Starting phenix.real_space_refine on Tue Aug 26 15:04:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8saw_40282/08_2025/8saw_40282_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8saw_40282/08_2025/8saw_40282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8saw_40282/08_2025/8saw_40282_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8saw_40282/08_2025/8saw_40282_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8saw_40282/08_2025/8saw_40282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8saw_40282/08_2025/8saw_40282.map" } resolution = 3.3 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= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians S 135 5.16 5 C 12327 2.51 5 N 3324 2.21 5 O 3957 1.98 5 H 18589 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38332 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7144 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "B" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1925 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1941 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1568 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7144 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "F" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1925 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "H" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1941 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1565 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 7145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7145 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "L" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1925 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "M" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1941 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1568 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "G" 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: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 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: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.72, per 1000 atoms: 0.20 Number of scatterers: 38332 At special positions: 0 Unit cell: (158.834, 157.768, 139.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 O 3957 8.00 N 3324 7.00 C 12327 6.00 H 18589 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " 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=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 121 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 43 " distance=2.03 Simple disulfide: pdb=" SG CYS K 88 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 95 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 100 " - pdb=" SG CYS K 116 " distance=2.03 Simple disulfide: pdb=" SG CYS K 162 " - pdb=" SG CYS K 390 " distance=2.03 Simple disulfide: pdb=" SG CYS K 179 " - pdb=" SG CYS K 208 " distance=2.03 Simple disulfide: pdb=" SG CYS K 189 " - pdb=" SG CYS K 200 " distance=2.03 Simple disulfide: pdb=" SG CYS K 257 " - pdb=" SG CYS K 291 " distance=2.03 Simple disulfide: pdb=" SG CYS K 337 " - pdb=" SG CYS K 402 " distance=2.03 Simple disulfide: pdb=" SG CYS K 344 " - pdb=" SG CYS K 375 " distance=2.03 Simple disulfide: pdb=" SG CYS K 458 " - pdb=" SG CYS L 73 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 72 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " 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=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG G 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN E 301 " " NAG R 1 " - " ASN E 332 " " NAG S 1 " - " ASN E 156 " " NAG T 1 " - " ASN E 442 " " NAG U 1 " - " ASN K 262 " " NAG V 1 " - " ASN K 292 " " NAG W 1 " - " ASN K 115 " " NAG X 1 " - " ASN K 399 " Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.4 microseconds 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 48 sheets defined 17.1% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.358A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.514A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.048A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.533A pdb=" N VAL B 539 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG B 542 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 4.280A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.701A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.103A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.625A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.370A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.513A pdb=" N THR E 373 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 4.047A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.529A pdb=" N VAL F 539 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG F 542 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 4.285A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.703A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.108A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.625A pdb=" N GLU I 116 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 removed outlier: 4.372A pdb=" N ASP K 71 " --> pdb=" O ASN K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 310 Processing helix chain 'K' and resid 327 through 332 removed outlier: 3.515A pdb=" N THR K 332 " --> pdb=" O MET K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 438 removed outlier: 4.046A pdb=" N TRP K 436 " --> pdb=" O MET K 432 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER