Starting phenix.real_space_refine on Sat Jul 4 05:47:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m8l_23719/07_2026/7m8l_23719.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m8l_23719/07_2026/7m8l_23719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7m8l_23719/07_2026/7m8l_23719.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m8l_23719/07_2026/7m8l_23719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m8l_23719/07_2026/7m8l_23719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m8l_23719/07_2026/7m8l_23719.map" model { file = "/net/cci-nas-00/data/ceres_data/7m8l_23719/07_2026/7m8l_23719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m8l_23719/07_2026/7m8l_23719.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 11838 2.51 5 N 3147 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18753 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1028 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "J" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "M" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "P" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "B" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1028 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "Q" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1028 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "O" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "R" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" 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 chiralities: 2 Chain: "C" 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 chiralities: 2 Time building chain proxies: 4.38, per 1000 atoms: 0.23 Number of scatterers: 18753 At special positions: 0 Unit cell: (141.11, 152.44, 119.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 3711 8.00 N 3147 7.00 C 11838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 101 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 101 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.02 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.05 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 101 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.02 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.05 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 97 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 401 " - " ASN A 268 " " NAG A 402 " - " ASN A 238 " " NAG B 401 " - " ASN B 268 " " NAG B 402 " - " ASN B 238 " " NAG C 401 " - " ASN C 268 " " NAG C 402 " - " ASN C 238 " " NAG S 1 " - " ASN A 257 " " NAG T 1 " - " ASN A 228 " " NAG U 1 " - " ASN D 563 " " NAG V 1 " - " ASN B 257 " " NAG W 1 " - " ASN B 228 " " NAG X 1 " - " ASN E 563 " " NAG Y 1 " - " ASN C 257 " " NAG Z 1 " - " ASN C 228 " " NAG a 1 " - " ASN F 563 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 788.5 milliseconds 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 45 sheets defined 12.9% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 249 through 263 Processing helix chain 'G' and resid 67 through 70 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 4.809A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 removed outlier: 3.590A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 66 Processing helix chain 'M' and resid 88 through 92 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 249 through 263 Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 92 through 96 Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'E' and resid 553 through 576 removed outlier: 4.809A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 removed outlier: 3.590A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 66 Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 249 through 263 Processing helix chain 'I' and resid 67 through 70 Processing helix chain 'I' and resid 92 through 96 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 4.809A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 removed outlier: 3.590A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 66 Processing helix chain 'O' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.713A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 114 through 119 removed outlier: 6.901A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 13.774A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.707A pdb=" N THR G 83 " --> pdb=" O ASP G 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.005A pdb=" N MET G 37 " --> pdb=" O ARG G 53 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG G 53 " --> pdb=" O MET G 37 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP G 39 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AB2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'M' and resid 11 through 12 removed outlier: 7.495A pdb=" N TYR M 34 " --> pdb=" O ASP M 54 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP M 54 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP M 36 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'P' and resid 5 through 7 removed outlier: 5.744A pdb=" N THR P 69 " --> pdb=" O ALA P 25 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N GLN P 27 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER P 67 " --> pdb=" O GLN P 27 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL P 29 " --> pdb=" O SER P 65 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N SER P 65 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.634A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.712A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 114 through 119 removed outlier: 6.900A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 13.774A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.707A pdb=" N THR H 83 " --> pdb=" O ASP H 78 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.005A pdb=" N MET H 37 " --> pdb=" O ARG H 53 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG H 53 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP H 39 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.911A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.911A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AC8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.495A pdb=" N TYR N 34 " --> pdb=" O ASP N 54 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP N 54 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP N 36 " --> pdb=" O TYR N 52 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR N 52 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP N 38 " --> pdb=" O