : angle 1.58288 ( 82) covalent geometry : bond 0.00528 (19775) covalent geometry : angle 0.87759 (26832) Misc. bond : bond 0.01308 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 220 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 LEU cc_start: 0.7905 (tp) cc_final: 0.7668 (tt) REVERT: E 427 TRP cc_start: 0.6495 (m100) cc_final: 0.6161 (m100) REVERT: F 584 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6822 (tm-30) REVERT: H 32 TYR cc_start: 0.7912 (m-10) cc_final: 0.7653 (m-80) REVERT: H 82 LEU cc_start: 0.8110 (mp) cc_final: 0.7718 (tt) REVERT: X 108 MET cc_start: 0.6123 (tpt) cc_final: 0.5819 (tpt) outliers start: 11 outliers final: 3 residues processed: 230 average time/residue: 0.3969 time to fit residues: 131.9678 Evaluate side-chains 143 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.0870 chunk 135 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 185 ASN D 625 ASN E 103 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.049962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.035193 restraints weight = 125146.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.036399 restraints weight = 68463.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037224 restraints weight = 47485.810| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19890 Z= 0.155 Angle : 0.793 13.344 27130 Z= 0.381 Chirality : 0.046 0.441 3192 Planarity : 0.005 0.067 3357 Dihedral : 11.749 113.914 4022 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.13 % Favored : 90.48 % Rotamer: Outliers : 4.43 % Allowed : 28.92 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.88 (0.17), residues: 2312 helix: 0.68 (0.29), residues: 366 sheet: -0.69 (0.23), residues: 542 loop : -2.13 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 78 HIS 0.007 0.001 HIS X 35 PHE 0.022 0.002 PHE F 519 TYR 0.017 0.001 TYR H 100B ARG 0.012 0.001 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 49) link_NAG-ASN : angle 3.85911 ( 147) link_BETA1-4 : bond 0.00448 ( 22) link_BETA1-4 : angle 2.15393 ( 66) link_ALPHA1-3 : bond 0.02607 ( 1) link_ALPHA1-3 : angle 2.71482 ( 3) hydrogen bonds : bond 0.03824 ( 536) hydrogen bonds : angle 5.46237 ( 1449) SS BOND : bond 0.00375 ( 41) SS BOND : angle 1.24317 ( 82) covalent geometry : bond 0.00338 (19775) covalent geometry : angle 0.73287 (26832) Misc. bond : bond 0.00241 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 167 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 VAL cc_start: 0.9507 (OUTLIER) cc_final: 0.9247 (p) REVERT: A 252 LYS cc_start: 0.9560 (OUTLIER) cc_final: 0.9298 (mmmm) REVERT: A 426 MET cc_start: 0.8881 (tpp) cc_final: 0.8524 (tpp) REVERT: A 427 TRP cc_start: 0.8447 (m100) cc_final: 0.8223 (m100) REVERT: B 530 MET cc_start: 0.8867 (mtp) cc_final: 0.8080 (mtm) REVERT: B 584 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8313 (pt0) REVERT: B 588 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.8409 (mmt-90) REVERT: B 589 ASP cc_start: 0.8474 (m-30) cc_final: 0.8060 (p0) REVERT: C 121 LYS cc_start: 0.9381 (tptp) cc_final: 0.9157 (tptp) REVERT: C 164 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8922 (mt-10) REVERT: C 262 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8797 (t0) REVERT: C 293 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8721 (tt0) REVERT: C 369 LEU cc_start: 0.9102 (tp) cc_final: 0.8537 (tt) REVERT: C 377 ASN cc_start: 0.8696 (t0) cc_final: 0.8482 (t0) REVERT: D 530 MET cc_start: 0.8800 (mmm) cc_final: 0.8382 (tpt) REVERT: D 540 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8578 (mp10) REVERT: D 626 MET cc_start: 0.8866 (tpp) cc_final: 0.8416 (tpp) REVERT: D 632 ASP cc_start: 0.8686 (p0) cc_final: 0.8222 (p0) REVERT: D 633 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9405 (mmmt) REVERT: D 651 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8563 (m110) REVERT: E 161 MET cc_start: 0.8921 (mmm) cc_final: 0.8243 (tmm) REVERT: E 162 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8560 (p) REVERT: E 426 MET cc_start: 0.7854 (tpp) cc_final: 0.7417 (tpp) REVERT: E 427 TRP cc_start: 0.7593 (m100) cc_final: 0.7107 (m100) REVERT: E 475 MET cc_start: 0.8137 (tpp) cc_final: 0.7923 (tpp) REVERT: F 584 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8678 (tm-30) REVERT: H 3 GLN cc_start: 0.8774 (pp30) cc_final: 0.8543 (tm-30) REVERT: H 30 GLU cc_start: 0.8961 (pm20) cc_final: 0.8714 (pm20) REVERT: H 31 ASN cc_start: 0.9205 (t0) cc_final: 0.8910 (t0) REVERT: H 39 GLN cc_start: 0.9237 (tp-100) cc_final: 0.8911 (tp-100) REVERT: H 55 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8603 (ttpt) REVERT: H 82 LEU cc_start: 0.9308 (mp) cc_final: 0.8406 (tt) REVERT: I 11 LEU cc_start: 0.9537 (mm) cc_final: 0.9138 (tp) REVERT: I 55 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.9021 (ttmt) REVERT: I 82 MET cc_start: 0.7125 (mpp) cc_final: 0.6839 (mpp) REVERT: I 97 ARG cc_start: 0.9066 (tpp80) cc_final: 0.8818 (mmm160) REVERT: I 100 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9156 (p) REVERT: X 34 MET cc_start: 0.7460 (mmp) cc_final: 0.7168 (mmp) REVERT: X 100 GLU cc_start: 0.8233 (pt0) cc_final: 0.7590 (mp0) REVERT: X 100 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8486 (mp0) REVERT: X 100 LYS cc_start: 0.8622 (tppt) cc_final: 0.8244 (tptp) REVERT: J 18 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8235 (mm) REVERT: J 87 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8735 (m) outliers start: 90 outliers final: 33 residues processed: 249 average time/residue: 0.3255 time to fit residues: 123.4455 Evaluate side-chains 187 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 171 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 166 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.049340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.034492 restraints weight = 126675.