K 438 " --> pdb=" O ASP K 434 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 25 through 31 removed outlier: 3.533A pdb=" N VAL L 28 " --> pdb=" O THR L 25 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG L 31 " --> pdb=" O VAL L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 63 removed outlier: 4.294A pdb=" N LEU L 44 " --> pdb=" O GLY L 40 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG L 47 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 90 Processing helix chain 'L' and resid 95 through 104 Processing helix chain 'L' and resid 106 through 132 removed outlier: 3.703A pdb=" N ILE L 110 " --> pdb=" O TYR L 106 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP L 132 " --> pdb=" O LEU L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 removed outlier: 4.101A pdb=" N THR M 91 " --> pdb=" O SER M 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.624A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.424A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.834A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 7.129A pdb=" N HIS A 66 " --> pdb=" O THR A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.823A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.634A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.941A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.576A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.056A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.392A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.056A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 304 removed outlier: 6.721A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'C' and resid 9 through 11 removed outlier: 5.201A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.729A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.729A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.436A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.830A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC2, first strand: chain 'E' and resid 66 through 67 removed outlier: 7.126A pdb=" N HIS E 66 " --> pdb=" O THR E 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.824A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.634A pdb=" N ASN E 156 " --> pdb=" O SER E 132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.953A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.575A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.398A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 302 through 304 removed outlier: 6.738A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AD2, first strand: chain 'H' and resid 9 through 11 removed outlier: 5.136A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 41 through 43 removed outlier: 6.725A pdb=" N VAL I 41 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLN I 70 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU I 79 " --> pdb=" O GLN I 70 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 41 through 43 removed outlier: 6.725A pdb=" N VAL I 41 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N THR I 129 " --> pdb=" O ALA I 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 49 through 54 Processing sheet with id=AD6, first strand: chain 'K' and resid 452 through 456 removed outlier: 5.423A pdb=" N VAL K 5 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR L 74 " --> pdb=" O VAL K 5 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL K 7 " --> pdb=" O CYS L 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 14 through 16 removed outlier: 3.831A pdb=" N ILE K 186 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL K 203 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 44 through 45 Processing sheet with id=AD9, first strand: chain 'K' and resid 35 through 36 removed outlier: 7.124A pdb=" N HIS K 35 " --> pdb=" O THR K 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'K' and resid 60 through 61 removed outlier: 3.822A pdb=" N GLU K 60 " --> pdb=" O CYS K 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 128 through 136 removed outlier: 3.637A pdb=" N ASN K 115 " --> pdb=" O SER K 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 163 through 164 removed outlier: 6.937A pdb=" N THR K 163 " --> pdb=" O TYR K 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 220 through 222 removed outlier: 6.573A pdb=" N LEU K 221 " --> pdb=" O THR K 407 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE K 400 " --> pdb=" O ARG K 259 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY K 408 " --> pdb=" O THR K 251 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N THR K 251 " --> pdb=" O GLY K 408 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N LEU K 410 " --> pdb=" O LEU K 249 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU K 249 " --> pdb=" O LEU K 410 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N THR K 412 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N VAL K 247 " --> pdb=" O THR K 412 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLU K 254 " --> pdb=" O SER K 294 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER K 294 " --> pdb=" O GLU K 254 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE K 341 " --> pdb=" O LYS K 378 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 232 through 234 removed outlier: 11.395A pdb=" N VAL K 247 " --> pdb=" O THR K 412 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N THR K 412 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU K 249 " --> pdb=" O LEU K 410 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N LEU K 410 " --> pdb=" O LEU K 249 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N THR K 251 " --> pdb=" O GLY K 408 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY K 408 " --> pdb=" O THR K 251 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE K 400 " --> pdb=" O ARG K 259 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS K 319 " --> pdb=" O PHE K 425 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 263 through 265 removed outlier: 6.716A pdb=" N THR K 264 " --> pdb=" O GLY K 280 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 268 through 269 Processing sheet with id=AE8, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AE9, first strand: chain 'M' and resid 9 through 11 removed outlier: 5.168A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.725A pdb=" N VAL N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.725A pdb=" N VAL N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR N 98 " --> pdb=" O ALA N 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 18 through 23 672 hydrogen bonds defined for protein. 1746 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: 10.45 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 18586 1.04 - 1.23: 368 1.23 - 1.43: 8122 1.43 - 1.62: 11487 1.62 - 1.82: 183 Bond restraints: 38746 Sorted by residual: bond pdb=" C THR K 92 " pdb=" N PRO K 93 " ideal model delta sigma weight residual 1.334 1.349 -0.015 8.40e-03 1.42e+04 3.34e+00 bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.334 1.348 -0.015 8.40e-03 1.42e+04 3.06e+00 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.97e+00 ... (remaining 38741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 68074 1.61 - 3.21: 1219 3.21 - 4.82: 171 4.82 - 6.42: 47 6.42 - 8.03: 9 Bond angle restraints: 69520 Sorted by residual: angle pdb=" C LEU K 91 " pdb=" N THR K 92 " pdb=" CA THR K 92 " ideal model delta sigma weight residual 121.80 129.83 -8.03 2.44e+00 1.68e-01 1.08e+01 angle pdb=" C LEU E 122 " pdb=" N THR E 123 " pdb=" CA THR E 123 " ideal model delta sigma weight residual 121.80 129.78 -7.98 2.44e+00 1.68e-01 1.07e+01 angle pdb=" C LEU A 122 " pdb=" N THR A 123 " pdb=" CA THR A 123 " ideal model delta sigma weight residual 121.80 129.75 -7.95 2.44e+00 1.68e-01 1.06e+01 angle pdb=" C GLU I 83 " pdb=" N VAL I 84 " pdb=" CA VAL I 84 " ideal model delta sigma weight residual 121.97 126.84 -4.87 1.80e+00 3.09e-01 7.31e+00 angle pdb=" CA VAL N 53 " pdb=" CB VAL N 53 " pdb=" CG2 VAL N 53 " ideal model delta sigma weight residual 110.40 114.98 -4.58 1.70e+00 3.46e-01 7.27e+00 ... (remaining 69515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 18181 22.00 - 44.01: 693 44.01 - 66.01: 207 66.01 - 88.02: 36 88.02 - 110.02: 24 Dihedral angle restraints: 19141 sinusoidal: 10843 harmonic: 8298 Sorted by residual: dihedral pdb=" CA THR E 123 " pdb=" C THR E 123 " pdb=" N PRO E 124 " pdb=" CA PRO E 124 " ideal model delta harmonic sigma weight residual -180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA THR A 123 " pdb=" C THR A 123 " pdb=" N PRO A 124 " pdb=" CA PRO A 124 " ideal model delta harmonic sigma weight residual -180.00 -158.31 -21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR K 92 " pdb=" C THR K 92 " pdb=" N PRO K 93 " pdb=" CA PRO K 93 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 19138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2696 0.055 - 0.111: 343 0.111 - 0.166: 159 0.166 - 0.221: 0 0.221 - 0.277: 6 Chirality restraints: 3204 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3201 not shown) Planarity restraints: 5799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 123 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO E 124 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 124 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 124 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 92 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO K 93 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO K 93 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO K 93 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 124 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.030 5.00e-02 4.00e+02 ... (remaining 5796 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4298 2.26 - 2.84: 82821 2.84 - 3.43: 88618 3.43 - 4.01: 127124 4.01 - 4.60: 191942 Nonbonded interactions: 494803 Sorted by model distance: nonbonded pdb=" O GLU D 52 " pdb=" H SER D 54 " model vdw 1.675 2.450 nonbonded pdb=" O GLU N 52 " pdb=" H SER N 54 " model vdw 1.676 2.450 nonbonded pdb=" O GLU I 83 " pdb=" H SER I 85 " model vdw 1.676 2.450 nonbonded pdb=" O VAL A 496 " pdb=" HE1 TRP B 631 " model vdw 1.679 2.450 nonbonded pdb=" O VAL E 496 " pdb=" HE1 TRP F 631 " model vdw 1.681 2.450 ... (remaining 494798 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 'E' selection = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 2 through 462)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = (chain 'D' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 2 through 110)) selection = chain 'I' selection = (chain 'N' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 2 through 110)) } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' } 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 individual isotropic 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: 0.460 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: 0.270 