ILE N 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AD2, first strand: chain 'Q' and resid 5 through 7 removed outlier: 5.744A pdb=" N THR Q 69 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N GLN Q 27 " --> pdb=" O SER Q 67 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER Q 67 " --> pdb=" O GLN Q 27 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N VAL Q 29 " --> pdb=" O SER Q 65 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N SER Q 65 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.634A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 43 through 45 removed outlier: 6.712A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 114 through 119 removed outlier: 6.901A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 13.773A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.707A pdb=" N THR I 83 " --> pdb=" O ASP I 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.005A pdb=" N MET I 37 " --> pdb=" O ARG I 53 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG I 53 " --> pdb=" O MET I 37 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP I 39 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 49 through 50 Processing sheet with id=AE5, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'O' and resid 11 through 12 removed outlier: 7.495A pdb=" N TYR O 34 " --> pdb=" O ASP O 54 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP O 54 " --> pdb=" O TYR O 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP O 36 " --> pdb=" O TYR O 52 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR O 52 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP O 38 " --> pdb=" O ILE O 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AE8, first strand: chain 'R' and resid 5 through 7 removed outlier: 5.744A pdb=" N THR R 69 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N GLN R 27 " --> pdb=" O SER R 67 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER R 67 " --> pdb=" O GLN R 27 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL R 29 " --> pdb=" O SER R 65 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N SER R 65 " --> pdb=" O VAL R 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.634A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3581 1.32 - 1.46: 6795 1.46 - 1.60: 8701 1.60 - 1.73: 60 1.73 - 1.87: 57 Bond restraints: 19194 Sorted by residual: bond pdb=" CB TYR A 99 " pdb=" CG TYR A 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.77e+01 bond pdb=" CB TYR B 99 " pdb=" CG TYR B 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.77e+01 bond pdb=" CB TYR C 99 " pdb=" CG TYR C 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.76e+01 bond pdb=" CB ILE J 107 " pdb=" CG1 ILE J 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CB ILE L 107 " pdb=" CG1 ILE L 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.72e+01 ... (remaining 19189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 21498 2.26 - 4.51: 3759 4.51 - 6.77: 690 6.77 - 9.02: 115 9.02 - 11.28: 26 Bond angle restraints: 26088 Sorted by residual: angle pdb=" N GLN N 41 " pdb=" CA GLN N 41 " pdb=" C GLN N 41 " ideal model delta sigma weight residual 111.36 120.62 -9.26 1.09e+00 8.42e-01 7.21e+01 angle pdb=" N GLN M 41 " pdb=" CA GLN M 41 " pdb=" C GLN M 41 " ideal model delta sigma weight residual 111.36 120.61 -9.25 1.09e+00 8.42e-01 7.21e+01 angle pdb=" N GLN O 41 " pdb=" CA GLN O 41 " pdb=" C GLN O 41 " ideal model delta sigma weight residual 111.36 120.61 -9.25 1.09e+00 8.42e-01 7.20e+01 angle pdb=" CA ASP H 78 " pdb=" CB ASP H 78 " pdb=" CG ASP H 78 " ideal model delta sigma weight residual 112.60 120.72 -8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" CA ASP I 78 " pdb=" CB ASP I 78 " pdb=" CG ASP I 78 " ideal model delta sigma weight residual 112.60 120.71 -8.11 1.00e+00 1.00e+00 6.58e+01 ... (remaining 26083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 10563 17.31 - 34.63: 252 34.63 - 51.94: 90 51.94 - 69.25: 33 69.25 - 86.56: 9 Dihedral angle restraints: 10947 sinusoidal: 4275 harmonic: 6672 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 101 " pdb=" CB CYS I 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.57 60.43 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 101 " pdb=" CB CYS H 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.58 60.42 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 101 " pdb=" CB CYS G 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.60 60.40 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 10944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2104 0.105 - 0.211: 656 0.211 - 0.316: 149 0.316 - 0.421: 54 0.421 - 0.527: 19 Chirality restraints: 2982 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.67e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.61e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.55e+01 ... (remaining 2979 not shown) Planarity restraints: 3297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 99 " 0.104 2.00e-02 2.50e+03 5.63e-02 6.33e+01 pdb=" CG TYR B 99 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 99 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR B 99 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR B 99 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 99 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 99 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 99 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 99 " -0.105 2.00e-02 2.50e+03 5.63e-02 6.33e+01 pdb=" CG TYR C 99 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 99 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR C 99 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR C 99 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR C 99 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR C 99 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 99 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 99 " -0.104 2.00e-02 2.50e+03 5.62e-02 6.31e+01 pdb=" CG TYR A 99 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 99 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 99 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 99 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 99 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 99 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 99 " -0.083 2.00e-02 2.50e+03 ... (remaining 3294 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 6995 2.88 - 3.39: 16279 3.39 - 3.89: 32370 3.89 - 4.40: 37598 4.40 - 4.90: 61464 