Starting phenix.real_space_refine on Sun Aug 24 11:04:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tni_41417/08_2025/8tni_41417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tni_41417/08_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_41417/08_2025/8tni_41417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tni_41417/08_2025/8tni_41417.map" model { file = "/net/cci-nas-00/data/ceres_data/8tni_41417/08_2025/8tni_41417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tni_41417/08_2025/8tni_41417.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.38, per 1000 atoms: 0.23 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: 1.91 Conformation dependent library (CDL) restraints added in 828.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.66 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: 2.76 Time building geometry restraints manager: 2.43 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 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: 10.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.040 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- 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 : 13.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (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 ARG 0.030 0.001 ARG E 166 TYR 0.019 0.001 TYR H 100B PHE 0.014 0.002 PHE B 522 TRP 0.032 0.002 TRP E 69 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00528 (19775) covalent geometry : angle 0.87759 (26832) SS BOND : bond 0.00438 ( 41) SS BOND : angle 1.58288 ( 82) hydrogen bonds : bond 0.13625 ( 536) hydrogen bonds : angle 6.16684 ( 1449) Misc. bond : bond 0.01308 ( 2) link_ALPHA1-3 : bond 0.02166 ( 1) link_ALPHA1-3 : angle 3.48526 ( 3) link_BETA1-4 : bond 0.00716 ( 22) link_BETA1-4 : angle 2.40316 ( 66) link_NAG-ASN : bond 0.00880 ( 49) link_NAG-ASN : angle 5.63134 ( 147) *********************** 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 : 0.739 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: 0.1585 time to fit residues: 52.7605 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 : 0.507 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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** B 591 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN D 590 GLN D 625 ASN ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.048435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.033561 restraints weight = 129798.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.034743 restraints weight = 70328.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.035558 restraints weight = 48864.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036077 restraints weight = 38735.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.036415 restraints weight = 33372.147| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19890 Z= 0.276 Angle : 0.840 13.345 27130 Z= 0.405 Chirality : 0.046 0.466 3192 Planarity : 0.005 0.061 3357 Dihedral : 11.788 114.445 4022 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.25 % Favored : 89.36 % Rotamer: Outliers : 5.37 % Allowed : 29.06 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.17), residues: 2312 helix: 0.63 (0.28), residues: 372 sheet: -0.84 (0.22), residues: 558 loop : -2.16 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 166 TYR 0.016 0.002 TYR H 100B PHE 0.027 0.002 PHE B 519 TRP 0.019 0.002 TRP F 631 HIS 0.006 0.001 HIS X 35 Details of bonding type rmsd covalent geometry : bond 0.00594 (19775) covalent geometry : angle 0.77989 (26832) SS BOND : bond 0.00406 ( 41) SS BOND : angle 1.38991 ( 82) hydrogen bonds : bond 0.04062 ( 536) hydrogen bonds : angle 5.55165 ( 1449) Misc. bond : bond 0.00267 ( 2) link_ALPHA1-3 : bond 0.02666 ( 1) link_ALPHA1-3 : angle 2.66758 ( 3) link_BETA1-4 : bond 0.00279 ( 22) link_BETA1-4 : angle 2.20587 ( 66) link_NAG-ASN : bond 0.00730 ( 49) link_NAG-ASN : angle 3.99204 ( 147) *********************** 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 268 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 159 time to evaluate : 0.451 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: 0.9543 (OUTLIER) cc_final: 0.9328 (p) REVERT: A 252 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9338 (mmmm) REVERT: A 426 MET cc_start: 0.8841 (tpp) cc_final: 0.8465 (tpp) REVERT: B 584 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8285 (pt0) REVERT: B 589 ASP cc_start: 0.8473 (m-30) cc_final: 0.8148 (p0) REVERT: B 626 MET cc_start: 0.8811 (ttt) cc_final: 0.8296 (tpp) REVERT: C 164 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8931 (mt-10) REVERT: C 262 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8911 (t0) REVERT: C 293 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: C 369 LEU cc_start: 0.9161 (tp) cc_final: 0.8627 (tt) REVERT: C 377 ASN cc_start: 0.8641 (t0) cc_final: 0.8433 (t0) REVERT: D 626 MET cc_start: 0.8858 (tpp) cc_final: 0.8438 (tpp) REVERT: D 632 ASP cc_start: 0.8689 (p0) cc_final: 0.8470 (p0) REVERT: D 633 LYS cc_start: 0.9615 (mmmt) cc_final: 0.9360 (mmmt) REVERT: D 651 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8461 (m110) REVERT: E 171 LYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9045 (tptm) REVERT: E 426 MET cc_start: 0.7848 (tpp) cc_final: 0.7406 (tpp) REVERT: E 427 TRP cc_start: 0.7636 (m100) cc_final: 0.7134 (m100) REVERT: H 3 GLN cc_start: 0.8716 (pp30) cc_final: 0.8463 (tm-30) REVERT: H 30 GLU cc_start: 0.8936 (pm20) cc_final: 0.8657 (pm20) REVERT: H 31 ASN cc_start: 0.9212 (t0) cc_final: 0.8713 (t0) REVERT: H 82 LEU cc_start: 0.9291 (mp) cc_final: 0.8443 (tt) REVERT: I 100 THR cc_start: 0.9427 (OUTLIER) cc_final: 0.9183 (p) REVERT: X 34 MET cc_start: 0.7468 (mmp) cc_final: 0.7183 (mmp) REVERT: X 100 GLU cc_start: 0.8270 (pt0) cc_final: 0.7668 (mp0) REVERT: X 100 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8477 (mp0) REVERT: X 100 LYS cc_start: 0.8629 (tppt) cc_final: 0.8274 (tptp) REVERT: J 18 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8188 (mm) REVERT: J 87 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8735 (m) outliers start: 109 outliers final: 52 residues processed: 258 average time/residue: 0.1323 time to fit residues: 52.0754 Evaluate side-chains 196 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 134 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 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 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 416 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 651 ASN 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 171 LYS Chi-restraints excluded: chain E residue 198 THR 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 F residue 545 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 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 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 1 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN F 658 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 100NGLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.047154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.032309 restraints weight = 132662.