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 38.370 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.130 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 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 : 0.004 0.047 20247 Z= 0.180 Angle : 0.657 8.028 27624 Z= 0.312 Chirality : 0.047 0.277 3204 Planarity : 0.003 0.054 3435 Dihedral : 12.110 110.019 8031 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Rotamer: Outliers : 1.27 % Allowed : 3.80 % Favored : 94.93 % 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: -0.32 (0.17), residues: 2439 helix: 2.04 (0.30), residues: 330 sheet: 0.31 (0.20), residues: 658 loop : -1.03 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.008 0.001 TYR I 69 PHE 0.006 0.001 PHE M 29 TRP 0.008 0.001 TRP M 50 HIS 0.002 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00384 (20157) covalent geometry : angle 0.64853 (27396) SS BOND : bond 0.00247 ( 42) SS BOND : angle 0.84522 ( 84) hydrogen bonds : bond 0.12261 ( 645) hydrogen bonds : angle 5.46315 ( 1746) link_ALPHA1-2 : bond 0.00496 ( 6) link_ALPHA1-2 : angle 1.70042 ( 18) link_ALPHA1-3 : bond 0.00413 ( 6) link_ALPHA1-3 : angle 1.74655 ( 18) link_ALPHA1-6 : bond 0.00542 ( 6) link_ALPHA1-6 : angle 1.54028 ( 18) link_BETA1-4 : bond 0.00342 ( 18) link_BETA1-4 : angle 1.18362 ( 54) link_NAG-ASN : bond 0.00210 ( 12) link_NAG-ASN : angle 1.67266 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 476 time to evaluate : 1.008 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: 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: symmetry clash REVERT: A 113 ASP cc_start: 0.7037 (t0) cc_final: 0.6818 (t0) REVERT: A 114 GLN cc_start: 0.7928 (tt0) cc_final: 0.7550 (tt0) REVERT: B 530 MET cc_start: 0.8462 (mmm) cc_final: 0.8087 (mtp) REVERT: B 630 GLN cc_start: 0.7339 (tp-100) cc_final: 0.7105 (tp-100) REVERT: C 89 ASP cc_start: 0.6219 (p0) cc_final: 0.5872 (p0) REVERT: E 66 HIS cc_start: 0.6564 (p-80) cc_final: 0.6324 (p-80) REVERT: F 630 GLN cc_start: 0.7269 (tp-100) cc_final: 0.7054 (tp-100) REVERT: M 82 GLU cc_start: 0.7601 (tt0) cc_final: 0.7369 (tt0) outliers start: 27 outliers final: 12 residues processed: 500 average time/residue: 0.3206 time to fit residues: 243.8729 Evaluate side-chains 280 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 268 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 121 CYS Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 653 GLN E 195 ASN K 156 ASN K 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.180576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152593 restraints weight = 67756.826| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.23 r_work: 0.3480 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20247 Z= 0.251 Angle : 0.669 8.841 27624 Z= 0.341 Chirality : 0.046 0.190 3204 Planarity : 0.005 0.056 3435 Dihedral : 9.464 62.230 3632 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Rotamer: Outliers : 2.21 % Allowed : 8.22 % Favored : 89.58 % 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: -0.59 (0.17), residues: 2439 helix: 1.45 (0.30), residues: 345 sheet: -0.01 (0.20), residues: 705 loop : -1.09 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.016 0.002 TYR N 51 PHE 0.014 0.002 PHE K 342 TRP 0.012 0.002 TRP E 45 HIS 0.004 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00579 (20157) covalent geometry : angle 0.64492 (27396) SS BOND : bond 0.00936 ( 42) SS BOND : angle 2.09583 ( 84) hydrogen bonds : bond 0.04297 ( 645) hydrogen bonds : angle 5.07590 ( 1746) link_ALPHA1-2 : bond 0.00250 ( 6) link_ALPHA1-2 : angle 2.17513 ( 18) link_ALPHA1-3 : bond 0.00413 ( 6) link_ALPHA1-3 : angle 2.26173 ( 18) link_ALPHA1-6 : bond 0.00193 ( 6) link_ALPHA1-6 : angle 1.86108 ( 18) link_BETA1-4 : bond 0.00545 ( 18) link_BETA1-4 : angle 2.08856 ( 54) link_NAG-ASN : bond 0.00306 ( 12) link_NAG-ASN : angle 1.96185 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 1.032 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 95 MET cc_start: 0.7831 (ttp) cc_final: 0.7577 (ttp) REVERT: A 114 GLN cc_start: 0.8315 (tt0) cc_final: 0.7900 (tt0) REVERT: A 500 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7204 (mtp-110) REVERT: B 630 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7631 (tp-100) REVERT: B 652 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7422 (tm-30) REVERT: E 66 HIS cc_start: 0.6776 (p-80) cc_final: 0.6400 (p-80) REVERT: E 502 LYS cc_start: 0.7366 (pttm) cc_final: 0.7072 (mmmt) REVERT: F 634 GLU cc_start: 0.8375 (tt0) cc_final: 0.8126 (tt0) REVERT: F 652 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7851 (tm-30) REVERT: K 269 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7638 (mmm-85) REVERT: K 457 ARG cc_start: 0.7862 (mtp180) cc_final: 0.7523 (mtp-110) REVERT: K 459 LYS cc_start: 0.7402 (pttm) cc_final: 0.7062 (mmmt) REVERT: L 19 MET cc_start: 0.8714 (mmm) cc_final: 0.8455 (mtp) REVERT: M 82 GLU cc_start: 0.8009 (tt0) cc_final: 0.7754 (tt0) outliers start: 47 outliers final: 40 residues processed: 299 average time/residue: 0.2858 time to fit residues: 132.3736 Evaluate side-chains 272 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 121 CYS Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 228 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN K 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148274 restraints weight = 67816.699| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.25 r_work: 0.3485 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20247 