Nonbonded interactions: 154706 Sorted by model distance: nonbonded pdb=" N THR Q 31 " pdb=" N ASN Q 32 " model vdw 2.378 2.560 nonbonded pdb=" N THR P 31 " pdb=" N ASN P 32 " model vdw 2.379 2.560 nonbonded pdb=" N THR R 31 " pdb=" N ASN R 32 " model vdw 2.380 2.560 nonbonded pdb=" OD2 ASP O 74 " pdb=" NZ LYS O 77 " model vdw 2.405 3.120 nonbonded pdb=" OD2 ASP M 74 " pdb=" NZ LYS M 77 " model vdw 2.406 3.120 ... (remaining 154701 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.140 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.022 0.181 19257 Z= 1.120 Angle : 1.864 12.656 26256 Z= 1.215 Chirality : 0.117 0.527 2982 Planarity : 0.009 0.060 3282 Dihedral : 9.769 86.563 6660 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.65 % Allowed : 1.69 % Favored : 97.65 % Rotamer: Outliers : 0.15 % Allowed : 1.68 % Favored : 98.17 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.75 (0.17), residues: 2301 helix: 1.11 (0.34), residues: 150 sheet: 0.34 (0.17), residues: 903 loop : 0.74 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 77 TYR 0.105 0.011 TYR C 99 PHE 0.027 0.006 PHE N 80 TRP 0.034 0.008 TRP L 36 HIS 0.007 0.003 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.02136 / 1.11 (19194) covalent geometry : angle 1.84380 / 1.21 (26088) SS BOND : bond 0.01108 / 0.79 ( 21) SS BOND : angle 3.01019 / 1.77 ( 42) hydrogen bonds : bond 0.15724 / 11.09 ( 684) hydrogen bonds : angle 8.18736 / 5.44 ( 1719) link_ALPHA1-3 : bond 0.08211 / 4.79 ( 6) link_ALPHA1-3 : angle 4.44048 / 2.54 ( 18) link_ALPHA1-6 : bond 0.06486 / 3.73 ( 6) link_ALPHA1-6 : angle 3.69320 / 2.13 ( 18) link_BETA1-4 : bond 0.07454 / 4.96 ( 15) link_BETA1-4 : angle 5.47145 / 3.27 ( 45) link_NAG-ASN : bond 0.07779 / 4.97 ( 15) link_NAG-ASN : angle 2.16940 / 1.47 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 623 time to evaluate : 0.733 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: A 44 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7800 (mt0) REVERT: A 99 TYR cc_start: 0.7365 (m-10) cc_final: 0.6853 (m-10) REVERT: A 106 GLU cc_start: 0.8431 (tt0) cc_final: 0.8229 (tt0) REVERT: G 39 TRP cc_start: 0.6916 (m100) cc_final: 0.6034 (m100) REVERT: G 87 GLN cc_start: 0.5925 (tp40) cc_final: 0.5601 (mp10) REVERT: J 32 LYS cc_start: 0.8084 (pttt) cc_final: 0.7838 (ptmm) REVERT: J 61 ASP cc_start: 0.6822 (p0) cc_final: 0.6361 (t0) REVERT: J 97 TRP cc_start: 0.6069 (m-10) cc_final: 0.5667 (m-10) REVERT: D 565 THR cc_start: 0.9022 (p) cc_final: 0.8672 (t) REVERT: D 596 ARG cc_start: 0.6937 (mtp85) cc_final: 0.6628 (mtt-85) REVERT: D 597 TRP cc_start: 0.5878 (m-90) cc_final: 0.5416 (m100) REVERT: M 6 GLU cc_start: 0.8301 (mp0) cc_final: 0.7971 (mp0) REVERT: M 17 THR cc_start: 0.8712 (m) cc_final: 0.8392 (p) REVERT: M 54 ASP cc_start: 0.8273 (t0) cc_final: 0.7830 (t0) REVERT: M 74 ASP cc_start: 0.7031 (t0) cc_final: 0.6064 (p0) REVERT: M 116 THR cc_start: 0.8140 (t) cc_final: 0.7940 (t) REVERT: P 37 GLN cc_start: 0.8729 (tt0) cc_final: 0.8270 (tt0) REVERT: P 85 VAL cc_start: 0.8704 (t) cc_final: 0.8329 (m) REVERT: H 39 TRP cc_start: 0.6885 (m100) cc_final: 0.6172 (m100) REVERT: H 87 GLN cc_start: 0.6064 (tp40) cc_final: 0.5557 (mp10) REVERT: K 59 ILE cc_start: 0.1979 (mm) cc_final: 0.1565 (mm) REVERT: K 61 ASP cc_start: 0.6732 (p0) cc_final: 0.6295 (t70) REVERT: K 73 THR cc_start: 0.7988 (m) cc_final: 0.7785 (t) REVERT: E 565 THR cc_start: 0.8976 (p) cc_final: 0.8606 (t) REVERT: E 597 TRP cc_start: 0.6089 (m-90) cc_final: 0.5537 (m100) REVERT: N 6 GLU cc_start: 0.8245 (mp0) cc_final: 0.7849 (mp0) REVERT: N 17 THR cc_start: 0.8885 (m) cc_final: 0.8579 (p) REVERT: N 54 ASP cc_start: 0.8336 (t0) cc_final: 0.7818 (t0) REVERT: N 74 ASP cc_start: 0.7170 (t0) cc_final: 0.6277 (p0) REVERT: Q 39 LYS cc_start: 0.8411 (mttt) cc_final: 0.8050 (mttt) REVERT: Q 85 VAL cc_start: 0.8614 (t) cc_final: 0.8322 (m) REVERT: Q 105 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6777 (mm-30) REVERT: C 44 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7648 (mt0) REVERT: C 99 TYR cc_start: 0.7404 (m-10) cc_final: 0.6527 (m-10) REVERT: C 103 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8333 (mt-10) REVERT: I 39 TRP cc_start: 0.7032 (m100) cc_final: 0.5925 (m100) REVERT: I 87 GLN cc_start: 0.5948 (tp40) cc_final: 0.5475 (mp10) REVERT: I 88 MET cc_start: 0.7390 (mtm) cc_final: 0.7090 (ptp) REVERT: L 61 ASP cc_start: 0.7097 (p0) cc_final: 0.6619 (t70) REVERT: F 565 THR cc_start: 0.8892 (p) cc_final: 0.8605 (t) REVERT: F 597 TRP cc_start: 0.6067 (m-90) cc_final: 0.5642 (m100) REVERT: O 6 GLU cc_start: 0.8430 (mp0) cc_final: 0.8115 (mp0) REVERT: O 17 THR cc_start: 0.8954 (m) cc_final: 0.8627 (p) REVERT: O 34 TYR cc_start: 0.8830 (m-80) cc_final: 0.8613 (m-80) REVERT: O 54 ASP cc_start: 0.8298 (t0) cc_final: 0.7804 (t0) REVERT: O 74 ASP cc_start: 0.6916 (t0) cc_final: 0.6094 (p0) REVERT: R 4 MET cc_start: 0.7684 (mmm) cc_final: 0.7215 (mmm) REVERT: R 11 LEU cc_start: 0.8752 (tp) cc_final: 0.8529 (tt) REVERT: R 37 GLN cc_start: 0.8602 (tt0) cc_final: 0.8150 (tt0) REVERT: R 85 VAL cc_start: 0.8713 (t) cc_final: 0.8400 (m) outliers start: 3 outliers final: 0 residues processed: 623 average time/residue: 0.1796 time to fit residues: 160.1099 Evaluate side-chains 392 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN M 41 GLN M 78 ASN M 79 HIS P 92 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN N 78 ASN N 79 HIS Q 37 GLN Q 79 GLN Q 89 GLN C 39 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN O 78 ASN O 79 HIS O 114 GLN R 79 GLN R 92 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102562 restraints weight = 30983.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101120 restraints weight = 63125.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101892 restraints weight = 60127.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103894 restraints weight = 38452.