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.033485 restraints weight = 73327.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.034257 restraints weight = 51360.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.034764 restraints weight = 41100.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.035087 restraints weight = 35573.813| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 19890 Z= 0.335 Angle : 0.842 13.337 27130 Z= 0.407 Chirality : 0.046 0.358 3192 Planarity : 0.005 0.045 3357 Dihedral : 10.193 115.038 4020 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.47 % Favored : 89.14 % Rotamer: Outliers : 6.35 % Allowed : 28.03 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.17), residues: 2312 helix: 0.30 (0.27), residues: 390 sheet: -0.59 (0.24), residues: 486 loop : -2.13 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 166 TYR 0.016 0.002 TYR H 100B PHE 0.018 0.002 PHE D 519 TRP 0.022 0.002 TRP E 69 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00715 (19775) covalent geometry : angle 0.78916 (26832) SS BOND : bond 0.00465 ( 41) SS BOND : angle 1.62053 ( 82) hydrogen bonds : bond 0.03975 ( 536) hydrogen bonds : angle 5.50217 ( 1449) Misc. bond : bond 0.00118 ( 2) link_ALPHA1-3 : bond 0.03603 ( 1) link_ALPHA1-3 : angle 3.60789 ( 3) link_BETA1-4 : bond 0.00299 ( 22) link_BETA1-4 : angle 2.02792 ( 66) link_NAG-ASN : bond 0.00790 ( 49) link_NAG-ASN : angle 3.66638 ( 147) *********************** 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 279 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 150 time to evaluate : 0.623 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: 0.9497 (t0) cc_final: 0.9160 (p0) REVERT: A 252 LYS cc_start: 0.9597 (OUTLIER) cc_final: 0.9303 (mmmm) REVERT: A 426 MET cc_start: 0.8899 (tpp) cc_final: 0.8666 (tpp) REVERT: A 427 TRP cc_start: 0.8598 (m100) cc_final: 0.8163 (m100) REVERT: A 475 MET cc_start: 0.7047 (ptp) cc_final: 0.6601 (ptp) REVERT: B 530 MET cc_start: 0.8987 (mtp) cc_final: 0.8149 (mtm) REVERT: B 588 ARG cc_start: 0.8740 (tpp-160) cc_final: 0.8324 (tpp-160) REVERT: B 589 ASP cc_start: 0.8614 (m-30) cc_final: 0.8221 (p0) REVERT: B 601 LYS cc_start: 0.7377 (ttpt) cc_final: 0.6224 (pttt) REVERT: B 626 MET cc_start: 0.8948 (ttt) cc_final: 0.8387 (ttt) REVERT: C 104 MET cc_start: 0.9447 (ppp) cc_final: 0.9206 (ppp) REVERT: C 121 LYS cc_start: 0.9340 (tptp) cc_final: 0.9069 (tppt) REVERT: C 164 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.8963 (mt-10) REVERT: C 262 ASN cc_start: 0.9375 (OUTLIER) cc_final: 0.9155 (t0) REVERT: C 293 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8795 (tt0) REVERT: C 369 LEU cc_start: 0.9209 (tp) cc_final: 0.8694 (tt) REVERT: C 373 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.8998 (p) REVERT: C 426 MET cc_start: 0.8470 (tpp) cc_final: 0.8061 (tpp) REVERT: C 427 TRP cc_start: 0.8494 (m100) cc_final: 0.8078 (m100) REVERT: D 540 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8687 (mp10) REVERT: D 626 MET cc_start: 0.8943 (tpp) cc_final: 0.8501 (tpp) REVERT: D 633 LYS cc_start: 0.9677 (mmmt) cc_final: 0.9466 (mmmt) REVERT: D 651 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8426 (m110) REVERT: E 104 MET cc_start: 0.9528 (ppp) cc_final: 0.9101 (ppp) REVERT: E 161 MET cc_start: 0.8744 (mmm) cc_final: 0.8383 (tmm) REVERT: E 171 LYS cc_start: 0.9577 (OUTLIER) cc_final: 0.9206 (tptm) REVERT: E 373 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9247 (p) REVERT: E 426 MET cc_start: 0.8045 (tpp) cc_final: 0.7658 (tpp) REVERT: F 530 MET cc_start: 0.9218 (tpp) cc_final: 0.8852 (tpt) REVERT: H 76 ASN cc_start: 0.9586 (m-40) cc_final: 0.9036 (t0) REVERT: H 82 LEU cc_start: 0.9451 (mp) cc_final: 0.8621 (tt) REVERT: H 97 ARG cc_start: 0.9229 (mmm160) cc_final: 0.8834 (mmm-85) REVERT: I 82 MET cc_start: 0.7668 (mpp) cc_final: 0.7085 (mpp) REVERT: I 100 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9185 (p) REVERT: X 34 MET cc_start: 0.7368 (mmp) cc_final: 0.7108 (mmp) REVERT: X 100 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8691 (mm-40) REVERT: J 18 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8108 (mm) outliers start: 129 outliers final: 75 residues processed: 270 average time/residue: 0.1212 time to fit residues: 50.7155 Evaluate side-chains 217 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 130 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 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 201 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 621 GLU 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 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 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 373 THR 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 489 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 651 ASN 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 135 THR Chi-restraints excluded: chain E residue 171 LYS 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 244 THR Chi-restraints excluded: chain E residue 254 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 373 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 592 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 57 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 THR 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 X residue 100 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 192 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 100NGLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.048355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.033541 restraints weight = 129487.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.034711 restraints weight = 69841.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.035529 restraints weight = 48404.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.036021 restraints weight = 38327.