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.035722 restraints weight = 68307.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.036552 restraints weight = 47316.595| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19890 Z= 0.169 Angle : 0.743 13.163 27130 Z= 0.356 Chirality : 0.045 0.346 3192 Planarity : 0.004 0.040 3357 Dihedral : 10.223 113.649 4020 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.13 % Favored : 90.48 % Rotamer: Outliers : 3.99 % Allowed : 28.72 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.81 (0.17), residues: 2312 helix: 0.67 (0.29), residues: 372 sheet: -0.64 (0.23), residues: 542 loop : -2.06 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 479 HIS 0.004 0.001 HIS A 216 PHE 0.015 0.001 PHE D 519 TYR 0.015 0.001 TYR H 100B ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 49) link_NAG-ASN : angle 3.48321 ( 147) link_BETA1-4 : bond 0.00332 ( 22) link_BETA1-4 : angle 1.97539 ( 66) link_ALPHA1-3 : bond 0.02991 ( 1) link_ALPHA1-3 : angle 3.31866 ( 3) hydrogen bonds : bond 0.03583 ( 536) hydrogen bonds : angle 5.25957 ( 1449) SS BOND : bond 0.00483 ( 41) SS BOND : angle 1.33079 ( 82) covalent geometry : bond 0.00371 (19775) covalent geometry : angle 0.68903 (26832) Misc. bond : bond 0.00101 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 155 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9520 (t0) cc_final: 0.9222 (p0) REVERT: A 252 LYS cc_start: 0.9578 (OUTLIER) cc_final: 0.9281 (mmmm) REVERT: A 426 MET cc_start: 0.8921 (tpp) cc_final: 0.8556 (tpp) REVERT: B 523 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9199 (mp) REVERT: C 65 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8244 (tmtt) REVERT: C 104 MET cc_start: 0.9403 (ppp) cc_final: 0.9199 (ppp) REVERT: C 121 LYS cc_start: 0.9343 (tptp) cc_final: 0.9143 (tptp) REVERT: C 164 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.8945 (mt-10) REVERT: C 262 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8943 (t0) REVERT: C 293 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8759 (tt0) REVERT: C 369 LEU cc_start: 0.9127 (tp) cc_final: 0.8528 (tt) REVERT: C 377 ASN cc_start: 0.8807 (t0) cc_final: 0.8557 (t0) REVERT: D 535 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8657 (mmm) REVERT: D 626 MET cc_start: 0.8973 (tpp) cc_final: 0.8501 (tpp) REVERT: D 633 LYS cc_start: 0.9671 (mmmt) cc_final: 0.9441 (mmmt) REVERT: E 161 MET cc_start: 0.8952 (mmm) cc_final: 0.8150 (tmm) REVERT: E 162 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8532 (p) REVERT: E 373 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9114 (p) REVERT: E 426 MET cc_start: 0.7969 (tpp) cc_final: 0.7550 (tpp) REVERT: E 427 TRP cc_start: 0.7649 (m100) cc_final: 0.7067 (m100) REVERT: E 475 MET cc_start: 0.8240 (tpp) cc_final: 0.7985 (tpp) REVERT: F 530 MET cc_start: 0.9102 (tpp) cc_final: 0.8641 (tpt) REVERT: F 584 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8775 (tm-30) REVERT: H 3 GLN cc_start: 0.8912 (pp30) cc_final: 0.8651 (tm-30) REVERT: H 31 ASN cc_start: 0.9171 (t0) cc_final: 0.8792 (t0) REVERT: H 39 GLN cc_start: 0.9285 (tp-100) cc_final: 0.8938 (tp-100) REVERT: H 55 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8816 (ttmt) REVERT: H 97 ARG cc_start: 0.9182 (mmm160) cc_final: 0.8730 (mmm160) REVERT: I 5 GLN cc_start: 0.9196 (pp30) cc_final: 0.8933 (pp30) REVERT: I 11 LEU cc_start: 0.9504 (mm) cc_final: 0.9147 (tp) REVERT: I 55 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9052 (ttpt) REVERT: I 82 MET cc_start: 0.7441 (mpp) cc_final: 0.7159 (mpp) REVERT: I 97 ARG cc_start: 0.9092 (tpp80) cc_final: 0.8854 (mmm160) REVERT: X 34 MET cc_start: 0.7333 (mmp) cc_final: 0.7100 (mmp) REVERT: X 100 GLU cc_start: 0.8263 (pt0) cc_final: 0.7643 (mp0) REVERT: X 100 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8513 (mp0) REVERT: X 100 LYS cc_start: 0.8580 (tppt) cc_final: 0.8190 (tptp) REVERT: J 18 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8210 (mm) REVERT: J 87 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8676 (m) outliers start: 81 outliers final: 39 residues processed: 226 average time/residue: 0.3201 time to fit residues: 111.4283 Evaluate side-chains 188 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 142 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 214 optimal weight: 0.0670 chunk 123 optimal weight: 2.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN D 590 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.048672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.033752 restraints weight = 129935.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.034974 restraints weight = 70264.