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104053 restraints weight = 26506.949| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19257 Z= 0.177 Angle : 0.807 18.528 26256 Z= 0.399 Chirality : 0.049 0.272 2982 Planarity : 0.005 0.043 3282 Dihedral : 5.604 22.673 2577 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.56 % Favored : 97.31 % Rotamer: Outliers : 1.93 % Allowed : 10.33 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: 0.38 (0.17), residues: 2301 helix: 2.17 (0.37), residues: 156 sheet: 0.06 (0.17), residues: 969 loop : 0.32 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 587 TYR 0.022 0.002 TYR G 100 PHE 0.039 0.002 PHE K 72 TRP 0.037 0.002 TRP R 94 HIS 0.008 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (19194) covalent geometry : angle 0.74796 / 0.39 (26088) SS BOND : bond 0.00399 / 0.25 ( 21) SS BOND : angle 1.31069 / 0.80 ( 42) hydrogen bonds : bond 0.04724 / 3.24 ( 684) hydrogen bonds : angle 6.42181 / 4.33 ( 1719) link_ALPHA1-3 : bond 0.01530 / 0.89 ( 6) link_ALPHA1-3 : angle 1.58195 / 0.91 ( 18) link_ALPHA1-6 : bond 0.01219 / 0.62 ( 6) link_ALPHA1-6 : angle 1.49629 / 0.87 ( 18) link_BETA1-4 : bond 0.02330 / 1.91 ( 15) link_BETA1-4 : angle 4.19300 / 2.59 ( 45) link_NAG-ASN : bond 0.00975 / 0.70 ( 15) link_NAG-ASN : angle 5.86235 / 3.91 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 428 time to evaluate : 0.745 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 100 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6714 (mp0) REVERT: G 53 ARG cc_start: 0.5847 (ttp-170) cc_final: 0.5574 (ptm-80) REVERT: D 565 THR cc_start: 0.8728 (p) cc_final: 0.8328 (t) REVERT: D 597 TRP cc_start: 0.6218 (m-90) cc_final: 0.5806 (m100) REVERT: M 3 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8221 (mp10) REVERT: M 6 GLU cc_start: 0.8312 (mp0) cc_final: 0.7997 (mp0) REVERT: M 17 THR cc_start: 0.8565 (m) cc_final: 0.8261 (p) REVERT: M 74 ASP cc_start: 0.6439 (t0) cc_final: 0.5490 (p0) REVERT: B 100 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6855 (mp0) REVERT: B 150 ASP cc_start: 0.7565 (m-30) cc_final: 0.7356 (m-30) REVERT: K 80 GLU cc_start: 0.6384 (mm-30) cc_final: 0.5641 (tp30) REVERT: E 565 THR cc_start: 0.8517 (p) cc_final: 0.8125 (t) REVERT: E 597 TRP cc_start: 0.6313 (m-90) cc_final: 0.5850 (m100) REVERT: N 3 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8178 (mp10) REVERT: N 6 GLU cc_start: 0.8211 (mp0) cc_final: 0.7886 (mp0) REVERT: N 17 THR cc_start: 0.8516 (m) cc_final: 0.8252 (p) REVERT: N 74 ASP cc_start: 0.6379 (t0) cc_final: 0.5644 (p0) REVERT: Q 39 LYS cc_start: 0.8056 (mttt) cc_final: 0.7775 (mttt) REVERT: C 100 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7238 (mp0) REVERT: I 33 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5172 (mptt) REVERT: L 13 LEU cc_start: 0.6808 (mt) cc_final: 0.6581 (mt) REVERT: L 80 GLU cc_start: 0.6218 (mm-30) cc_final: 0.5887 (tp30) REVERT: F 565 THR cc_start: 0.8693 (p) cc_final: 0.8369 (t) REVERT: F 597 TRP cc_start: 0.6376 (m-90) cc_final: 0.5859 (m100) REVERT: O 6 GLU cc_start: 0.8425 (mp0) cc_final: 0.8114 (mp0) REVERT: O 74 ASP cc_start: 0.6344 (t0) cc_final: 0.5458 (p0) REVERT: R 98 TYR cc_start: 0.8501 (m-80) cc_final: 0.8260 (m-80) REVERT: R 105 GLU cc_start: 0.5629 (mm-30) cc_final: 0.5078 (mm-30) outliers start: 38 outliers final: 24 residues processed: 447 average time/residue: 0.1730 time to fit residues: 112.4699 Evaluate side-chains 394 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 369 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 106 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 197 optimal weight: 0.0270 chunk 121 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 514 ASN D 595 GLN M 41 GLN M 79 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN H 3 GLN E 514 ASN N 78 ASN N 79 HIS Q 79 GLN I 3 GLN L 43 GLN F 514 ASN F 595 GLN O 79 HIS O 114 GLN R 79 GLN R 92 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099135 restraints weight = 31363.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099372 restraints weight = 72703.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100119 restraints weight = 60522.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100034 restraints weight = 41042.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100824 restraints weight = 34474.539| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19257 Z= 0.235 Angle : 0.771 15.488 26256 Z= 0.381 Chirality : 0.048 0.295 2982 Planarity : 0.005 0.046 3282 Dihedral : 5.414 21.802 2577 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.87 % Favored : 97.00 % Rotamer: Outliers : 3.26 % Allowed : 12.88 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: -0.11 (0.17), residues: 2301 helix: 1.37 (0.38), residues: 174 sheet: -0.31 (0.16), residues: 1065 loop : 0.14 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 587 TYR 0.025 0.002 TYR L 92 PHE 0.021 0.002 PHE J 99 TRP 0.030 0.002 TRP Q 94 HIS 0.008 0.002 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 (19194) covalent geometry : angle 0.73133 / 0.37 (26088) SS BOND : bond 0.00434 / 0.29 ( 21) SS BOND : angle 1.44751 / 0.86 ( 42) hydrogen bonds : bond 0.04595 / 3.12 ( 684) hydrogen bonds : angle 5.96319 / 4.05 ( 1719) link_ALPHA1-3 : bond 0.01193 / 0.70 ( 6) link_ALPHA1-3 : angle 1.74223 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00565 / 0.35 ( 6) link_ALPHA1-6 : angle 1.58737 / 0.90 ( 18) link_BETA1-4 : bond 0.01734 / 1.41 ( 15) link_BETA1-4 : angle 3.74614 / 2.34 ( 45) link_NAG-ASN : bond 0.00825 / 0.45 ( 15) link_NAG-ASN : angle 4.30271 / 2.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 383 time to evaluate : 0.797 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: A 100 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6901 (mp0) REVERT: A 184 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8986 (pp) REVERT: A 261 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: D 565 THR cc_start: 0.8815 (p) cc_final: 0.8370 (t) REVERT: D 578 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7424 (tt0) REVERT: D 597 TRP cc_start: 0.6394 (m-90) cc_final: 0.5939 (m100) REVERT: M 3 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8344 (mp10) REVERT: M 6 GLU cc_start: 0.8413 (mp0) cc_final: 0.8102 (mp0) REVERT: M 17 THR cc_start: 0.8588 (m) cc_final: 0.8233 (p) REVERT: M 74 ASP cc_start: 0.6315 (t0) cc_final: 0.5653 (p0) REVERT: B 100 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7006 (mp0) REVERT: K 80 GLU cc_start: 0.6117 (mm-30) cc_final: 0.5782 (tp30) REVERT: E 565 THR cc_start: 0.8699 (p) cc_final: 0.8253 (t) REVERT: E 597 TRP cc_start: 0.6357 (m-90) cc_final: 0.5941 (m100) REVERT: N 3 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8262 (mp10) REVERT: N 6 GLU cc_start: 0.8247 (mp0) cc_final: 0.7752 (mp0) REVERT: N 17 THR cc_start: 0.8602 (m) cc_final: 0.8336 (p) REVERT: N 74 ASP cc_start: 0.6463 (t0) cc_final: 0.5773 (p0) REVERT: N 100 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7445 (mm-30) REVERT: C 130 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: L 32 LYS cc_start: 0.8420 (ptmm) cc_final: 0.7909 (mmtt) REVERT: L 92 TYR cc_start: 0.5449 (OUTLIER) cc_final: 0.4652 (m-80) REVERT: F 565 THR cc_start: 0.8719 (p) cc_final: 0.8350 (t) REVERT: F 597 TRP cc_start: 0.6437 (m-90) cc_final: 0.5963 (m100) REVERT: O 3 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8214 (mp10) REVERT: O 6 GLU cc_start: 0.8529 (mp0) cc_final: 0.8216 (mp0) REVERT: O 74 ASP cc_start: 0.6507 (t0) cc_final: 0.5778 (p0) REVERT: R 98 TYR cc_start: 0.8527 (m-80) cc_final: 0.8222 (m-80) outliers start: 64 outliers final: 41 residues processed: 419 average time/residue: 0.1686 time to fit residues: 103.3734 Evaluate side-chains 402 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 357 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 545 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 114 GLN Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 203 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 79 HIS P 79 GLN P 92 ASN K 43 GLN N 41 GLN N 79 HIS Q 37 GLN Q 79 GLN F 514 ASN O 79 HIS R 79 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096021 restraints weight = 31705.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094701 restraints weight = 65213.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095443 restraints weight = 61054.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097674 restraints weight = 39341.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098009 restraints weight = 25752.346| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19257 Z= 0.177 Angle : 0.707 11.934 26256 Z= 0.347 Chirality : 0.046 0.243 2982 Planarity : 0.005 0.058 3282 Dihedral : 5.247 23.418 2577 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.82 % Favored : 97.00 % Rotamer: Outliers : 3.61 % Allowed : 12.93 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: -0.14 (0.18), residues: 2301 helix: 1.50 (0.38), residues: 174 sheet: -0.16 (0.16), residues: 1032 loop : -0.13 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 587 TYR 0.022 0.002 TYR G 100 PHE 0.015 0.002 PHE J 63 TRP 0.033 0.002 TRP J 36 HIS 0.008 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (19194) covalent geometry : angle 0.67662 / 0.34 (26088) SS BOND : bond 0.00379 / 0.21 ( 21) SS BOND : angle 1.15186 / 0.71 ( 42) hydrogen bonds : bond 0.03930 / 2.67 ( 684) hydrogen bonds : angle 5.63525 / 3.84 ( 1719) link_ALPHA1-3 : bond 0.01054 / 0.62 ( 6) link_ALPHA1-3 : angle 1.73376 / 1.02 ( 18) link_ALPHA1-6 : bond 0.00451 / 0.28 ( 6) link_ALPHA1-6 : angle 1.54447 / 0.89 ( 18) link_BETA1-4 : bond 0.01540 / 1.27 ( 15) link_BETA1-4 : angle 3.32977 / 2.09 ( 45) link_NAG-ASN : bond 0.00674 / 0.37 ( 15) link_NAG-ASN : angle 3.47704 / 2.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 383 time to evaluate : 0.758 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: A 100 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6791 (mp0) REVERT: A 231 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: A 261 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: J 32 LYS cc_start: 0.8568 (pttp) cc_final: 0.8054 (mmtt) REVERT: D 565 THR cc_start: 0.8806 (p) cc_final: 0.8341 (t) REVERT: D 578 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7348 (tt0) REVERT: D 597 TRP cc_start: 0.6329 (m-90) cc_final: 0.5842 (m100) REVERT: M 6 GLU cc_start: 0.8437 (mp0) cc_final: 0.8094 (mp0) REVERT: M 17 THR cc_start: 0.8547 (m) cc_final: 0.8204 (p) REVERT: M 74 ASP cc_start: 0.6385 (t0) cc_final: 0.5689 (p0) REVERT: P 10 THR cc_start: 0.8700 (m) cc_final: 0.8333 (p) REVERT: B 99 TYR cc_start: 0.6844 (OUTLIER) cc_final: 0.6127 (m-10) REVERT: B 100 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: H 57 ARG cc_start: 0.7277 (mtp180) cc_final: 0.7035 (ttt-90) REVERT: K 80 GLU cc_start: 0.6182 (mm-30) cc_final: 0.5806 (tp30) REVERT: E 551 GLN cc_start: 0.7836 (tp40) cc_final: 0.7568 (tp40) REVERT: E 565 THR cc_start: 0.8681 (p) cc_final: 0.8282 (t) REVERT: E 597 TRP cc_start: 0.6356 (m-90) cc_final: 0.5938 (m100) REVERT: N 3 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8338 (mp10) REVERT: N 6 GLU cc_start: 0.8279 (mp0) cc_final: 0.7795 (mp0) REVERT: N 17 THR cc_start: 0.8569 (m) cc_final: 0.8292 (p) REVERT: N 74 ASP cc_start: 0.6543 (t0) cc_final: 0.5857 (p0) REVERT: C 130 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7217 (mtm-85) REVERT: C 261 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: L 91 GLN cc_start: 0.6247 (pp30) cc_final: 0.5776 (pp30) REVERT: F 565 THR cc_start: 0.8653 (p) cc_final: 0.8351 (t) REVERT: F 597 TRP cc_start: 0.6418 (m-90) cc_final: 0.6028 (m100) REVERT: O 6 GLU cc_start: 0.8477 (mp0) cc_final: 0.8099 (mp0) REVERT: O 74 ASP cc_start: 0.6508 (t0) cc_final: 0.5812 (p0) REVERT: O 75 THR cc_start: 0.7920 (p) cc_final: 0.7698 (t) REVERT: O 100 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7607 (mm-30) REVERT: R 98 TYR cc_start: 0.8489 (m-80) cc_final: 0.8170 (m-80) outliers start: 71 outliers final: 43 residues processed: 420 average time/residue: 0.1635 time to fit residues: 102.1830 Evaluate side-chains 408 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 514 ASN Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 126 optimal weight: 0.5980 chunk 176 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 ASN M 79 HIS P 79 GLN N 79 HIS Q 32 ASN Q 79 GLN L 43 GLN O 79 HIS R 37 GLN R 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097699 restraints weight = 31363.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097160 restraints weight = 73979.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098053 restraints weight = 65201.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098192 restraints weight = 41228.