Z= 0.205 Angle : 0.613 12.807 27624 Z= 0.313 Chirality : 0.045 0.180 3204 Planarity : 0.005 0.059 3435 Dihedral : 8.124 59.427 3631 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.73 % Favored : 96.02 % Rotamer: Outliers : 2.35 % Allowed : 9.20 % Favored : 88.45 % 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: -0.85 (0.17), residues: 2439 helix: 1.26 (0.29), residues: 347 sheet: -0.23 (0.19), residues: 727 loop : -1.25 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 87 TYR 0.013 0.002 TYR C 111 PHE 0.017 0.002 PHE K 342 TRP 0.016 0.002 TRP B 628 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00481 (20157) covalent geometry : angle 0.59216 (27396) SS BOND : bond 0.01016 ( 42) SS BOND : angle 1.66373 ( 84) hydrogen bonds : bond 0.04165 ( 645) hydrogen bonds : angle 4.99978 ( 1746) link_ALPHA1-2 : bond 0.00425 ( 6) link_ALPHA1-2 : angle 1.57892 ( 18) link_ALPHA1-3 : bond 0.00540 ( 6) link_ALPHA1-3 : angle 1.75572 ( 18) link_ALPHA1-6 : bond 0.00428 ( 6) link_ALPHA1-6 : angle 1.96511 ( 18) link_BETA1-4 : bond 0.00276 ( 18) link_BETA1-4 : angle 1.99586 ( 54) link_NAG-ASN : bond 0.00130 ( 12) link_NAG-ASN : angle 2.05994 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 0.656 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 114 GLN cc_start: 0.8475 (tt0) cc_final: 0.8037 (tt0) REVERT: B 630 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7621 (tp-100) REVERT: B 652 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7729 (tm-30) REVERT: E 66 HIS cc_start: 0.6851 (p-80) cc_final: 0.6523 (p-80) REVERT: F 652 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7882 (tm-30) REVERT: K 230 GLU cc_start: 0.7528 (tt0) cc_final: 0.7300 (tt0) REVERT: K 269 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7581 (mmm-85) REVERT: K 457 ARG cc_start: 0.7930 (mtp180) cc_final: 0.7561 (mtp-110) REVERT: M 82 GLU cc_start: 0.8043 (tt0) cc_final: 0.7826 (tt0) outliers start: 50 outliers final: 43 residues processed: 283 average time/residue: 0.2922 time to fit residues: 127.6812 Evaluate side-chains 261 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 121 CYS Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 337 CYS Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 458 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.176321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148208 restraints weight = 67863.277| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.22 r_work: 0.3548 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 20247 Z= 0.158 Angle : 0.571 13.791 27624 Z= 0.292 Chirality : 0.043 0.174 3204 Planarity : 0.005 0.062 3435 Dihedral : 7.170 57.430 3631 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.90 % Favored : 95.86 % Rotamer: Outliers : 2.58 % Allowed : 9.77 % Favored : 87.65 % 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: -0.82 (0.17), residues: 2439 helix: 1.33 (0.29), residues: 348 sheet: -0.22 (0.19), residues: 722 loop : -1.25 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.009 0.001 TYR D 51 PHE 0.013 0.001 PHE K 342 TRP 0.009 0.001 TRP M 101 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00375 (20157) covalent geometry : angle 0.54740 (27396) SS BOND : bond 0.00605 ( 42) SS BOND : angle 1.97015 ( 84) hydrogen bonds : bond 0.03808 ( 645) hydrogen bonds : angle 4.84318 ( 1746) link_ALPHA1-2 : bond 0.00333 ( 6) link_ALPHA1-2 : angle 1.66393 ( 18) link_ALPHA1-3 : bond 0.00584 ( 6) link_ALPHA1-3 : angle 1.66582 ( 18) link_ALPHA1-6 : bond 0.00342 ( 6) link_ALPHA1-6 : angle 1.76829 ( 18) link_BETA1-4 : bond 0.00301 ( 18) link_BETA1-4 : angle 1.78053 ( 54) link_NAG-ASN : bond 0.00134 ( 12) link_NAG-ASN : angle 1.90770 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 1.043 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 114 GLN cc_start: 0.8370 (tt0) cc_final: 0.7915 (tt0) REVERT: B 630 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7623 (tp-100) REVERT: B 652 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7661 (tm-30) REVERT: C 38 ARG cc_start: 0.7802 (tmm-80) cc_final: 0.7584 (ttp-170) REVERT: D 44 LYS cc_start: 0.6826 (ptmt) cc_final: 0.6458 (pttt) REVERT: E 66 HIS cc_start: 0.6905 (p-80) cc_final: 0.6592 (p-80) REVERT: F 652 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7824 (tm-30) REVERT: M 82 GLU cc_start: 0.7981 (tt0) cc_final: 0.7773 (tt0) outliers start: 55 outliers final: 45 residues processed: 271 average time/residue: 0.2940 time to fit residues: 123.0319 Evaluate side-chains 263 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 218 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 121 CYS Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 336 ASN Chi-restraints excluded: chain K residue 337 CYS Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 73 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 174 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 232 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** 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 = 0.3996 r_free = 0.3996 target = 0.175428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145819 restraints weight = 67927.059| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.26 r_work: 0.3414 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 20247 Z= 0.156 Angle : 0.565 13.821 27624 Z= 0.288 Chirality : 0.043 0.159 3204 Planarity : 0.005 0.066 3435 Dihedral : 6.630 57.443 3631 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.18 % Favored : 95.57 % Rotamer: Outliers : 2.39 % Allowed : 10.19 % Favored : 87.42 % 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: -0.83 (0.17), residues: 2439 helix: 1.31 (0.29), residues: 349 sheet: -0.20 (0.19), residues: 725 loop : -1.27 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.009 0.001 TYR N 51 PHE 0.016 0.001 PHE K 342 TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00372 (20157) covalent geometry : angle 0.54333 (27396) SS BOND : bond 0.00695 ( 42) SS BOND : angle 1.89761 ( 84) hydrogen bonds : bond 0.03737 ( 645) hydrogen bonds : angle 4.75515 ( 1746) link_ALPHA1-2 : bond 0.00338 ( 6) link_ALPHA1-2 : angle 1.60817 ( 18) link_ALPHA1-3 : bond 0.00562 ( 6) link_ALPHA1-3 : angle 1.71478 ( 18) link_ALPHA1-6 : bond 0.00317 ( 6) link_ALPHA1-6 : angle 1.80649 ( 18) link_BETA1-4 : bond 0.00309 ( 18) link_BETA1-4 : angle 1.54775 ( 54) link_NAG-ASN : bond 0.00148 ( 12) link_NAG-ASN : angle 1.93319 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 0.985 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 114 GLN cc_start: 0.8363 (tt0) cc_final: 0.7894 (tt0) REVERT: C 38 ARG cc_start: 0.7689 (tmm-80) cc_final: 0.7444 (ttp-170) REVERT: D 44 LYS cc_start: 0.6811 (ptmt) cc_final: 0.6476 (pttt) REVERT: E 66 HIS cc_start: 0.6963 (p-80) cc_final: 0.6620 (p-80) REVERT: F 652 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7843 (tm-30) REVERT: K 64 MET cc_start: 0.7770 (ttp) cc_final: 0.7391 (ttp) outliers start: 51 outliers final: 44 residues processed: 280 average time/residue: 0.3150 time to fit residues: 135.6204 Evaluate side-chains 267 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 121 CYS Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 158 ASN Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 336 ASN Chi-restraints excluded: chain K residue 337 CYS Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain L residue 73 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 3 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.172293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142095 restraints weight = 68050.489| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.26 r_work: 0.3366 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 20247 Z= 0.221 Angle : 0.606 12.464 27624 Z= 0.310 Chirality : 0.044 0.168 3204 Planarity : 0.005 0.065 3435 Dihedral : 6.852 58.185 3631 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.41 % Favored : 94.34 % Rotamer: Outliers : 2.63 % Allowed : 10.66 % Favored : 86.71 % 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: -1.05 (0.17), residues: 2439 helix: 0.98 (0.29), residues: 346 sheet: -0.28 (0.19), residues: 742 loop : -1.41 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.010 0.002 TYR D 51 PHE 0.020 0.002 PHE K 342 TRP 0.011 0.002 TRP H 50 HIS 0.005 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00527 (20157) covalent geometry : angle 0.58216 (27396) SS BOND : bond 0.00797 ( 42) SS BOND : angle 1.99889 ( 84) hydrogen bonds : bond 0.04141 ( 645) hydrogen bonds : angle 4.91081 ( 1746) link_ALPHA1-2 : bond 0.00248 ( 6) link_ALPHA1-2 : angle 1.78648 ( 18) link_ALPHA1-3 : bond 0.00480 ( 6) link_ALPHA1-3 : angle 1.86516 ( 18) link_ALPHA1-6 : bond 0.00411 ( 6) link_ALPHA1-6 : angle 1.88404 ( 18) link_BETA1-4 : bond 0.00307 ( 18) link_BETA1-4 : angle 1.71897 ( 54) link_NAG-ASN : bond 0.00177 ( 12) link_NAG-ASN : angle 2.31857 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 1.074 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 114 GLN cc_start: 0.8533 (tt0) cc_final: 0.8061 (tt0) REVERT: A 500 ARG cc_start: 0.7608 (mtp180) cc_final: 0.7273 (mtp-110) REVERT: C 38 ARG cc_start: 0.7886 (tmm-80) cc_final: 0.7604 (ttp-170) REVERT: C 60 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: D 44 LYS cc_start: 0.6832 (ptmt) cc_final: 0.6521 (pttt) REVERT: E 66 HIS cc_start: 0.7083 (p-80) cc_final: 0.6772 (p-80) REVERT: F 652 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7973 (tm-30) REVERT: K 64 MET cc_start: 0.7974 (ttp) cc_final: 0.7733 (ttp) outliers start: 56 outliers final: 47 residues processed: 291 average time/residue: 0.3217 time to fit residues: 143.4565 Evaluate side-chains 272 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 121 CYS Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 158 ASN Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 336 ASN Chi-restraints excluded: chain K residue 337 CYS Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 179 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 227 optimal weight: 0.6980 chunk 230 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN H 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.173746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143071 restraints weight = 68035.070| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.35 r_work: 0.3386 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 20247 Z= 0.149 Angle : 0.553 11.151 27624 Z= 0.283 Chirality : 0.043 0.153 3204 Planarity : 0.005 0.064 3435 Dihedral : 6.416 57.145 3631 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.22 % Favored : 95.53 % Rotamer: Outliers : 2.35 % Allowed : 11.31 % Favored : 86.34 % 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: -0.99 (0.17), residues: 2439 helix: 1.15 (0.29), residues: 346 sheet: -0.23 (0.20), residues: 742 loop : -1.42 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 125 TYR 0.009 0.001 TYR D 51 PHE 0.015 0.001 PHE K 342 TRP 0.009 0.001 TRP H 50 HIS 0.005 