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035790 restraints weight = 48641.615| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19890 Z= 0.189 Angle : 0.735 13.141 27130 Z= 0.353 Chirality : 0.044 0.298 3192 Planarity : 0.004 0.043 3357 Dihedral : 9.068 114.017 4020 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.69 % Favored : 89.92 % Rotamer: Outliers : 5.02 % Allowed : 27.44 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.17), residues: 2312 helix: 0.78 (0.29), residues: 372 sheet: -0.68 (0.23), residues: 542 loop : -2.00 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 69 HIS 0.004 0.001 HIS C 374 PHE 0.039 0.001 PHE D 519 TYR 0.015 0.001 TYR H 100B ARG 0.006 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 49) link_NAG-ASN : angle 3.29973 ( 147) link_BETA1-4 : bond 0.00297 ( 22) link_BETA1-4 : angle 1.84571 ( 66) link_ALPHA1-3 : bond 0.03096 ( 1) link_ALPHA1-3 : angle 3.27027 ( 3) hydrogen bonds : bond 0.03385 ( 536) hydrogen bonds : angle 5.13232 ( 1449) SS BOND : bond 0.00652 ( 41) SS BOND : angle 1.38657 ( 82) covalent geometry : bond 0.00409 (19775) covalent geometry : angle 0.68642 (26832) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 154 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6728 (m) REVERT: A 80 ASN cc_start: 0.9521 (t0) cc_final: 0.9208 (p0) REVERT: A 95 MET cc_start: 0.9262 (ppp) cc_final: 0.9053 (ppp) REVERT: A 252 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9276 (mmmm) REVERT: A 475 MET cc_start: 0.7791 (ttp) cc_final: 0.7456 (ttp) REVERT: B 540 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8356 (mp10) REVERT: B 589 ASP cc_start: 0.8549 (m-30) cc_final: 0.8158 (p0) REVERT: B 626 MET cc_start: 0.8648 (tpp) cc_final: 0.8396 (tpp) REVERT: C 54 CYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6785 (m) REVERT: C 65 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8259 (tmtt) REVERT: C 95 MET cc_start: 0.9066 (ptm) cc_final: 0.8544 (tmm) REVERT: C 104 MET cc_start: 0.9405 (ppp) cc_final: 0.9171 (ppp) REVERT: C 164 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.8969 (mt-10) REVERT: C 262 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.9073 (t0) REVERT: C 293 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: C 369 LEU cc_start: 0.9191 (tp) cc_final: 0.8580 (tt) REVERT: C 377 ASN cc_start: 0.8836 (t0) cc_final: 0.8601 (t0) REVERT: C 426 MET cc_start: 0.8536 (tpp) cc_final: 0.8180 (tpp) REVERT: C 427 TRP cc_start: 0.8399 (m100) cc_final: 0.8077 (m100) REVERT: D 540 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8669 (mp10) REVERT: D 626 MET cc_start: 0.9044 (tpp) cc_final: 0.8510 (tpp) REVERT: D 632 ASP cc_start: 0.9167 (p0) cc_final: 0.8784 (p0) REVERT: D 633 LYS cc_start: 0.9702 (mmmt) cc_final: 0.9468 (mmmt) REVERT: E 104 MET cc_start: 0.9465 (ppp) cc_final: 0.9027 (ppp) REVERT: E 161 MET cc_start: 0.8873 (mmm) cc_final: 0.8124 (tmm) REVERT: E 162 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8521 (p) REVERT: E 373 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9178 (p) REVERT: E 426 MET cc_start: 0.7937 (tpp) cc_final: 0.7554 (tpp) REVERT: E 427 TRP cc_start: 0.7655 (m100) cc_final: 0.7030 (m100) REVERT: F 584 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8747 (tm-30) REVERT: F 626 MET cc_start: 0.8422 (tpp) cc_final: 0.7990 (tpp) REVERT: H 55 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8854 (ttmt) REVERT: H 82 MET cc_start: 0.8855 (mtp) cc_final: 0.8267 (tpt) REVERT: H 82 LEU cc_start: 0.9422 (mp) cc_final: 0.9177 (tt) REVERT: H 97 ARG cc_start: 0.9161 (mmm160) cc_final: 0.8864 (mmm160) REVERT: I 11 LEU cc_start: 0.9493 (mm) cc_final: 0.9140 (tp) REVERT: I 70 SER cc_start: 0.9485 (OUTLIER) cc_final: 0.9178 (p) REVERT: I 82 MET cc_start: 0.7825 (mpp) cc_final: 0.7285 (mpp) REVERT: I 97 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8856 (mmm160) REVERT: I 100 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9171 (p) REVERT: X 34 MET cc_start: 0.7311 (mmp) cc_final: 0.7040 (mmp) REVERT: J 18 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8150 (mm) outliers start: 102 outliers final: 57 residues processed: 249 average time/residue: 0.3346 time to fit residues: 126.6493 Evaluate side-chains 203 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 132 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 145 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 540 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 GLN X 100NGLN J 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.048552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.033685 restraints weight = 130285.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.034911 restraints weight = 70445.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.035709 restraints weight = 48852.766| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19890 Z= 0.174 Angle : 0.723 12.180 27130 Z= 0.351 Chirality : 0.044 0.263 3192 Planarity : 0.004 0.042 3357 Dihedral : 8.680 113.672 4020 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.43 % Favored : 90.14 % Rotamer: Outliers : 5.52 % Allowed : 27.49 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2312 helix: 0.45 (0.28), residues: 390 sheet: -0.63 (0.22), residues: 552 loop : -1.98 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 69 HIS 0.003 0.001 HIS X 35 PHE 0.022 0.001 PHE D 519 TYR 0.013 0.001 TYR H 100B ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 49) link_NAG-ASN : angle 3.09466 ( 147) link_BETA1-4 : bond 0.00300 ( 22) link_BETA1-4 : angle 1.72736 ( 66) link_ALPHA1-3 : bond 0.03077 ( 1) link_ALPHA1-3 : angle 3.19138 ( 3) hydrogen bonds : bond 0.03306 ( 536) hydrogen bonds : angle 5.01880 ( 1449) SS BOND : bond 0.00340 ( 41) SS BOND : angle 1.63341 ( 82) covalent geometry : bond 0.00382 (19775) covalent geometry : angle 0.67828 (26832) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 145 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6806 (m) REVERT: A 80 ASN cc_start: 0.9526 (t0) cc_final: 0.9225 (p0) REVERT: A 95 MET cc_start: 0.9273 (ppp) cc_final: 0.8998 (ppp) REVERT: A 150 MET cc_start: 0.8539 (ttp) cc_final: 0.8121 (mtm) REVERT: A 252 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9283 (mmmm) REVERT: A 287 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: A 426 MET cc_start: 0.8890 (tpp) cc_final: 0.8527 (tpp) REVERT: B 530 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8123 (mtm) REVERT: B 589 ASP cc_start: 0.8541 (m-30) cc_final: 0.8161 (p0) REVERT: C 54 CYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6688 (m) REVERT: C 65 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8233 (tmtt) REVERT: C 95 MET cc_start: 0.9095 (ptm) cc_final: 0.8620 (tmm) REVERT: C 104 MET cc_start: 0.9420 (ppp) cc_final: 0.9177 (ppp) REVERT: C 164 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.8977 (mt-10) REVERT: C 262 ASN cc_start: 0.9328 (OUTLIER) cc_final: 0.9112 (t0) REVERT: C 293 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: C 369 LEU cc_start: 0.9194 (tp) cc_final: 0.8569 (tt) REVERT: C 377 ASN cc_start: 0.8845 (t0) cc_final: 0.8617 (t0) REVERT: C 426 MET cc_start: 0.8504 (tpp) cc_final: 0.8258 (tpp) REVERT: C 427 TRP cc_start: 0.8360 (m100) cc_final: 0.7969 (m100) REVERT: D 540 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8651 (mp10) REVERT: D 605 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7881 (m) REVERT: D 632 ASP cc_start: 0.9206 (p0) cc_final: 0.8816 (p0) REVERT: D 633 LYS cc_start: 0.9716 (mmmt) cc_final: 0.9484 (mmmt) REVERT: E 125 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9337 (tt) REVERT: E 150 MET cc_start: 0.7378 (mtm) cc_final: 0.6881 (mtm) REVERT: E 161 MET cc_start: 0.8870 (mmm) cc_final: 0.8122 (tmm) REVERT: E 162 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.8569 (p) REVERT: E 426 MET cc_start: 0.7960 (tpp) cc_final: 0.7606 (tpp) REVERT: E 427 TRP cc_start: 0.7590 (m100) cc_final: 0.7010 (m100) REVERT: F 584 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8755 (tm-30) REVERT: F 626 MET cc_start: 0.8472 (tpp) cc_final: 0.7986 (tpp) REVERT: H 76 ASN cc_start: 0.9683 (m110) cc_final: 0.9096 (t0) REVERT: H 82 LEU cc_start: 0.9421 (mp) cc_final: 0.8446 (tt) REVERT: I 11 LEU cc_start: 0.9476 (mm) cc_final: 0.9151 (tp) REVERT: I 82 MET cc_start: 0.8005 (mpp) cc_final: 0.7461 (mpp) REVERT: I 97 ARG cc_start: 0.9083 (tpp80) cc_final: 0.8870 (mmm160) REVERT: I 100 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9172 (p) REVERT: X 34 MET cc_start: 0.7394 (mmp) cc_final: 0.7026 (mmp) REVERT: J 18 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8164 (mm) REVERT: J 1098 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.5223 (m-80) outliers start: 112 outliers final: 58 residues processed: 248 average time/residue: 0.2894 time to fit residues: 113.6708 Evaluate side-chains 202 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 128 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 211 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 HIS ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 GLN X 100NGLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.048386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.033495 restraints weight = 130060.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.034709 restraints weight = 70517.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.035516 restraints weight = 49056.849| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19890 Z= 0.172 Angle : 0.724 12.577 27130 Z= 0.350 Chirality : 0.044 0.246 3192 Planarity : 0.004 0.044 3357 Dihedral : 8.489 112.880 4020 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.47 % Favored : 90.10 % Rotamer: Outliers : 4.58 % Allowed : 28.18 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.17), residues: 2312 helix: 0.50 (0.28), residues: 390 sheet: -0.58 (0.23), residues: 539 loop : -1.96 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 427 HIS 0.004 0.001 HIS C 352 PHE 0.013 0.001 PHE E 382 TYR 0.013 0.001 TYR H 100B ARG 0.004 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 49) link_NAG-ASN : angle 3.00518 ( 147) link_BETA1-4 : bond 0.00303 ( 22) link_BETA1-4 : angle 1.67016 ( 66) link_ALPHA1-3 : bond 0.03080 ( 1) link_ALPHA1-3 : angle 3.20455 ( 3) hydrogen bonds : bond 0.03233 ( 536) hydrogen bonds : angle 4.95257 ( 1449) SS BOND : bond 0.00410 ( 41) SS BOND : angle 1.58628 ( 82) covalent geometry : bond 0.00377 (19775) covalent geometry : angle 0.68200 (26832) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 142 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6852 (m) REVERT: A 80 ASN cc_start: 0.9540 (t0) cc_final: 0.9239 (p0) REVERT: A 95 MET cc_start: 0.9321 (ppp) cc_final: 0.9022 (ppp) REVERT: A 150 MET cc_start: 0.8511 (ttp) cc_final: 0.8040 (mtm) REVERT: A 252 LYS cc_start: 0.9578 (OUTLIER) cc_final: 0.9253 (mmmm) REVERT: A 425 ASN cc_start: 0.9059 (t0) cc_final: 0.8729 (t0) REVERT: B 530 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8110 (mtm) REVERT: B 626 MET cc_start: 0.8449 (tpp) cc_final: 0.8025 (tpp) REVERT: C 54 CYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6289 (m) REVERT: C 65 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8228 (tmtt) REVERT: C 95 MET cc_start: 0.9094 (ptm) cc_final: 0.8661 (tmm) REVERT: C 104 MET cc_start: 0.9416 (ppp) cc_final: 0.9164 (ppp) REVERT: C 164 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.8994 (mt-10) REVERT: C 293 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: C 369 LEU cc_start: 0.9208 (tp) cc_final: 0.8585 (tt) REVERT: C 377 ASN cc_start: 0.8863 (t0) cc_final: 0.8645 (t0) REVERT: C 426 MET cc_start: 0.8522 (tpp) cc_final: 0.8025 (tpp) REVERT: C 427 TRP cc_start: 0.8344 (m100) cc_final: 0.7606 (m100) REVERT: D 530 MET cc_start: 0.8896 (tpp) cc_final: 0.8667 (tpp) REVERT: D 540 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8676 (mp10) REVERT: D 571 TRP cc_start: 0.6598 (m100) cc_final: 0.6310 (m100) REVERT: D 605 CYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7891 (m) REVERT: D 626 MET cc_start: 0.9035 (tpp) cc_final: 0.8199 (tpp) REVERT: D 632 ASP cc_start: 0.9221 (p0) cc_final: 0.8850 (p0) REVERT: E 104 MET cc_start: 0.9481 (ppp) cc_final: 0.9127 (ppp) REVERT: E 125 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9307 (tt) REVERT: E 161 MET cc_start: 0.8846 (mmm) cc_final: 0.8073 (tmm) REVERT: E 162 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.8572 (p) REVERT: E 426 MET cc_start: 0.8042 (tpp) cc_final: 0.7698 (tpp) REVERT: E 427 TRP cc_start: 0.7610 (m100) cc_final: 0.7023 (m100) REVERT: F 584 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8762 (tm-30) REVERT: F 626 MET cc_start: 0.8410 (tpp) cc_final: 0.7909 (tpp) REVERT: H 76 ASN cc_start: 0.9671 (m110) cc_final: 0.9081 (t0) REVERT: H 82 LEU cc_start: 0.9433 (mp) cc_final: 0.8465 (tt) REVERT: I 11 LEU cc_start: 0.9460 (mm) cc_final: 0.9165 (tp) REVERT: I 82 MET cc_start: 0.8132 (mpp) cc_final: 0.7605 (mpp) REVERT: I 97 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8870 (mmm160) REVERT: I 100 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9188 (p) REVERT: X 34 MET cc_start: 0.7536 (mmp) cc_final: 0.7182 (mmp) REVERT: J 18 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8172 (mm) REVERT: J 1098 PHE cc_start: 0.5724 (OUTLIER) cc_final: 0.5136 (m-80) outliers start: 93 outliers final: 64 residues processed: 224 average time/residue: 0.3083 time to fit residues: 108.2463 Evaluate side-chains 208 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 130 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 71 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN F 590 GLN F 658 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.047239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032452 restraints weight = 131966.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.033625 restraints weight = 72993.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.034387 restraints weight = 51293.769| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19890 Z= 0.255 Angle : 0.774 12.536 27130 Z= 0.376 Chirality : 0.044 0.252 3192 Planarity : 0.004 0.043 3357 Dihedral : 8.426 111.759 4020 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.25 % Favored : 89.36 % Rotamer: Outliers : 5.17 % Allowed : 28.52 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.17), residues: 2312 helix: 0.43 (0.28), residues: 390 sheet: -0.64 (0.23), residues: 533 loop : -1.97 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 427 HIS 0.004 0.001 HIS A 352 PHE 0.015 0.001 PHE A 288 TYR 0.015 0.001 TYR H 95 ARG 0.005 0.000 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 49) link_NAG-ASN : angle 3.02310 ( 147) link_BETA1-4 : bond 0.00248 ( 22) link_BETA1-4 : angle 1.77560 ( 66) link_ALPHA1-3 : bond 0.02557 ( 1) link_ALPHA1-3 : angle 2.82124 ( 3) hydrogen bonds : bond 0.03426 ( 536) hydrogen bonds : angle 5.08495 ( 1449) SS BOND : bond 0.00382 ( 41) SS BOND : angle 1.53989 ( 82) covalent geometry : bond 0.00548 (19775) covalent geometry : angle 0.73499 (26832) Misc. bond : bond 0.00062 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 136 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9555 (t0) cc_final: 0.9227 (p0) REVERT: A 95 MET cc_start: 0.9424 (ppp) cc_final: 0.9111 (ppp) REVERT: A 150 MET cc_start: 0.8523 (ttp) cc_final: 0.8115 (mtm) REVERT: A 252 LYS cc_start: 0.9575 (OUTLIER) cc_final: 0.9253 (mmmm) REVERT: A 425 ASN cc_start: 0.9123 (t0) cc_final: 0.8791 (t0) REVERT: B 589 ASP cc_start: 0.8668 (m-30) cc_final: 0.8271 (p0) REVERT: B 626 MET cc_start: 0.8591 (tpp) cc_final: 0.8345 (tpp) REVERT: C 54 CYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6534 (m) REVERT: C 104 MET cc_start: 0.9440 (ppp) cc_final: 0.9177 (ppp) REVERT: C 164 GLU cc_start: 0.9413 (OUTLIER) cc_final: 0.8979 (mt-10) REVERT: C 271 MET cc_start: 0.7867 (mmm) cc_final: 0.7630 (mmm) REVERT: C 293 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8578 (tt0) REVERT: C 369 LEU cc_start: 0.9251 (tp) cc_final: 0.8673 (tt) REVERT: C 377 ASN cc_start: 0.8864 (t0) cc_final: 0.8659 (t0) REVERT: C 426 MET cc_start: 0.8555 (tpp) cc_final: 0.8160 (tpp) REVERT: C 427 TRP cc_start: 0.8329 (m100) cc_final: 0.7626 (m100) REVERT: D 530 MET cc_start: 0.8791 (tpp) cc_final: 0.8493 (tpp) REVERT: D 540 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8706 (mp10) REVERT: D 605 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7838 (m) REVERT: D 626 MET cc_start: 0.9027 (tpp) cc_final: 0.8207 (tpp) REVERT: E 104 MET cc_start: 0.9517 (ppp) cc_final: 0.9148 (ppp) REVERT: E 150 MET cc_start: 0.7152 (mtm) cc_final: 0.6800 (mpp) REVERT: E 161 MET cc_start: 0.8766 (mmm) cc_final: 0.8504 (mmm) REVERT: E 426 MET cc_start: 0.8077 (tpp) cc_final: 0.7700 (tpp) REVERT: E 427 TRP cc_start: 0.7727 (m100) cc_final: 0.7197 (m100) REVERT: F 535 MET cc_start: 0.8434 (mmm) cc_final: 0.8228 (mmm) REVERT: F 584 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8728 (tm-30) REVERT: F 589 ASP cc_start: 0.8869 (m-30) cc_final: 0.8384 (p0) REVERT: F 599 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8801 (m) REVERT: F 626 MET cc_start: 0.8449 (tpp) cc_final: 0.8189 (tpp) REVERT: H 55 LYS cc_start: 0.9239 (ttpt) cc_final: 0.9027 (pttt) REVERT: H 76 ASN cc_start: 0.9684 (m110) cc_final: 0.9105 (t0) REVERT: H 82 LEU cc_start: 0.9443 (mp) cc_final: 0.8504 (tt) REVERT: I 11 LEU cc_start: 0.9425 (mm) cc_final: 0.9143 (tp) REVERT: I 18 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7505 (mm) REVERT: I 82 MET cc_start: 0.8313 (mpp) cc_final: 0.7807 (mpp) REVERT: I 100 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9230 (p) REVERT: I 102 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: X 98 GLU cc_start: 0.8692 (tp30) cc_final: 0.8415 (mm-30) REVERT: J 18 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8123 (mm) REVERT: J 1098 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.5082 (m-80) outliers start: 105 outliers final: 73 residues processed: 233 average time/residue: 0.3779 time to fit residues: 140.2555 Evaluate side-chains 214 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 129 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 102 PHE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 135 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 287 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.048130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.033325 restraints weight = 129845.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.034523 restraints weight = 71436.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.035308 restraints weight = 50004.817| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19890 Z= 0.149 Angle : 0.737 12.512 27130 Z= 0.355 Chirality : 0.044 0.247 3192 Planarity : 0.004 0.043 3357 Dihedral : 8.139 111.038 4020 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.74 % Favored : 90.87 % Rotamer: Outliers : 4.19 % Allowed : 29.75 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), residues: 2312 helix: 0.48 (0.28), residues: 390 sheet: -0.68 (0.23), residues: 535 loop : -1.88 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 427 HIS 0.004 0.001 HIS X 35 PHE 0.014 0.001 PHE E 382 TYR 0.014 0.001 TYR H 100B ARG 0.006 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 49) link_NAG-ASN : angle 2.82743 ( 147) link_BETA1-4 : bond 0.00343 ( 22) link_BETA1-4 : angle 1.59865 ( 66) link_ALPHA1-3 : bond 0.02900 ( 1) link_ALPHA1-3 : angle 3.27159 ( 3) hydrogen bonds : bond 0.03237 ( 536) hydrogen bonds : angle 4.91485 ( 1449) SS BOND : bond 0.00356 ( 41) SS BOND : angle 1.28850 ( 82) covalent geometry : bond 0.00331 (19775) covalent geometry : angle 0.70165 (26832) Misc. bond : bond 0.00051 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 143 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9516 (t0) cc_final: 0.9212 (p0) REVERT: A 95 MET cc_start: 0.9332 (ppp) cc_final: 0.9014 (ppp) REVERT: A 150 MET cc_start: 0.8443 (ttp) cc_final: 0.8050 (mtm) REVERT: A 252 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9277 (mmmm) REVERT: A 287 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8687 (tt0) REVERT: A 425 ASN cc_start: 0.9099 (t0) cc_final: 0.8710 (t0) REVERT: B 530 MET cc_start: 0.8992 (mtp) cc_final: 0.8148 (mtm) REVERT: B 589 ASP cc_start: 0.8586 (m-30) cc_final: 0.8218 (p0) REVERT: B 626 MET cc_start: 0.8582 (tpp) cc_final: 0.8330 (tpp) REVERT: C 54 CYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6501 (m) REVERT: C 95 MET cc_start: 0.9161 (ptm) cc_final: 0.8742 (ppp) REVERT: C 104 MET cc_start: 0.9397 (ppp) cc_final: 0.9127 (ppp) REVERT: C 164 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.8975 (mt-10) REVERT: C 293 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: C 369 LEU cc_start: 0.9221 (tp) cc_final: 0.8639 (tt) REVERT: C 377 ASN cc_start: 0.8754 (t0) cc_final: 0.8469 (t0) REVERT: C 426 MET cc_start: 0.8556 (tpp) cc_final: 0.8206 (tpp) REVERT: C 427 TRP cc_start: 0.8209 (m100) cc_final: 0.7548 (m100) REVERT: D 530 MET cc_start: 0.8795 (tpp) cc_final: 0.8594 (tpp) REVERT: D 540 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8697 (mp10) REVERT: D 574 LYS cc_start: 0.8936 (mmtm) cc_final: 0.8684 (mppt) REVERT: D 605 CYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7749 (m) REVERT: D 626 MET cc_start: 0.8992 (tpp) cc_final: 0.8209 (tpp) REVERT: D 632 ASP cc_start: 0.9169 (p0) cc_final: 0.8890 (p0) REVERT: D 647 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8555 (tm-30) REVERT: E 104 MET cc_start: 0.9500 (ppp) cc_final: 0.9218 (ppp) REVERT: E 150 MET cc_start: 0.7152 (mtm) cc_final: 0.6731 (mpp) REVERT: E 161 MET cc_start: 0.8736 (mmm) cc_final: 0.8501 (mmm) REVERT: E 287 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8424 (tm-30) REVERT: F 535 MET cc_start: 0.8442 (mmm) cc_final: 0.8217 (mmm) REVERT: H 76 ASN cc_start: 0.9691 (m110) cc_final: 0.9118 (t0) REVERT: H 82 LEU cc_start: 0.9406 (mp) cc_final: 0.8481 (tt) REVERT: I 11 LEU cc_start: 0.9398 (mm) cc_final: 0.9159 (tp) REVERT: I 18 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7509 (mm) REVERT: I 82 MET cc_start: 0.8323 (mpp) cc_final: 0.7796 (mpp) REVERT: I 100 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9223 (p) REVERT: J 18 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8182 (mm) REVERT: J 1098 PHE cc_start: 0.5638 (OUTLIER) cc_final: 0.5128 (m-80) outliers start: 85 outliers final: 62 residues processed: 221 average time/residue: 0.5451 time to fit residues: 193.4082 Evaluate side-chains 203 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 129 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 29 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 141 optimal weight: 0.0040 chunk 136 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 227 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 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 = 0.3389 r_free = 0.3389 target = 0.048368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.033560 restraints weight = 129852.