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098840 restraints weight = 34872.693| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19257 Z= 0.171 Angle : 0.685 10.452 26256 Z= 0.336 Chirality : 0.045 0.239 2982 Planarity : 0.005 0.061 3282 Dihedral : 5.142 23.856 2577 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.30 % Favored : 96.52 % Rotamer: Outliers : 3.51 % Allowed : 13.38 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: -0.26 (0.18), residues: 2301 helix: 1.56 (0.39), residues: 174 sheet: -0.29 (0.16), residues: 1050 loop : -0.17 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 587 TYR 0.037 0.002 TYR I 85 PHE 0.018 0.001 PHE K 72 TRP 0.038 0.002 TRP K 36 HIS 0.008 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (19194) covalent geometry : angle 0.65935 / 0.33 (26088) SS BOND : bond 0.00353 / 0.21 ( 21) SS BOND : angle 1.15630 / 0.71 ( 42) hydrogen bonds : bond 0.03834 / 2.61 ( 684) hydrogen bonds : angle 5.45864 / 3.73 ( 1719) link_ALPHA1-3 : bond 0.01025 / 0.60 ( 6) link_ALPHA1-3 : angle 1.79841 / 1.05 ( 18) link_ALPHA1-6 : bond 0.00497 / 0.29 ( 6) link_ALPHA1-6 : angle 1.53553 / 0.89 ( 18) link_BETA1-4 : bond 0.01467 / 1.21 ( 15) link_BETA1-4 : angle 3.17638 / 2.00 ( 45) link_NAG-ASN : bond 0.00576 / 0.31 ( 15) link_NAG-ASN : angle 2.85079 / 2.07 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 370 time to evaluate : 0.811 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: A 99 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6023 (m-10) REVERT: A 100 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6794 (mp0) REVERT: A 184 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8939 (pp) REVERT: A 261 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: J 32 LYS cc_start: 0.8486 (pttp) cc_final: 0.8033 (mmtt) REVERT: D 565 THR cc_start: 0.8813 (p) cc_final: 0.8354 (t) REVERT: D 578 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7398 (tt0) REVERT: D 597 TRP cc_start: 0.6350 (m-90) cc_final: 0.5916 (m100) REVERT: M 6 GLU cc_start: 0.8463 (mp0) cc_final: 0.8070 (mp0) REVERT: M 17 THR cc_start: 0.8476 (m) cc_final: 0.7974 (p) REVERT: M 74 ASP cc_start: 0.6456 (t0) cc_final: 0.5813 (p0) REVERT: P 10 THR cc_start: 0.8476 (m) cc_final: 0.8117 (p) REVERT: B 99 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6144 (m-10) REVERT: B 231 GLU cc_start: 0.7047 (mp0) cc_final: 0.6806 (mp0) REVERT: H 57 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6914 (ttt-90) REVERT: E 565 THR cc_start: 0.8699 (p) cc_final: 0.8258 (t) REVERT: E 597 TRP cc_start: 0.6447 (m-90) cc_final: 0.6038 (m100) REVERT: N 3 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8362 (mp10) REVERT: N 6 GLU cc_start: 0.8299 (mp0) cc_final: 0.7766 (mp0) REVERT: N 17 THR cc_start: 0.8724 (m) cc_final: 0.8426 (p) REVERT: Q 70 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7527 (mm-30) REVERT: Q 103 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7756 (ttp80) REVERT: C 130 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7139 (mtm-85) REVERT: C 261 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: L 32 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7996 (mmtt) REVERT: L 91 GLN cc_start: 0.6132 (pp30) cc_final: 0.5788 (pp30) REVERT: L 92 TYR cc_start: 0.5591 (OUTLIER) cc_final: 0.4760 (m-80) REVERT: F 547 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7749 (mp) REVERT: F 565 THR cc_start: 0.8686 (p) cc_final: 0.8365 (t) REVERT: F 597 TRP cc_start: 0.6431 (m-90) cc_final: 0.6024 (m100) REVERT: O 6 GLU cc_start: 0.8466 (mp0) cc_final: 0.8123 (mp0) REVERT: O 74 ASP cc_start: 0.6470 (t0) cc_final: 0.5832 (p0) REVERT: O 100 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7559 (mm-30) REVERT: R 37 GLN cc_start: 0.7996 (tt0) cc_final: 0.7729 (tt0) REVERT: R 98 TYR cc_start: 0.8473 (m-80) cc_final: 0.8164 (m-80) outliers start: 69 outliers final: 51 residues processed: 407 average time/residue: 0.1618 time to fit residues: 97.6841 Evaluate side-chains 418 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 358 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 78 ASN Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 211 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 162 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN M 78 ASN M 79 HIS P 79 GLN K 43 GLN E 551 GLN N 79 HIS Q 79 GLN L 43 GLN F 516 HIS O 79 HIS R 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096379 restraints weight = 31167.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095066 restraints weight = 63810.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096573 restraints weight = 59813.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096827 restraints weight = 36134.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098171 restraints weight = 30583.236| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19257 Z= 0.133 Angle : 0.659 11.242 26256 Z= 0.323 Chirality : 0.044 0.217 2982 Planarity : 0.005 0.064 3282 Dihedral : 4.973 22.868 2577 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.17 % Favored : 96.61 % Rotamer: Outliers : 3.46 % Allowed : 13.84 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: -0.26 (0.18), residues: 2301 helix: 1.78 (0.39), residues: 174 sheet: -0.32 (0.16), residues: 1065 loop : -0.17 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 587 TYR 0.019 0.001 TYR G 100 PHE 0.021 0.001 PHE F 592 TRP 0.049 0.002 TRP J 36 HIS 0.012 0.002 HIS M 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (19194) covalent geometry : angle 0.63590 / 0.32 (26088) SS BOND : bond 0.00275 / 0.15 ( 21) SS BOND : angle 1.11617 / 0.67 ( 42) hydrogen bonds : bond 0.03471 / 2.35 ( 684) hydrogen bonds : angle 5.32017 / 3.64 ( 1719) link_ALPHA1-3 : bond 0.01011 / 0.60 ( 6) link_ALPHA1-3 : angle 1.80317 / 1.05 ( 18) link_ALPHA1-6 : bond 0.00572 / 0.33 ( 6) link_ALPHA1-6 : angle 1.52873 / 0.89 ( 18) link_BETA1-4 : bond 0.01458 / 1.19 ( 15) link_BETA1-4 : angle 2.99465 / 1.89 ( 45) link_NAG-ASN : bond 0.00532 / 0.30 ( 15) link_NAG-ASN : angle 2.53709 / 1.86 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 382 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.6020 (m-10) REVERT: A 100 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6693 (mp0) REVERT: A 184 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8865 (pp) REVERT: A 261 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: J 32 LYS cc_start: 0.8535 (pttp) cc_final: 0.8032 (mmtt) REVERT: D 565 THR cc_start: 0.8768 (p) cc_final: 0.8279 (t) REVERT: D 578 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7402 (tt0) REVERT: D 597 TRP cc_start: 0.6426 (m-90) cc_final: 0.5937 (m100) REVERT: M 6 GLU cc_start: 0.8476 (mp0) cc_final: 0.8119 (mp0) REVERT: M 78 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7494 (m-40) REVERT: P 10 THR cc_start: 0.8492 (m) cc_final: 0.8207 (p) REVERT: B 99 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.6032 (m-10) REVERT: B 231 GLU cc_start: 0.7000 (mp0) cc_final: 0.6700 (mp0) REVERT: H 57 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6955 (ttt180) REVERT: K 32 LYS cc_start: 0.8611 (ptmm) cc_final: 0.8254 (mmtt) REVERT: E 565 THR cc_start: 0.8645 (p) cc_final: 0.8245 (t) REVERT: E 597 TRP cc_start: 0.6420 (m-90) cc_final: 0.6018 (m100) REVERT: N 6 GLU cc_start: 0.8340 (mp0) cc_final: 0.7863 (mp0) REVERT: N 47 LEU cc_start: 0.8924 (mt) cc_final: 