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00359 (20157) covalent geometry : angle 0.53306 (27396) SS BOND : bond 0.00489 ( 42) SS BOND : angle 1.77631 ( 84) hydrogen bonds : bond 0.03754 ( 645) hydrogen bonds : angle 4.80654 ( 1746) link_ALPHA1-2 : bond 0.00276 ( 6) link_ALPHA1-2 : angle 1.62237 ( 18) link_ALPHA1-3 : bond 0.00627 ( 6) link_ALPHA1-3 : angle 1.62211 ( 18) link_ALPHA1-6 : bond 0.00344 ( 6) link_ALPHA1-6 : angle 1.71776 ( 18) link_BETA1-4 : bond 0.00298 ( 18) link_BETA1-4 : angle 1.48786 ( 54) link_NAG-ASN : bond 0.00135 ( 12) link_NAG-ASN : angle 1.89061 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 1.016 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: A 114 GLN cc_start: 0.8417 (tt0) cc_final: 0.8064 (tt0) REVERT: A 500 ARG cc_start: 0.7566 (mtp180) cc_final: 0.7225 (mtp-110) REVERT: C 38 ARG cc_start: 0.7699 (tmm-80) cc_final: 0.7424 (ttp-170) REVERT: D 44 LYS cc_start: 0.6874 (ptmt) cc_final: 0.6556 (pttt) REVERT: E 66 HIS cc_start: 0.6979 (p-80) cc_final: 0.6687 (p-80) REVERT: F 652 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7877 (tm-30) REVERT: K 49 SER cc_start: 0.5889 (OUTLIER) cc_final: 0.5680 (m) REVERT: K 64 MET cc_start: 0.7778 (ttp) cc_final: 0.7542 (ttp) outliers start: 50 outliers final: 44 residues processed: 277 average time/residue: 0.3114 time to fit residues: 132.7556 Evaluate side-chains 268 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 121 CYS Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 336 ASN Chi-restraints excluded: chain K residue 337 CYS Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 194 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** 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 = 0.3964 r_free = 0.3964 target = 0.172271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143650 restraints weight = 67850.474| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.13 r_work: 0.3404 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20247 Z= 0.182 Angle : 0.580 11.024 27624 Z= 0.297 Chirality : 0.043 0.157 3204 Planarity : 0.005 0.065 3435 Dihedral : 6.350 56.891 3629 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.08 % Favored : 94.67 % Rotamer: Outliers : 2.30 % Allowed : 11.69 % Favored : 86.01 % 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: -1.07 (0.17), residues: 2439 helix: 1.07 (0.29), residues: 346 sheet: -0.26 (0.20), residues: 747 loop : -1.49 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.009 0.001 TYR D 51 PHE 0.016 0.002 PHE K 342 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00439 (20157) covalent geometry : angle 0.55678 (27396) SS BOND : bond 0.00561 ( 42) SS BOND : angle 2.01327 ( 84) hydrogen bonds : bond 0.03871 ( 645) hydrogen bonds : angle 4.85435 ( 1746) link_ALPHA1-2 : bond 0.00242 ( 6) link_ALPHA1-2 : angle 1.73441 ( 18) link_ALPHA1-3 : bond 0.00529 ( 6) link_ALPHA1-3 : angle 1.70662 ( 18) link_ALPHA1-6 : bond 0.00360 ( 6) link_ALPHA1-6 : angle 1.77666 ( 18) link_BETA1-4 : bond 0.00322 ( 18) link_BETA1-4 : angle 1.57387 ( 54) link_NAG-ASN : bond 0.00143 ( 12) link_NAG-ASN : angle 2.11456 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8485 (tt0) cc_final: 0.8119 (tt0) REVERT: A 500 ARG cc_start: 0.7772 (mtp180) cc_final: 0.7410 (mtp-110) REVERT: A 502 LYS cc_start: 0.7555 (pttm) cc_final: 0.7142 (mmmt) REVERT: C 38 ARG cc_start: 0.7819 (tmm-80) cc_final: 0.7525 (ttp-170) REVERT: C 60 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: D 44 LYS cc_start: 0.6882 (ptmt) cc_final: 0.6591 (pttt) REVERT: E 66 HIS cc_start: 0.7059 (p-80) cc_final: 0.6753 (p-80) REVERT: E 308 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7627 (mmm-85) REVERT: F 652 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7950 (tm-30) REVERT: K 64 MET cc_start: 0.7950 (ttp) cc_final: 0.7706 (ttp) outliers start: 49 outliers final: 44 residues processed: 275 average time/residue: 0.3361 time to fit residues: 141.5278 Evaluate side-chains 270 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 121 CYS Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 158 ASN Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 336 ASN Chi-restraints excluded: chain K residue 337 CYS Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 61 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 236 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 151 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.172318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142210 restraints weight = 68123.951| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.27 r_work: 0.3339 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20247 Z= 0.164 Angle : 0.569 10.515 27624 Z= 0.291 Chirality : 0.043 0.153 3204 Planarity : 0.005 0.063 3435 Dihedral : 6.057 56.901 3628 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.80 % Favored : 94.96 % Rotamer: Outliers : 2.11 % Allowed : 11.97 % Favored : 85.92 % 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: -1.07 (0.17), residues: 2439 helix: 1.14 (0.29), residues: 346 sheet: -0.24 (0.20), residues: 747 loop : -1.53 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.011 0.001 TYR M 80 PHE 0.016 0.002 PHE E 383 TRP 0.009 0.001 TRP H 50 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00394 (20157) covalent geometry : angle 0.54807 (27396) SS BOND : bond 0.00528 ( 42) SS BOND : angle 1.87216 ( 84) hydrogen bonds : bond 0.03768 ( 645) hydrogen bonds : angle 4.83077 ( 1746) link_ALPHA1-2 : bond 0.00220 ( 6) link_ALPHA1-2 : angle 