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.036389 restraints weight = 33153.803| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2401 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= 0.147 Angle : 0.754 13.310 27130 Z= 0.363 Chirality : 0.045 0.288 3192 Planarity : 0.004 0.043 3357 Dihedral : 9.179 114.474 4020 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.21 % Favored : 90.35 % Rotamer: Outliers : 4.68 % Allowed : 29.06 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.17), residues: 2312 helix: 0.52 (0.28), residues: 384 sheet: -0.58 (0.23), residues: 522 loop : -2.06 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 542 TYR 0.015 0.001 TYR H 100B PHE 0.046 0.002 PHE D 519 TRP 0.021 0.001 TRP E 69 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00324 (19775) covalent geometry : angle 0.70450 (26832) SS BOND : bond 0.00380 ( 41) SS BOND : angle 1.76967 ( 82) hydrogen bonds : bond 0.03493 ( 536) hydrogen bonds : angle 5.19301 ( 1449) Misc. bond : bond 0.00073 ( 2) link_ALPHA1-3 : bond 0.03233 ( 1) link_ALPHA1-3 : angle 3.21143 ( 3) link_BETA1-4 : bond 0.00357 ( 22) link_BETA1-4 : angle 1.78865 ( 66) link_NAG-ASN : bond 0.00497 ( 49) link_NAG-ASN : angle 3.31592 ( 147) *********************** 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 248 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 153 time to evaluate : 0.706 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: 0.9486 (t0) cc_final: 0.9175 (p0) REVERT: A 252 LYS cc_start: 0.9587 (OUTLIER) cc_final: 0.9292 (mmmm) REVERT: A 374 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7921 (t-90) REVERT: A 426 MET cc_start: 0.8905 (tpp) cc_final: 0.8657 (tpp) REVERT: A 427 TRP cc_start: 0.8558 (m100) cc_final: 0.8121 (m100) REVERT: A 466 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8083 (tp30) REVERT: A 475 MET cc_start: 0.6948 (ptp) cc_final: 0.6471 (ptp) REVERT: B 530 MET cc_start: 0.9022 (mtp) cc_final: 0.8244 (mtm) REVERT: B 588 ARG cc_start: 0.8776 (tpp-160) cc_final: 0.8407 (tpp-160) REVERT: B 626 MET cc_start: 0.8943 (ttt) cc_final: 0.8550 (tpp) REVERT: C 54 CYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6741 (m) REVERT: C 95 MET cc_start: 0.9050 (ptm) cc_final: 0.8666 (tmm) REVERT: C 104 MET cc_start: 0.9391 (ppp) cc_final: 0.9144 (ppp) REVERT: C 121 LYS cc_start: 0.9312 (tptp) cc_final: 0.9108 (tptp) REVERT: C 164 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.8929 (mt-10) REVERT: C 262 ASN cc_start: 0.9305 (OUTLIER) cc_final: 0.9099 (t0) REVERT: C 293 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8809 (tt0) REVERT: C 369 LEU cc_start: 0.9173 (tp) cc_final: 0.8589 (tt) REVERT: D 535 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8773 (mmm) REVERT: D 540 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8647 (mp10) REVERT: D 542 ARG cc_start: 0.9179 (ttp80) cc_final: 0.8939 (ttp80) REVERT: D 626 MET cc_start: 0.8983 (tpp) cc_final: 0.8550 (tpp) REVERT: D 632 ASP cc_start: 0.9140 (p0) cc_final: 0.8751 (p0) REVERT: D 633 LYS cc_start: 0.9691 (mmmt) cc_final: 0.9476 (mmmt) REVERT: E 104 MET cc_start: 0.9516 (ppp) cc_final: 0.9305 (ppp) REVERT: E 161 MET cc_start: 0.8776 (mmm) cc_final: 0.7885 (tmm) REVERT: F 626 MET cc_start: 0.8260 (tpp) cc_final: 0.8059 (tpp) REVERT: H 76 ASN cc_start: 0.9609 (m-40) cc_final: 0.9045 (t0) REVERT: H 97 ARG cc_start: 0.9252 (mmm160) cc_final: 0.8791 (mmm-85) REVERT: I 55 LYS cc_start: 0.9579 (tmtt) cc_final: 0.9370 (tmmt) REVERT: I 82 MET cc_start: 0.7859 (mpp) cc_final: 0.7270 (mpp) REVERT: X 87 THR cc_start: 0.7418 (p) cc_final: 0.7206 (p) REVERT: J 18 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8160 (mm) outliers start: 95 outliers final: 48 residues processed: 238 average time/residue: 0.1333 time to fit residues: 48.4119 Evaluate side-chains 191 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 133 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 573 ILE 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 208 VAL Chi-restraints excluded: chain C residue 244 THR 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 416 LEU 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 540 GLN Chi-restraints excluded: chain D residue 599 SER 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 208 VAL 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 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 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 11 LEU 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 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 28 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.0170 chunk 160 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 overall best weight: 2.7624 ------------------------------------------------------------------------------- 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** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 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** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 GLN ** J 76 ASN ** 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 = 0.3355 r_free = 0.3355 target = 0.046945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.032312 restraints weight = 128871.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.033483 restraints weight = 70594.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.034264 restraints weight = 49504.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.034757 restraints weight = 39413.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.035053 restraints weight = 34226.262| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19890 Z= 0.265 Angle : 0.789 13.266 27130 Z= 0.380 Chirality : 0.044 0.273 3192 Planarity : 0.004 0.045 3357 Dihedral : 8.821 113.513 4020 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.47 % Favored : 89.10 % Rotamer: Outliers : 6.11 % Allowed : 27.64 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.17), residues: 2312 helix: 0.53 (0.28), residues: 384 sheet: -0.69 (0.22), residues: 559 loop : -2.08 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 166 TYR 0.014 0.001 TYR H 100B PHE 0.021 0.002 PHE D 519 TRP 0.016 0.002 TRP E 96 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00571 (19775) covalent geometry : angle 0.74285 (26832) SS BOND : bond 0.00420 ( 41) SS BOND : angle 1.59898 ( 82) hydrogen bonds : bond 0.03486 ( 536) hydrogen bonds : angle 5.21384 ( 1449) Misc. bond : bond 0.00063 ( 2) link_ALPHA1-3 : bond 0.02930 ( 1) link_ALPHA1-3 : angle 3.08428 ( 3) link_BETA1-4 : bond 0.00244 ( 22) link_BETA1-4 : angle 1.85403 ( 66) link_NAG-ASN : bond 0.00657 ( 49) link_NAG-ASN : angle 3.31378 ( 147) *********************** 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 263 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 139 time to evaluate : 0.502 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: A 80 ASN cc_start: 0.9529 (t0) cc_final: 0.9198 (p0) REVERT: A 104 MET cc_start: 0.9642 (OUTLIER) cc_final: 0.9350 (tpp) REVERT: A 150 MET cc_start: 0.8534 (ttp) cc_final: 0.8064 (mtm) REVERT: A 252 LYS cc_start: 0.9597 (OUTLIER) cc_final: 0.9257 (mmmm) REVERT: A 426 MET cc_start: 0.8981 (tpp) cc_final: 0.8666 (tpp) REVERT: A 427 TRP cc_start: 0.8624 (m100) cc_final: 0.8151 (m100) REVERT: A 466 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8146 (tp30) REVERT: A 475 MET cc_start: 0.7277 (ptp) cc_final: 0.6745 (ptp) REVERT: B 530 MET cc_start: 0.9093 (mtp) cc_final: 0.8248 (mtm) REVERT: B 589 ASP cc_start: 0.8646 (m-30) cc_final: 0.8211 (p0) REVERT: B 605 CYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7544 (m) REVERT: B 626 MET cc_start: 0.8953 (ttt) cc_final: 0.8459 (ttt) REVERT: C 54 CYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6603 (m) REVERT: C 104 MET cc_start: 0.9445 (ppp) cc_final: 0.9184 (ppp) REVERT: C 164 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.8974 (mt-10) REVERT: C 293 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8731 (tt0) REVERT: C 369 LEU cc_start: 0.9215 (tp) cc_final: 0.8638 (tt) REVERT: C 426 MET cc_start: 0.8400 (tpp) cc_final: 0.8095 (tpp) REVERT: C 427 TRP cc_start: 0.8333 (m100) cc_final: 0.7904 (m100) REVERT: C 475 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7773 (ppp) REVERT: D 535 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8836 (mmm) REVERT: D 540 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8718 (mp10) REVERT: D 542 ARG cc_start: 0.9204 (ttp80) cc_final: 0.8946 (ttp80) REVERT: D 605 CYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7880 (m) REVERT: D 626 MET cc_start: 0.9069 (tpp) cc_final: 0.8627 (tpp) REVERT: D 632 ASP cc_start: 0.9238 (p0) cc_final: 0.8880 (p0) REVERT: D 633 LYS cc_start: 0.9723 (mmmt) cc_final: 0.9510 (mmmt) REVERT: D 661 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8858 (tt) REVERT: E 42 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8582 (p) REVERT: E 104 MET cc_start: 0.9529 (ppp) cc_final: 0.9294 (tmm) REVERT: E 150 MET cc_start: 0.7519 (mtm) cc_final: 0.6967 (mtm) REVERT: E 161 MET cc_start: 0.8751 (mmm) cc_final: 0.8409 (mmm) REVERT: E 426 MET cc_start: 0.8037 (tpp) cc_final: 0.7625 (tpp) REVERT: F 626 MET cc_start: 0.8384 (tpp) cc_final: 0.7844 (tpp) REVERT: H 76 ASN cc_start: 0.9614 (m-40) cc_final: 0.9120 (t0) REVERT: H 97 ARG cc_start: 0.9224 (mmm160) cc_final: 0.8750 (mmm-85) REVERT: I 55 LYS cc_start: 0.9597 (tmtt) cc_final: 0.9334 (tmmt) REVERT: I 82 MET cc_start: 0.8117 (mpp) cc_final: 0.7593 (mpp) REVERT: I 100 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9178 (p) REVERT: I 102 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: J 18 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8082 (mm) REVERT: J 1098 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.5299 (m-80) outliers start: 124 outliers final: 73 residues processed: 251 average time/residue: 0.1175 time to fit residues: 46.2344 Evaluate side-chains 217 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 127 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 605 CYS 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 44 VAL 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 244 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 330 HIS 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 540 GLN Chi-restraints excluded: chain D residue 599 SER 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 D residue 650 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 42 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 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 446 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 592 LEU 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 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 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 107 THR 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 104 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.047530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.032847 restraints weight = 130126.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034001 restraints weight = 71956.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.034769 restraints weight = 50265.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.035271 restraints weight = 40258.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.035602 restraints weight = 34878.733| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2864 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= 0.185 Angle : 0.749 13.266 27130 Z= 0.362 Chirality : 0.044 0.247 3192 Planarity : 0.004 0.045 3357 Dihedral : 8.548 113.479 4020 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.47 % Favored : 90.10 % Rotamer: Outliers : 5.07 % Allowed : 28.77 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.17), residues: 2312 helix: 0.50 (0.27), residues: 390 sheet: -0.69 (0.23), residues: 543 loop : -1.98 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.013 0.001 TYR H 100B PHE 0.013 0.001 PHE J 37 TRP 0.014 0.001 TRP E 112 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00405 (19775) covalent geometry : angle 0.70696 (26832) SS BOND : bond 0.00373 ( 41) SS BOND : angle 1.41537 ( 82) hydrogen bonds : bond 0.03362 ( 536) hydrogen bonds : angle 5.06955 ( 1449) Misc. bond : bond 0.00052 ( 2) link_ALPHA1-3 : bond 0.03028 ( 1) link_ALPHA1-3 : angle 3.10543 ( 3) link_BETA1-4 : bond 0.00294 ( 22) link_BETA1-4 : angle 1.70406 ( 66) link_NAG-ASN : bond 0.00494 ( 49) link_NAG-ASN : angle 3.13399 ( 147) *********************** 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 246 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 143 time to evaluate : 0.655 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: A 80 ASN cc_start: 0.9502 (t0) cc_final: 0.9202 (p0) REVERT: A 104 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.9302 (tpp) REVERT: A 150 MET cc_start: 0.8503 (ttp) cc_final: 0.8107 (mtm) REVERT: A 252 LYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9272 (mmmm) REVERT: A 374 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.8021 (t-90) REVERT: A 426 MET cc_start: 0.8952 (tpp) cc_final: 0.8605 (tpp) REVERT: A 427 TRP cc_start: 0.8560 (OUTLIER) cc_final: 0.8000 (m100) REVERT: A 466 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: A 475 MET cc_start: 0.7271 (ptp) cc_final: 0.6898 (ptp) REVERT: B 530 MET cc_start: 0.9013 (mtp) cc_final: 0.8164 (mtm) REVERT: B 589 ASP cc_start: 0.8609 (m-30) cc_final: 0.8174 (p0) REVERT: B 626 MET cc_start: 0.8997 (ttt) cc_final: 0.8610 (ttt) REVERT: C 54 CYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6525 (m) REVERT: C 95 MET cc_start: 0.9139 (ptm) cc_final: 0.8552 (tmm) REVERT: C 104 MET cc_start: 0.9411 (ppp) cc_final: 0.9144 (ppp) REVERT: C 164 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.8947 (mt-10) REVERT: C 293 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8608 (tt0) REVERT: C 369 LEU cc_start: 0.9206 (tp) cc_final: 0.8642 (tt) REVERT: C 426 MET cc_start: 0.8429 (tpp) cc_final: 0.8142 (tpp) REVERT: C 427 TRP cc_start: 0.8269 (m100) cc_final: 0.7805 (m100) REVERT: C 475 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7763 (ppp) REVERT: D 540 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8701 (mp10) REVERT: D 542 ARG cc_start: 0.9176 (ttp80) cc_final: 0.8918 (ttp80) REVERT: D 605 CYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7904 (m) REVERT: D 626 MET cc_start: 0.9017 (tpp) cc_final: 0.8567 (tpp) REVERT: D 632 ASP cc_start: 0.9194 (p0) cc_final: 0.8792 (p0) REVERT: D 633 LYS cc_start: 0.9719 (mmmt) cc_final: 0.9498 (mmmt) REVERT: E 104 MET cc_start: 0.9528 (OUTLIER) cc_final: 0.9255 (tmm) REVERT: E 161 MET cc_start: 0.8748 (mmm) cc_final: 0.8451 (mmm) REVERT: F 626 MET cc_start: 0.8368 (tpp) cc_final: 0.7831 (tpp) REVERT: H 76 ASN cc_start: 0.9596 (m-40) cc_final: 0.9104 (t0) REVERT: H 97 ARG cc_start: 0.9242 (mmm160) cc_final: 0.8679 (mmm160) REVERT: I 55 LYS cc_start: 0.9569 (tmtt) cc_final: 0.9344 (tmmt) REVERT: I 82 MET cc_start: 0.8216 (mpp) cc_final: 0.7692 (mpp) REVERT: I 100 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9181 (p) REVERT: I 102 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: X 34 MET cc_start: 0.7433 (mmp) cc_final: 0.7068 (mmp) REVERT: J 18 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8121 (mm) REVERT: J 31 ASN cc_start: 0.9500 (p0) cc_final: 0.9268 (p0) REVERT: J 1098 PHE cc_start: 0.5943 (OUTLIER) cc_final: 0.5281 (m-80) outliers start: 103 outliers final: 69 residues processed: 233 average time/residue: 0.1209 time to fit residues: 44.7521 Evaluate side-chains 212 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 127 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 104 MET 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 182 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 44 VAL 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 244 THR 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 475 MET 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 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 116 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 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL 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 376 PHE 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 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE 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 86 ASP 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 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 107 THR 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 198 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 172 optimal weight: 0.0670 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 138 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** 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 = 0.3373 r_free = 0.3373 target = 0.047910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.033278 restraints weight = 130667.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.034479 restraints weight = 71470.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.035266 restraints weight = 49900.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.035800 restraints weight = 39724.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.036136 restraints weight = 34224.871| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19890 Z= 0.144 Angle : 0.733 13.207 27130 Z= 0.354 Chirality : 0.044 0.244 3192 Planarity : 0.004 0.043 3357 Dihedral : 8.280 112.111 4020 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.34 % Favored : 90.18 % Rotamer: Outliers : 4.78 % Allowed : 29.31 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.17), residues: 2312 helix: 0.50 (0.27), residues: 390 sheet: -0.65 (0.23), residues: 543 loop : -1.94 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.014 0.001 TYR H 100B PHE 0.013 0.001 PHE E 382 TRP 0.017 0.001 TRP E 427 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00323 (19775) covalent geometry : angle 0.69358 (26832) SS BOND : bond 0.00392 ( 41) SS BOND : angle 1.37996 ( 82) hydrogen bonds : bond 0.03197 ( 536) hydrogen bonds : angle 4.96721 ( 1449) Misc. bond : bond 0.00052 ( 2) link_ALPHA1-3 : bond 0.03000 ( 1) link_ALPHA1-3 : angle 3.25370 ( 3) link_BETA1-4 : bond 0.00356 ( 22) link_BETA1-4 : angle 1.61825 ( 66) link_NAG-ASN : bond 0.00418 ( 49) link_NAG-ASN : angle 2.96147 ( 147) *********************** 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 237 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 140 time to evaluate : 0.478 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: A 80 ASN cc_start: 0.9491 (t0) cc_final: 0.9204 (p0) REVERT: A 104 MET cc_start: 0.9565 (OUTLIER) cc_final: 0.9294 (tpp) REVERT: A 150 MET cc_start: 0.8470 (ttp) cc_final: 0.8061 (mtm) REVERT: A 252 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9260 (mmmm) REVERT: A 426 MET cc_start: 0.8967 (tpp) cc_final: 0.8619 (tpp) REVERT: A 427 TRP cc_start: 0.8539 (m100) cc_final: 0.7981 (m100) REVERT: A 466 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8154 (tp30) REVERT: A 475 MET cc_start: 0.7425 (ptp) cc_final: 0.7032 (ptp) REVERT: B 530 MET cc_start: 0.9021 (mtp) cc_final: 0.8156 (mtm) REVERT: B 589 ASP cc_start: 0.8607 (m-30) cc_final: 0.8161 (p0) REVERT: B 626 MET cc_start: 0.9026 (ttt) cc_final: 0.8667 (ttt) REVERT: C 54 CYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6490 (m) REVERT: C 104 MET cc_start: 0.9396 (ppp) cc_final: 0.9145 (ppp) REVERT: C 164 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.8972 (mt-10) REVERT: C 293 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: C 369 LEU cc_start: 0.9206 (tp) cc_final: 0.8640 (tt) REVERT: C 427 TRP cc_start: 0.8192 (m100) cc_final: 0.7751 (m100) REVERT: C 475 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7858 (ppp) REVERT: D 530 MET cc_start: 0.8761 (tpp) cc_final: 0.6942 (tpp) REVERT: D 540 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8668 (mp10) REVERT: D 542 ARG cc_start: 0.9181 (ttp80) cc_final: 0.8915 (ttp80) REVERT: D 605 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7849 (m) REVERT: D 626 MET cc_start: 0.9017 (tpp) cc_final: 0.8387 (tpp) REVERT: D 632 ASP cc_start: 0.9201 (p0) cc_final: 0.8793 (p0) REVERT: D 633 LYS cc_start: 0.9719 (mmmt) cc_final: 0.9499 (mmmt) REVERT: D 651 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.9083 (m110) REVERT: E 104 MET cc_start: 0.9537 (OUTLIER) cc_final: 0.9250 (tmm) REVERT: E 161 MET cc_start: 0.8793 (mmm) cc_final: 0.8544 (mmm) REVERT: E 162 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9060 (p) REVERT: E 427 TRP cc_start: 0.8011 (m100) cc_final: 0.7584 (m100) REVERT: F 530 MET cc_start: 0.9068 (tpp) cc_final: 0.8476 (tpp) REVERT: H 45 ARG cc_start: 0.9455 (OUTLIER) cc_final: 0.9016 (tmm-80) REVERT: H 76 ASN cc_start: 0.9605 (m-40) cc_final: 0.9109 (t0) REVERT: H 97 ARG cc_start: 0.9222 (mmm160) cc_final: 0.8647 (mmm160) REVERT: I 55 LYS cc_start: 0.9534 (tmtt) cc_final: 0.9302 (tmmt) REVERT: I 82 MET cc_start: 0.8286 (mpp) cc_final: 0.7757 (mpp) REVERT: I 102 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: X 34 