0.8719 (mp) REVERT: N 74 ASP cc_start: 0.6891 (t0) cc_final: 0.5732 (p0) REVERT: N 79 HIS cc_start: 0.6413 (m-70) cc_final: 0.6093 (m170) REVERT: N 106 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: C 130 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7098 (mtm-85) REVERT: C 261 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: L 32 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8035 (mmtt) REVERT: L 91 GLN cc_start: 0.6180 (pp30) cc_final: 0.5874 (pp30) REVERT: L 92 TYR cc_start: 0.5530 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: F 547 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7560 (mp) REVERT: F 565 THR cc_start: 0.8720 (p) cc_final: 0.8425 (t) REVERT: F 597 TRP cc_start: 0.6384 (m-90) cc_final: 0.5964 (m100) REVERT: O 74 ASP cc_start: 0.6513 (t0) cc_final: 0.5873 (p0) REVERT: O 100 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7556 (mm-30) REVERT: R 37 GLN cc_start: 0.7993 (tt0) cc_final: 0.7785 (tt0) REVERT: R 42 GLN cc_start: 0.8503 (pm20) cc_final: 0.8189 (pm20) REVERT: R 98 TYR cc_start: 0.8433 (m-80) cc_final: 0.8142 (m-80) outliers start: 68 outliers final: 46 residues processed: 418 average time/residue: 0.1655 time to fit residues: 101.8848 Evaluate side-chains 414 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 78 ASN Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 106 GLU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 188 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN M 78 ASN M 79 HIS Q 79 GLN O 79 HIS R 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099294 restraints weight = 31540.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099531 restraints weight = 79105.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100241 restraints weight = 56695.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099865 restraints weight = 40905.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101061 restraints weight = 32105.146| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19257 Z= 0.152 Angle : 0.668 11.763 26256 Z= 0.328 Chirality : 0.045 0.213 2982 Planarity : 0.005 0.070 3282 Dihedral : 4.940 22.813 2577 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.35 % Favored : 96.39 % Rotamer: Outliers : 3.87 % Allowed : 14.05 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: -0.28 (0.18), residues: 2301 helix: 1.55 (0.39), residues: 180 sheet: -0.17 (0.16), residues: 1032 loop : -0.36 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 587 TYR 0.019 0.002 TYR K 50 PHE 0.016 0.001 PHE M 80 TRP 0.038 0.002 TRP L 36 HIS 0.008 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (19194) covalent geometry : angle 0.64677 / 0.32 (26088) SS BOND : bond 0.00325 / 0.20 ( 21) SS BOND : angle 1.16297 / 0.73 ( 42) hydrogen bonds : bond 0.03545 / 2.40 ( 684) hydrogen bonds : angle 5.23004 / 3.58 ( 1719) link_ALPHA1-3 : bond 0.00981 / 0.58 ( 6) link_ALPHA1-3 : angle 1.82163 / 1.06 ( 18) link_ALPHA1-6 : bond 0.00551 / 0.31 ( 6) link_ALPHA1-6 : angle 1.51909 / 0.88 ( 18) link_BETA1-4 : bond 0.01384 / 1.14 ( 15) link_BETA1-4 : angle 2.95126 / 1.87 ( 45) link_NAG-ASN : bond 0.00477 / 0.25 ( 15) link_NAG-ASN : angle 2.29873 / 1.73 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 371 time to evaluate : 0.732 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 99 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6084 (m-10) REVERT: A 100 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6740 (mp0) REVERT: A 261 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: J 32 LYS cc_start: 0.8465 (pttp) cc_final: 0.8025 (mmtt) REVERT: D 565 THR cc_start: 0.8765 (p) cc_final: 0.8306 (t) REVERT: D 578 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7344 (tt0) REVERT: D 597 TRP cc_start: 0.6417 (m-90) cc_final: 0.5934 (m100) REVERT: M 6 GLU cc_start: 0.8460 (mp0) cc_final: 0.8123 (mp0) REVERT: M 74 ASP cc_start: 0.6737 (t0) cc_final: 0.5399 (p0) REVERT: M 79 HIS cc_start: 0.6749 (OUTLIER) cc_final: 0.6493 (m170) REVERT: P 10 THR cc_start: 0.8540 (m) cc_final: 0.8201 (p) REVERT: B 99 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6015 (m-10) REVERT: B 231 GLU cc_start: 0.7048 (mp0) cc_final: 0.6721 (mp0) REVERT: H 33 LYS cc_start: 0.5799 (OUTLIER) cc_final: 0.4831 (mmtp) REVERT: H 54 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6633 (tt) REVERT: H 57 ARG cc_start: 0.7081 (mtp180) cc_final: 0.6829 (ttt180) REVERT: K 32 LYS cc_start: 0.8452 (ptmm) cc_final: 0.8223 (mmtt) REVERT: E 565 THR cc_start: 0.8692 (p) cc_final: 0.8292 (t) REVERT: E 597 TRP cc_start: 0.6476 (m-90) cc_final: 0.6047 (m100) REVERT: N 6 GLU cc_start: 0.8353 (mp0) cc_final: 0.7935 (mp0) REVERT: N 74 ASP cc_start: 0.6741 (t0) cc_final: 0.5700 (p0) REVERT: N 79 HIS cc_start: 0.6689 (m-70) cc_final: 0.6150 (m170) REVERT: C 130 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7151 (mtm-85) REVERT: C 231 GLU cc_start: 0.7093 (mp0) cc_final: 0.6793 (mp0) REVERT: C 261 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: L 32 LYS cc_start: 0.8388 (ptmm) cc_final: 0.7959 (mmtt) REVERT: L 91 GLN cc_start: 0.6125 (pp30) cc_final: 0.5923 (pp30) REVERT: L 92 TYR cc_start: 0.5599 (OUTLIER) cc_final: 0.4874 (m-80) REVERT: F 547 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7443 (mp) REVERT: F 565 THR cc_start: 0.8691 (p) cc_final: 0.8380 (t) REVERT: F 597 TRP cc_start: 0.6383 (m-90) cc_final: 0.5985 (m100) REVERT: O 74 ASP cc_start: 0.6570 (t0) cc_final: 0.5921 (p0) REVERT: O 100 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7576 (mm-30) REVERT: R 37 GLN cc_start: 0.7979 (tt0) cc_final: 0.7778 (tt0) REVERT: R 61 ARG cc_start: 0.8334 (mtm110) cc_final: 0.8025 (mtm110) REVERT: R 98 TYR cc_start: 0.8421 (m-80) cc_final: 0.8111 (m-80) outliers start: 76 outliers final: 57 residues processed: 419 average time/residue: 0.1612 time to fit residues: 100.9849 Evaluate side-chains 424 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 357 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 78 ASN Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 30 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN P 79 GLN N 114 GLN Q 79 GLN O 78 ASN O 79 HIS R 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.093946 restraints weight = 31918.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095416 restraints weight = 78514.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094862 restraints weight = 42210.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094830 restraints weight = 31530.