1.68231 ( 18) link_ALPHA1-3 : bond 0.00609 ( 6) link_ALPHA1-3 : angle 1.62914 ( 18) link_ALPHA1-6 : bond 0.00325 ( 6) link_ALPHA1-6 : angle 1.73133 ( 18) link_BETA1-4 : bond 0.00307 ( 18) link_BETA1-4 : angle 1.49099 ( 54) link_NAG-ASN : bond 0.00120 ( 12) link_NAG-ASN : angle 1.98406 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8457 (tt0) cc_final: 0.8067 (tt0) REVERT: A 500 ARG cc_start: 0.7728 (mtp180) cc_final: 0.7360 (mtp-110) REVERT: A 502 LYS cc_start: 0.7568 (pttm) cc_final: 0.7119 (mmmt) REVERT: B 588 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7737 (mtm-85) REVERT: C 38 ARG cc_start: 0.7756 (tmm-80) cc_final: 0.7460 (ttp-170) REVERT: C 60 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: D 44 LYS cc_start: 0.6876 (ptmt) cc_final: 0.6584 (pttt) REVERT: E 66 HIS cc_start: 0.7049 (p-80) cc_final: 0.6773 (p-80) REVERT: E 269 GLU cc_start: 0.7545 (tt0) cc_final: 0.7333 (tt0) REVERT: E 308 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7614 (mmm-85) REVERT: F 652 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7952 (tm-30) outliers start: 45 outliers final: 42 residues processed: 268 average time/residue: 0.3503 time to fit residues: 143.9639 Evaluate side-chains 267 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 121 CYS Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 336 ASN Chi-restraints excluded: chain K residue 337 CYS Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 99 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 198 optimal weight: 0.0000 chunk 72 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.174086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144253 restraints weight = 67949.526| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.24 r_work: 0.3360 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20247 Z= 0.108 Angle : 0.519 10.104 27624 Z= 0.266 Chirality : 0.042 0.152 3204 Planarity : 0.004 0.062 3435 Dihedral : 5.604 57.979 3627 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.10 % Favored : 95.65 % Rotamer: Outliers : 1.36 % Allowed : 12.72 % Favored : 85.92 % 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: -0.90 (0.17), residues: 2439 helix: 1.45 (0.30), residues: 346 sheet: -0.15 (0.20), residues: 729 loop : -1.44 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.009 0.001 TYR K 441 PHE 0.010 0.001 PHE K 342 TRP 0.009 0.001 TRP H 50 HIS 0.004 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00254 (20157) covalent geometry : angle 0.50204 (27396) SS BOND : bond 0.00484 ( 42) SS BOND : angle 1.57641 ( 84) hydrogen bonds : bond 0.03361 ( 645) hydrogen bonds : angle 4.67438 ( 1746) link_ALPHA1-2 : bond 0.00347 ( 6) link_ALPHA1-2 : angle 1.58700 ( 18) link_ALPHA1-3 : bond 0.00708 ( 6) link_ALPHA1-3 : angle 1.48318 ( 18) link_ALPHA1-6 : bond 0.00344 ( 6) link_ALPHA1-6 : angle 1.64130 ( 18) link_BETA1-4 : bond 0.00321 ( 18) link_BETA1-4 : angle 1.29929 ( 54) link_NAG-ASN : bond 0.00146 ( 12) link_NAG-ASN : angle 1.65095 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8360 (tt0) cc_final: 0.7957 (tt0) REVERT: A 500 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7350 (mtp-110) REVERT: A 502 LYS cc_start: 0.7543 (pttm) cc_final: 0.7072 (mmmt) REVERT: B 588 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.7691 (mtm-85) REVERT: C 60 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: D 44 LYS cc_start: 0.6818 (ptmt) cc_final: 0.6530 (pttt) REVERT: E 66 HIS cc_start: 0.7006 (p-80) cc_final: 0.6731 (p-80) REVERT: F 652 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7855 (tm-30) outliers start: 29 outliers final: 28 residues processed: 254 average time/residue: 0.3398 time to fit residues: 131.7908 Evaluate side-chains 252 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain K residue 245 ILE Chi-restraints excluded: chain K residue 336 ASN Chi-restraints excluded: chain K residue 337 CYS Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 65 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142626 restraints weight = 68140.822| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.24 r_work: 0.3348 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20247 Z= 0.153 Angle : 0.551 10.017 27624 Z= 0.281 Chirality : 0.042 0.151 3204 Planarity : 0.004 0.063 3435 Dihedral : 5.652 57.828 3625 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.21 % Favored : 94.55 % Rotamer: Outliers : 1.60 % Allowed : 12.68 % Favored : 85.73 % 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: -0.98 (0.17), residues: 2439 helix: 1.34 (0.29), residues: 346 sheet: -0.20 (0.20), residues: 729 loop : -1.47 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.008 0.001 TYR D 51 PHE 0.016 0.001 PHE A 233 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS K 177 Details of bonding type rmsd covalent geometry : bond 0.00367 (20157) covalent geometry : angle 0.53114 (27396) SS BOND : bond 0.00476 ( 42) SS BOND : angle 1.71906 ( 84) hydrogen bonds : bond 0.03590 ( 645) hydrogen bonds : angle 4.72910 ( 1746) link_ALPHA1-2 : bond 0.00165 ( 6) link_ALPHA1-2 : angle 1.75414 ( 18) link_ALPHA1-3 : bond 0.00627 ( 6) link_ALPHA1-3 : angle 1.61897 ( 18) link_ALPHA1-6 : bond 0.00316 ( 6) link_ALPHA1-6 : angle 1.71853 ( 18) link_BETA1-4 : bond 0.00333 ( 18) link_BETA1-4 : angle 1.41538 ( 54) link_NAG-ASN : bond 0.00161 ( 12) link_NAG-ASN : angle 2.00794 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8505.17 seconds wall clock time: 145 minutes 4.73 seconds (8704.73 seconds total)