MET cc_start: 0.7499 (mmp) cc_final: 0.7120 (mmp) REVERT: J 18 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8148 (mm) REVERT: J 1098 PHE cc_start: 0.5698 (OUTLIER) cc_final: 0.5106 (m-80) outliers start: 97 outliers final: 67 residues processed: 224 average time/residue: 0.1201 time to fit residues: 42.2277 Evaluate side-chains 214 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 131 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 104 MET 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 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 44 VAL 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 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR 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 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 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL 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 376 PHE 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 621 GLU 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 45 ARG 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 70 SER Chi-restraints excluded: chain I residue 86 ASP 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 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 198 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 625 ASN ** 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 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.048231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.033529 restraints weight = 128654.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.034756 restraints weight = 69774.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.035564 restraints weight = 48351.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.036093 restraints weight = 38281.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.036396 restraints weight = 32924.434| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3062 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= 0.133 Angle : 0.735 13.135 27130 Z= 0.356 Chirality : 0.044 0.245 3192 Planarity : 0.004 0.054 3357 Dihedral : 8.096 110.759 4020 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.00 % Favored : 90.53 % Rotamer: Outliers : 4.33 % Allowed : 29.46 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.17), residues: 2312 helix: 0.81 (0.28), residues: 372 sheet: -0.74 (0.22), residues: 563 loop : -1.81 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 66 TYR 0.014 0.001 TYR H 100B PHE 0.012 0.001 PHE E 382 TRP 0.030 0.001 TRP E 69 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00303 (19775) covalent geometry : angle 0.69938 (26832) SS BOND : bond 0.00356 ( 41) SS BOND : angle 1.27000 ( 82) hydrogen bonds : bond 0.03165 ( 536) hydrogen bonds : angle 4.92493 ( 1449) Misc. bond : bond 0.00050 ( 2) link_ALPHA1-3 : bond 0.02927 ( 1) link_ALPHA1-3 : angle 3.34332 ( 3) link_BETA1-4 : bond 0.00372 ( 22) link_BETA1-4 : angle 1.58331 ( 66) link_NAG-ASN : bond 0.00404 ( 49) link_NAG-ASN : angle 2.83593 ( 147) *********************** 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: 88 poor density : 140 time to evaluate : 0.489 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: 0.9447 (t0) cc_final: 0.9183 (p0) REVERT: A 104 MET cc_start: 0.9504 (OUTLIER) cc_final: 0.9224 (tpp) REVERT: A 150 MET cc_start: 0.8365 (ttp) cc_final: 0.8002 (mtm) REVERT: A 161 MET cc_start: 0.9272 (tpp) cc_final: 0.8903 (tpp) REVERT: A 252 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9284 (mmmm) REVERT: A 426 MET cc_start: 0.8921 (tpp) cc_final: 0.8628 (tpp) REVERT: A 427 TRP cc_start: 0.8415 (m100) cc_final: 0.7917 (m100) REVERT: A 466 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8232 (tp30) REVERT: A 475 MET cc_start: 0.7482 (ptp) cc_final: 0.7058 (ptp) REVERT: B 530 MET cc_start: 0.8967 (mtp) cc_final: 0.8097 (mtm) REVERT: B 589 ASP cc_start: 0.8535 (m-30) cc_final: 0.8126 (p0) REVERT: B 605 CYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7545 (m) REVERT: B 626 MET cc_start: 0.9024 (ttt) cc_final: 0.8787 (ttt) REVERT: C 54 CYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6488 (m) REVERT: C 95 MET cc_start: 0.9102 (ptm) cc_final: 0.8673 (ppp) REVERT: C 104 MET cc_start: 0.9361 (ppp) cc_final: 0.9126 (ppp) REVERT: C 164 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.9001 (mt-10) REVERT: C 293 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8578 (tt0) REVERT: C 369 LEU cc_start: 0.9237 (tp) cc_final: 0.8684 (tt) REVERT: C 426 MET cc_start: 0.8358 (tpp) cc_final: 0.7767 (tpp) REVERT: C 427 TRP cc_start: 0.8039 (m100) cc_final: 0.7369 (m100) REVERT: C 475 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7317 (ppp) REVERT: D 540 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: D 542 ARG cc_start: 0.9124 (ttp80) cc_final: 0.8865 (ttp80) REVERT: D 605 CYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7821 (m) REVERT: D 626 MET cc_start: 0.8959 (tpp) cc_final: 0.8284 (tpp) REVERT: D 632 ASP cc_start: 0.9145 (p0) cc_final: 0.8727 (p0) REVERT: D 633 LYS cc_start: 0.9695 (mmmt) cc_final: 0.9487 (mmmt) REVERT: D 651 ASN cc_start: 0.9369 (OUTLIER) cc_final: 0.9060 (m110) REVERT: E 104 MET cc_start: 0.9514 (OUTLIER) cc_final: 0.9247 (tmm) REVERT: E 161 MET cc_start: 0.8731 (mmm) cc_final: 0.7704 (tmm) REVERT: E 162 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.8457 (p) REVERT: E 426 MET cc_start: 0.7852 (tpp) cc_final: 0.7458 (tpp) REVERT: E 427 TRP cc_start: 0.7731 (m100) cc_final: 0.7312 (m100) REVERT: F 530 MET cc_start: 0.9053 (tpp) cc_final: 0.8502 (tpp) REVERT: H 76 ASN cc_start: 0.9587 (m-40) cc_final: 0.9066 (t0) REVERT: H 97 ARG cc_start: 0.9194 (mmm160) cc_final: 0.8662 (mmm160) REVERT: I 55 LYS cc_start: 0.9496 (tmtt) cc_final: 0.8908 (tmtt) REVERT: I 82 MET cc_start: 0.8349 (mpp) cc_final: 0.7837 (mpp) REVERT: I 97 ARG cc_start: 0.8749 (mmm160) cc_final: 0.8067 (mmm160) REVERT: I 102 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: X 34 MET cc_start: 0.7529 (mmp) cc_final: 0.7198 (mmp) REVERT: X 108 MET cc_start: 0.8844 (mmm) cc_final: 0.8305 (tpt) REVERT: J 18 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8209 (mm) REVERT: J 1098 PHE cc_start: 0.5606 (OUTLIER) cc_final: 0.5014 (m-80) outliers start: 88 outliers final: 60 residues processed: 217 average time/residue: 0.1244 time to fit residues: 42.0175 Evaluate side-chains 208 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 132 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 44 VAL 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 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 244 THR 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 535 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN 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 D residue 651 ASN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 205 CYS 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 376 PHE 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 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 91 THR Chi-restraints excluded: chain I residue 100 VAL 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 107 THR 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 140 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN D 543 ASN ** D 625 ASN ** 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 658 GLN H 3 GLN ** 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 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.046836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.032179 restraints weight = 131249.