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.034789 restraints weight = 70173.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.035595 restraints weight = 48614.642| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19890 Z= 0.139 Angle : 0.745 12.423 27130 Z= 0.361 Chirality : 0.045 0.246 3192 Planarity : 0.004 0.046 3357 Dihedral : 8.000 110.091 4020 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.82 % Favored : 90.70 % Rotamer: Outliers : 3.99 % Allowed : 29.70 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.18), residues: 2312 helix: 0.71 (0.28), residues: 372 sheet: -0.81 (0.22), residues: 586 loop : -1.76 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP A 427 HIS 0.003 0.001 HIS X 35 PHE 0.012 0.001 PHE E 382 TYR 0.014 0.001 TYR H 100B ARG 0.015 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 49) link_NAG-ASN : angle 2.75450 ( 147) link_BETA1-4 : bond 0.00348 ( 22) link_BETA1-4 : angle 1.57111 ( 66) link_ALPHA1-3 : bond 0.02850 ( 1) link_ALPHA1-3 : angle 3.36032 ( 3) hydrogen bonds : bond 0.03157 ( 536) hydrogen bonds : angle 4.87572 ( 1449) SS BOND : bond 0.00416 ( 41) SS BOND : angle 1.40312 ( 82) covalent geometry : bond 0.00313 (19775) covalent geometry : angle 0.71175 (26832) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 142 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9531 (t0) cc_final: 0.9243 (p0) REVERT: A 95 MET cc_start: 0.9349 (ppp) cc_final: 0.8998 (ppp) REVERT: A 104 MET cc_start: 0.9595 (OUTLIER) cc_final: 0.9339 (tpp) REVERT: A 150 MET cc_start: 0.8492 (ttp) cc_final: 0.8083 (mtm) REVERT: A 252 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.9270 (mmmm) REVERT: A 425 ASN cc_start: 0.9151 (t0) cc_final: 0.8812 (t0) REVERT: B 589 ASP cc_start: 0.8610 (m-30) cc_final: 0.8216 (p0) REVERT: B 626 MET cc_start: 0.8546 (tpp) cc_final: 0.8107 (tpp) REVERT: C 54 CYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6487 (m) REVERT: C 95 MET cc_start: 0.9232 (ptm) cc_final: 0.8772 (ppp) REVERT: C 104 MET cc_start: 0.9404 (ppp) cc_final: 0.9147 (ppp) REVERT: C 164 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.8989 (mt-10) REVERT: C 271 MET cc_start: 0.8046 (mmm) cc_final: 0.7795 (mmm) REVERT: C 293 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: C 369 LEU cc_start: 0.9197 (tp) cc_final: 0.8620 (tt) REVERT: C 377 ASN cc_start: 0.8757 (t0) cc_final: 0.8530 (t0) REVERT: C 426 MET cc_start: 0.8628 (tpp) cc_final: 0.8359 (tpp) REVERT: C 427 TRP cc_start: 0.8181 (m100) cc_final: 0.7672 (m100) REVERT: D 530 MET cc_start: 0.8754 (tpp) cc_final: 0.8552 (tpp) REVERT: D 540 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8666 (mp10) REVERT: D 605 CYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7753 (m) REVERT: D 626 MET cc_start: 0.9012 (tpp) cc_final: 0.8220 (tpp) REVERT: D 647 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8582 (tm-30) REVERT: E 100 MET cc_start: 0.9250 (mtp) cc_final: 0.8975 (ptp) REVERT: E 104 MET cc_start: 0.9515 (ppp) cc_final: 0.9138 (ppp) REVERT: E 150 MET cc_start: 0.7076 (mtm) cc_final: 0.6650 (mpp) REVERT: E 161 MET cc_start: 0.8750 (mmm) cc_final: 0.8488 (mmm) REVERT: E 287 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8411 (tm-30) REVERT: E 426 MET cc_start: 0.7720 (tpp) cc_final: 0.7416 (tpp) REVERT: E 427 TRP cc_start: 0.7741 (m100) cc_final: 0.7379 (m100) REVERT: E 475 MET cc_start: 0.7056 (tmm) cc_final: 0.6761 (tmm) REVERT: F 535 MET cc_start: 0.8469 (mmm) cc_final: 0.8209 (mmm) REVERT: F 589 ASP cc_start: 0.8841 (m-30) cc_final: 0.8337 (p0) REVERT: H 76 ASN cc_start: 0.9704 (m110) cc_final: 0.9152 (t0) REVERT: H 82 LEU cc_start: 0.9431 (mp) cc_final: 0.8504 (tt) REVERT: I 11 LEU cc_start: 0.9381 (mm) cc_final: 0.9164 (tp) REVERT: I 18 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7391 (mm) REVERT: I 82 MET cc_start: 0.8337 (mpp) cc_final: 0.7802 (mpp) REVERT: I 97 ARG cc_start: 0.9056 (mmm160) cc_final: 0.8552 (mmm160) REVERT: I 100 THR cc_start: 0.9457 (OUTLIER) cc_final: 0.9223 (p) REVERT: I 102 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: X 34 MET cc_start: 0.7746 (mmp) cc_final: 0.7370 (mmp) REVERT: J 18 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (mm) REVERT: J 1098 PHE cc_start: 0.5637 (OUTLIER) cc_final: 0.5116 (m-80) outliers start: 81 outliers final: 55 residues processed: 214 average time/residue: 0.6035 time to fit residues: 204.5271 Evaluate side-chains 201 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 133 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 287 GLN Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 102 PHE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 155 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 chunk 83 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.047519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.032971 restraints weight = 128772.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.034162 restraints weight = 70376.