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.033336 restraints weight = 72652.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.034110 restraints weight = 51095.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.034607 restraints weight = 40877.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.034897 restraints weight = 35413.706| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19890 Z= 0.249 Angle : 0.776 13.108 27130 Z= 0.377 Chirality : 0.044 0.255 3192 Planarity : 0.004 0.044 3357 Dihedral : 8.210 109.747 4020 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.21 % Favored : 89.36 % Rotamer: Outliers : 4.43 % Allowed : 29.41 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.18), residues: 2312 helix: 0.84 (0.28), residues: 372 sheet: -0.77 (0.22), residues: 587 loop : -1.81 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 66 TYR 0.018 0.001 TYR I 32 PHE 0.018 0.002 PHE H 67 TRP 0.021 0.002 TRP E 69 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00541 (19775) covalent geometry : angle 0.73893 (26832) SS BOND : bond 0.00396 ( 41) SS BOND : angle 1.51921 ( 82) hydrogen bonds : bond 0.03325 ( 536) hydrogen bonds : angle 5.08845 ( 1449) Misc. bond : bond 0.00044 ( 2) link_ALPHA1-3 : bond 0.02680 ( 1) link_ALPHA1-3 : angle 3.14975 ( 3) link_BETA1-4 : bond 0.00243 ( 22) link_BETA1-4 : angle 1.73380 ( 66) link_NAG-ASN : bond 0.00562 ( 49) link_NAG-ASN : angle 2.94939 ( 147) *********************** 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: 90 poor density : 133 time to evaluate : 0.559 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: A 80 ASN cc_start: 0.9513 (t0) cc_final: 0.9222 (p0) REVERT: A 104 MET cc_start: 0.9576 (OUTLIER) cc_final: 0.9261 (tpp) REVERT: A 150 MET cc_start: 0.8510 (ttp) cc_final: 0.8138 (mtm) REVERT: A 252 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9251 (mmmm) REVERT: A 426 MET cc_start: 0.9013 (tpp) cc_final: 0.8781 (tpp) REVERT: A 427 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.8293 (m100) REVERT: A 466 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: A 475 MET cc_start: 0.7766 (ptp) cc_final: 0.7009 (ptp) REVERT: B 530 MET cc_start: 0.9045 (mtp) cc_final: 0.8054 (mtm) REVERT: B 589 ASP cc_start: 0.8645 (m-30) cc_final: 0.8237 (p0) REVERT: B 605 CYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7609 (m) REVERT: B 626 MET cc_start: 0.9069 (ttt) cc_final: 0.8738 (ttt) REVERT: C 54 CYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6445 (m) REVERT: C 95 MET cc_start: 0.9233 (ptm) cc_final: 0.8777 (ppp) REVERT: C 104 MET cc_start: 0.9416 (ppp) cc_final: 0.9175 (ppp) REVERT: C 164 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.8984 (mt-10) REVERT: C 293 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: C 369 LEU cc_start: 0.9274 (tp) cc_final: 0.8759 (tt) REVERT: C 426 MET cc_start: 0.8465 (tpp) cc_final: 0.7800 (tpp) REVERT: C 427 TRP cc_start: 0.8153 (m100) cc_final: 0.7392 (m100) REVERT: C 475 MET cc_start: 0.8224 (tmm) cc_final: 0.7728 (ppp) REVERT: D 535 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8778 (mmm) REVERT: D 540 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8683 (mp10) REVERT: D 542 ARG cc_start: 0.9224 (ttp80) cc_final: 0.8936 (ttp80) REVERT: D 605 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7761 (m) REVERT: D 626 MET cc_start: 0.9080 (tpp) cc_final: 0.8642 (tpp) REVERT: D 632 ASP cc_start: 0.9271 (p0) cc_final: 0.8950 (p0) REVERT: D 651 ASN cc_start: 0.9384 (OUTLIER) cc_final: 0.9086 (m110) REVERT: E 161 MET cc_start: 0.8724 (mmm) cc_final: 0.8433 (mmm) REVERT: F 626 MET cc_start: 0.8230 (tpp) cc_final: 0.7974 (tpp) REVERT: H 76 ASN cc_start: 0.9610 (m-40) cc_final: 0.9090 (t0) REVERT: H 97 ARG cc_start: 0.9181 (mmm160) cc_final: 0.8628 (mmm160) REVERT: I 13 GLN cc_start: 0.9058 (pp30) cc_final: 0.8825 (pp30) REVERT: I 55 LYS cc_start: 0.9538 (tmtt) cc_final: 0.9018 (tmtt) REVERT: I 82 MET cc_start: 0.8382 (mpp) cc_final: 0.7897 (mpp) REVERT: I 97 ARG cc_start: 0.8906 (mmm160) cc_final: 0.8041 (mmm160) REVERT: I 100 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9246 (p) REVERT: I 102 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: X 34 MET cc_start: 0.7597 (mmp) cc_final: 0.7261 (mmp) REVERT: J 18 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8124 (mm) REVERT: J 1098 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.5017 (m-80) outliers start: 90 outliers final: 67 residues processed: 210 average time/residue: 0.1206 time to fit residues: 40.4416 Evaluate side-chains 212 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 129 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 44 VAL 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 244 THR 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 455 THR 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 D residue 651 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 205 CYS 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 660 LEU Chi-restraints excluded: chain H residue 3 GLN 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 48 VAL 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 91 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 107 THR 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 79 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 149 optimal weight: 0.0970 chunk 182 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** D 625 ASN ** 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 658 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.047566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.033146 restraints weight = 130394.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.034342 restraints weight = 70980.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.035136 restraints weight = 49395.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.035593 restraints weight = 39231.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.035954 restraints weight = 34044.444| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19890 Z= 0.169 Angle : 0.759 13.065 27130 Z= 0.369 Chirality : 0.044 0.249 3192 Planarity : 0.004 0.043 3357 Dihedral : 8.085 109.672 4020 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.13 % Favored : 90.44 % Rotamer: Outliers : 4.14 % Allowed : 30.25 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.18), residues: 2312 helix: 0.87 (0.28), residues: 372 sheet: -0.80 (0.22), residues: 595 loop : -1.76 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 66 TYR 0.013 0.001 TYR H 100B PHE 0.013 0.001 PHE E 288 TRP 0.021 0.001 TRP E 69 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00379 (19775) covalent geometry : angle 0.72446 (26832) SS BOND : bond 0.00368 ( 41) SS BOND : angle 1.38052 ( 82) hydrogen bonds : bond 0.03278 ( 536) hydrogen bonds : angle 5.01379 ( 1449) Misc. bond : bond 0.00057 ( 2) link_ALPHA1-3 : bond 0.02765 ( 1) link_ALPHA1-3 : angle 3.24108 ( 3) link_BETA1-4 : bond 0.00299 ( 22) link_BETA1-4 : angle 1.61737 ( 66) link_NAG-ASN : bond 0.00420 ( 49) link_NAG-ASN : angle 2.83229 ( 147) ********************** 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 218 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 134 time to evaluate : 0.547 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: A 80 ASN cc_start: 0.9440 (t0) cc_final: 0.9177 (p0) REVERT: A 104 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9197 (tpp) REVERT: A 150 MET cc_start: 0.8431 (ttp) cc_final: 0.8074 (mtm) REVERT: A 161 MET cc_start: 0.9219 (tpp) cc_final: 0.8858 (tpp) REVERT: A 252 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9288 (mmmm) REVERT: A 466 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: A 475 MET cc_start: 0.7686 (ptp) cc_final: 0.6911 (ptp) REVERT: B 530 MET cc_start: 0.8975 (mtp) cc_final: 0.8040 (mtm) REVERT: B 589 ASP cc_start: 0.8583 (m-30) cc_final: 0.8197 (p0) REVERT: B 626 MET cc_start: 0.8998 (ttt) cc_final: 0.8784 (ttt) REVERT: C 54 CYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6328 (m) REVERT: C 95 MET cc_start: 0.9096 (ptm) cc_final: 0.8711 (ppp) REVERT: C 104 MET cc_start: 0.9379 (ppp) cc_final: 0.9136 (ppp) REVERT: C 164 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.8966 (mt-10) REVERT: C 293 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: C 369 LEU cc_start: 0.9266 (tp) cc_final: 0.8753 (tt) REVERT: C 426 MET cc_start: 0.8390 (tpp) cc_final: 0.7601 (tpp) REVERT: C 427 TRP cc_start: 0.8049 (m100) cc_final: 0.7227 (m100) REVERT: C 475 MET cc_start: 0.8154 (tmm) cc_final: 0.7722 (ppp) REVERT: D 535 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8679 (mmm) REVERT: D 540 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8665 (mp10) REVERT: D 542 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8907 (ttp80) REVERT: D 605 CYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7753 (m) REVERT: D 626 MET cc_start: 0.8961 (tpp) cc_final: 0.8330 (tpp) REVERT: D 651 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.9036 (m110) REVERT: E 104 MET cc_start: 0.9503 (OUTLIER) cc_final: 0.9234 (tmm) REVERT: E 161 MET cc_start: 0.8705 (mmm) cc_final: 0.8441 (mmm) REVERT: F 530 MET cc_start: 0.9118 (tpp) cc_final: 0.8908 (mmm) REVERT: F 589 ASP cc_start: 0.8803 (m-30) cc_final: 0.8343 (p0) REVERT: H 76 ASN cc_start: 0.9601 (m-40) cc_final: 0.9078 (t0) REVERT: H 97 ARG cc_start: 0.9168 (mmm160) cc_final: 0.8646 (mmm160) REVERT: I 13 GLN cc_start: 0.9022 (pp30) cc_final: 0.8785 (pp30) REVERT: I 55 LYS cc_start: 0.9513 (tmtt) cc_final: 0.9016 (tmtt) REVERT: I 82 MET cc_start: 0.8496 (mpp) cc_final: 0.7953 (mpp) REVERT: I 97 ARG cc_start: 0.8854 (mmm160) cc_final: 0.8016 (mmm160) REVERT: I 102 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: X 34 MET cc_start: 0.7574 (mmp) cc_final: 0.7222 (mmp) REVERT: J 18 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8196 (mm) REVERT: J 1098 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.5010 (m-80) outliers start: 84 outliers final: 63 residues processed: 209 average time/residue: 0.1233 time to fit residues: 40.9839 Evaluate side-chains 206 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 129 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 104 MET Chi-restraints excluded: chain A residue 123 THR 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 252 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 44 VAL 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 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR 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 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 D residue 651 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 205 CYS 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 615 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 63 VAL 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 100 VAL 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 107 THR 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 182 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 207 optimal weight: 0.0770 chunk 41 optimal weight: 6.9990 chunk 144 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN F 658 GLN H 3 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.047773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.032965 restraints weight = 130515.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.034154 restraints weight = 72732.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.034944 restraints weight = 51086.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.035445 restraints weight = 40787.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.035736 restraints weight = 35361.272| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3343 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= 0.149 Angle : 0.755 13.018 27130 Z= 0.366 Chirality : 0.044 0.248 3192 Planarity : 0.004 0.044 3357 Dihedral : 7.957 108.751 4020 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.00 % Favored : 90.53 % Rotamer: Outliers : 4.09 % Allowed : 30.34 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.18), residues: 2312 helix: 0.86 (0.28), residues: 372 sheet: -0.76 (0.22), residues: 595 loop : -1.75 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 66 TYR 0.016 0.001 TYR I 32 PHE 0.019 0.001 PHE E 288 TRP 0.071 0.002 TRP A 427 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00334 (19775) covalent geometry : angle 0.72206 (26832) SS BOND : bond 0.00354 ( 41) SS BOND : angle 1.31396 ( 82) hydrogen bonds : bond 0.03209 ( 536) hydrogen bonds : angle 4.95555 ( 1449) Misc. bond : bond 0.00058 ( 2) link_ALPHA1-3 : bond 0.02970 ( 1) link_ALPHA1-3 : angle 3.49705 ( 3) link_BETA1-4 : bond 0.00336 ( 22) link_BETA1-4 : angle 1.56909 ( 66) link_NAG-ASN : bond 0.00387 ( 49) link_NAG-ASN : angle 2.76372 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.63 seconds wall clock time: 62 minutes 11.07 seconds (3731.07 seconds total)