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.034955 restraints weight = 49042.734| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19890 Z= 0.196 Angle : 0.763 12.292 27130 Z= 0.371 Chirality : 0.044 0.252 3192 Planarity : 0.004 0.043 3357 Dihedral : 8.001 108.952 4020 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.39 % Favored : 90.14 % Rotamer: Outliers : 3.55 % Allowed : 30.49 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2312 helix: 0.67 (0.28), residues: 372 sheet: -0.84 (0.22), residues: 588 loop : -1.76 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 427 HIS 0.005 0.001 HIS A 374 PHE 0.012 0.001 PHE E 382 TYR 0.013 0.001 TYR H 100B ARG 0.014 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 49) link_NAG-ASN : angle 2.79893 ( 147) link_BETA1-4 : bond 0.00268 ( 22) link_BETA1-4 : angle 1.64422 ( 66) link_ALPHA1-3 : bond 0.02872 ( 1) link_ALPHA1-3 : angle 3.36890 ( 3) hydrogen bonds : bond 0.03225 ( 536) hydrogen bonds : angle 4.95317 ( 1449) SS BOND : bond 0.00383 ( 41) SS BOND : angle 1.48708 ( 82) covalent geometry : bond 0.00431 (19775) covalent geometry : angle 0.72901 (26832) Misc. bond : bond 0.00034 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 134 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9553 (t0) cc_final: 0.9249 (p0) REVERT: A 95 MET cc_start: 0.9412 (ppp) cc_final: 0.9088 (ppp) REVERT: A 104 MET cc_start: 0.9607 (OUTLIER) cc_final: 0.9336 (tpp) REVERT: A 150 MET cc_start: 0.8502 (ttp) cc_final: 0.8133 (mtm) REVERT: A 252 LYS cc_start: 0.9577 (OUTLIER) cc_final: 0.9235 (mmmm) REVERT: A 425 ASN cc_start: 0.9139 (t0) cc_final: 0.8778 (t0) REVERT: B 589 ASP cc_start: 0.8644 (m-30) cc_final: 0.8258 (p0) REVERT: C 54 CYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6451 (m) REVERT: C 95 MET cc_start: 0.9255 (ptm) cc_final: 0.8780 (ppp) REVERT: C 104 MET cc_start: 0.9422 (ppp) cc_final: 0.9165 (ppp) REVERT: C 164 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.8982 (mt-10) REVERT: C 271 MET cc_start: 0.8084 (mmm) cc_final: 0.7811 (mmm) REVERT: C 293 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8551 (tt0) REVERT: C 369 LEU cc_start: 0.9239 (tp) cc_final: 0.8688 (tt) REVERT: C 377 ASN cc_start: 0.8826 (t0) cc_final: 0.8560 (t0) REVERT: C 426 MET cc_start: 0.8596 (tpp) cc_final: 0.8282 (tpp) REVERT: C 427 TRP cc_start: 0.8232 (m100) cc_final: 0.7669 (m100) REVERT: D 530 MET cc_start: 0.8765 (tpp) cc_final: 0.8549 (tpp) REVERT: D 540 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8724 (mp10) REVERT: D 605 CYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7738 (m) REVERT: D 626 MET cc_start: 0.9048 (tpp) cc_final: 0.8294 (tpp) REVERT: D 647 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8578 (tm-30) REVERT: E 104 MET cc_start: 0.9522 (ppp) cc_final: 0.9150 (ppp) REVERT: E 161 MET cc_start: 0.8757 (mmm) cc_final: 0.8556 (mmm) REVERT: E 426 MET cc_start: 0.7692 (tpp) cc_final: 0.7422 (tpp) REVERT: E 475 MET cc_start: 0.7028 (tmm) cc_final: 0.6792 (tmm) REVERT: F 535 MET cc_start: 0.8500 (mmm) cc_final: 0.8222 (mmm) REVERT: F 589 ASP cc_start: 0.8863 (m-30) cc_final: 0.8357 (p0) REVERT: F 626 MET cc_start: 0.8454 (tpp) cc_final: 0.8188 (tpp) REVERT: H 55 LYS cc_start: 0.9179 (pttt) cc_final: 0.8915 (pttt) REVERT: H 76 ASN cc_start: 0.9711 (m110) cc_final: 0.9159 (t0) REVERT: H 82 LEU cc_start: 0.9435 (mp) cc_final: 0.8538 (tt) REVERT: I 11 LEU cc_start: 0.9408 (mm) cc_final: 0.9164 (tp) REVERT: I 18 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7397 (mm) REVERT: I 82 MET cc_start: 0.8378 (mpp) cc_final: 0.7827 (mpp) REVERT: I 100 THR cc_start: 0.9471 (OUTLIER) cc_final: 0.9234 (p) REVERT: I 102 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: X 34 MET cc_start: 0.7772 (mmp) cc_final: 0.7363 (mmp) REVERT: J 18 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8085 (mm) REVERT: J 1098 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.5091 (m-80) outliers start: 72 outliers final: 57 residues processed: 198 average time/residue: 0.3151 time to fit residues: 98.7073 Evaluate side-chains 201 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 132 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 102 PHE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 177 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 0.0970 chunk 221 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 650 GLN F 658 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.048686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.033913 restraints weight = 128744.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.035132 restraints weight = 69705.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.035945 restraints weight = 48342.881| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19890 Z= 0.127 Angle : 0.741 12.033 27130 Z= 0.360 Chirality : 0.044 0.246 3192 Planarity : 0.004 0.045 3357 Dihedral : 7.790 108.107 4020 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.65 % Favored : 90.87 % Rotamer: Outliers : 3.20 % Allowed : 30.94 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.56 (0.18), residues: 2312 helix: 0.69 (0.28), residues: 372 sheet: -0.76 (0.22), residues: 588 loop : -1.72 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 427 HIS 0.003 0.001 HIS X 35 PHE 0.012 0.001 PHE E 382 TYR 0.014 0.001 TYR H 100B ARG 0.013 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 49) link_NAG-ASN : angle 2.63148 ( 147) link_BETA1-4 : bond 0.00442 ( 22) link_BETA1-4 : angle 1.50293 ( 66) link_ALPHA1-3 : bond 0.02908 ( 1) link_ALPHA1-3 : angle 3.66739 ( 3) hydrogen bonds : bond 0.03044 ( 536) hydrogen bonds : angle 4.79264 ( 1449) SS BOND : bond 0.00375 ( 41) SS BOND : angle 1.28468 ( 82) covalent geometry : bond 0.00288 (19775) covalent geometry : angle 0.71053 (26832) Misc. bond : bond 0.00025 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8272.39 seconds wall clock time: 151 minutes 1.10 seconds (9061.10 seconds total)