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095162 restraints weight = 27591.071| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 19257 Z= 0.410 Angle : 0.876 11.751 26256 Z= 0.435 Chirality : 0.052 0.341 2982 Planarity : 0.007 0.066 3282 Dihedral : 5.808 29.562 2577 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.30 % Favored : 95.44 % Rotamer: Outliers : 4.12 % Allowed : 14.20 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: -0.83 (0.18), residues: 2301 helix: 1.84 (0.40), residues: 156 sheet: -0.67 (0.16), residues: 1044 loop : -0.65 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 587 TYR 0.029 0.003 TYR M 35 PHE 0.029 0.003 PHE M 80 TRP 0.058 0.003 TRP L 36 HIS 0.040 0.003 HIS M 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00984 / 0.41 (19194) covalent geometry : angle 0.85408 / 0.43 (26088) SS BOND : bond 0.00691 / 0.47 ( 21) SS BOND : angle 1.95175 / 1.17 ( 42) hydrogen bonds : bond 0.05426 / 3.65 ( 684) hydrogen bonds : angle 5.69189 / 3.91 ( 1719) link_ALPHA1-3 : bond 0.00902 / 0.52 ( 6) link_ALPHA1-3 : angle 1.95883 / 1.15 ( 18) link_ALPHA1-6 : bond 0.00231 / 0.14 ( 6) link_ALPHA1-6 : angle 1.57211 / 0.91 ( 18) link_BETA1-4 : bond 0.01346 / 1.13 ( 15) link_BETA1-4 : angle 3.55932 / 2.23 ( 45) link_NAG-ASN : bond 0.00636 / 0.41 ( 15) link_NAG-ASN : angle 2.37874 / 1.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 359 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6405 (m-80) REVERT: A 100 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7223 (mp0) REVERT: A 184 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9068 (pp) REVERT: A 231 GLU cc_start: 0.7039 (mp0) cc_final: 0.6809 (mp0) REVERT: J 32 LYS cc_start: 0.8464 (pttp) cc_final: 0.8117 (mmtt) REVERT: D 597 TRP cc_start: 0.6426 (m-90) cc_final: 0.6056 (m100) REVERT: M 6 GLU cc_start: 0.8491 (mp0) cc_final: 0.8022 (mp0) REVERT: M 83 ARG cc_start: 0.7097 (ttm-80) cc_final: 0.6819 (ttm-80) REVERT: B 99 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: B 184 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9053 (pt) REVERT: B 231 GLU cc_start: 0.7197 (mp0) cc_final: 0.6952 (mp0) REVERT: H 30 PHE cc_start: 0.4888 (m-10) cc_final: 0.4657 (m-10) REVERT: H 33 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.4851 (mmtp) REVERT: H 54 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6676 (tt) REVERT: H 57 ARG cc_start: 0.7337 (mtp180) cc_final: 0.7003 (ttt180) REVERT: K 32 LYS cc_start: 0.8501 (ptmm) cc_final: 0.8289 (mmtt) REVERT: E 565 THR cc_start: 0.8562 (p) cc_final: 0.8074 (t) REVERT: E 597 TRP cc_start: 0.6553 (m-90) cc_final: 0.6301 (m100) REVERT: N 6 GLU cc_start: 0.8352 (mp0) cc_final: 0.7670 (mp0) REVERT: N 74 ASP cc_start: 0.6800 (t0) cc_final: 0.5973 (p0) REVERT: N 79 HIS cc_start: 0.7101 (m-70) cc_final: 0.6855 (m170) REVERT: C 231 GLU cc_start: 0.7248 (mp0) cc_final: 0.6733 (mp0) REVERT: C 261 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: L 92 TYR cc_start: 0.5582 (OUTLIER) cc_final: 0.5054 (m-80) REVERT: F 547 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7775 (mp) REVERT: F 565 THR cc_start: 0.8574 (p) cc_final: 0.8190 (t) REVERT: F 597 TRP cc_start: 0.6527 (m-90) cc_final: 0.6193 (m100) REVERT: R 70 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7337 (mm-30) REVERT: R 98 TYR cc_start: 0.8534 (m-80) cc_final: 0.8258 (m-80) outliers start: 81 outliers final: 63 residues processed: 407 average time/residue: 0.1601 time to fit residues: 96.8401 Evaluate side-chains 413 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 341 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 113 PHE Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 87 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 180 optimal weight: 0.8980 chunk 159 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN Q 79 GLN O 79 HIS R 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097880 restraints weight = 31340.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097574 restraints weight = 76087.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098339 restraints weight = 63933.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098254 restraints weight = 41797.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098847 restraints weight = 35271.352| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19257 Z= 0.156 Angle : 0.723 12.934 26256 Z= 0.357 Chirality : 0.046 0.268 2982 Planarity : 0.005 0.068 3282 Dihedral : 5.363 27.920 2577 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.22 % Favored : 96.52 % Rotamer: Outliers : 3.51 % Allowed : 15.78 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: -0.68 (0.18), residues: 2301 helix: 1.37 (0.40), residues: 180 sheet: -0.50 (0.16), residues: 1008 loop : -0.59 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 587 TYR 0.022 0.002 TYR K 50 PHE 0.022 0.001 PHE K 72 TRP 0.073 0.002 TRP J 36 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (19194) covalent geometry : angle 0.69508 / 0.35 (26088) SS BOND : bond 0.00360 / 0.19 ( 21) SS BOND : angle 1.90914 / 1.12 ( 42) hydrogen bonds : bond 0.03761 / 2.53 ( 684) hydrogen bonds : angle 5.44873 / 3.76 ( 1719) link_ALPHA1-3 : bond 0.01014 / 0.60 ( 6) link_ALPHA1-3 : angle 1.78822 / 1.05 ( 18) link_ALPHA1-6 : bond 0.00476 / 0.27 ( 6) link_ALPHA1-6 : angle 1.50237 / 0.89 ( 18) link_BETA1-4 : bond 0.01501 / 1.23 ( 15) link_BETA1-4 : angle 3.06893 / 1.94 ( 45) link_NAG-ASN : bond 0.00417 / 0.23 ( 15) link_NAG-ASN : angle 3.21240 / 2.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 364 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: A 100 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6748 (mp0) REVERT: A 184 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8951 (pp) REVERT: A 231 GLU cc_start: 0.6960 (mp0) cc_final: 0.6665 (mp0) REVERT: A 261 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: J 32 LYS cc_start: 0.8427 (pttp) cc_final: 0.8103 (mmtt) REVERT: D 565 THR cc_start: 0.8799 (p) cc_final: 0.8298 (t) REVERT: D 597 TRP cc_start: 0.6358 (m-90) cc_final: 0.5903 (m100) REVERT: M 6 GLU cc_start: 0.8470 (mp0) cc_final: 0.8115 (mp0) REVERT: B 99 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6101 (m-10) REVERT: B 231 GLU cc_start: 0.7161 (mp0) cc_final: 0.6880 (mp0) REVERT: H 33 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.4892 (mmtp) REVERT: H 54 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6726 (tt) REVERT: H 57 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6961 (ttt180) REVERT: K 32 LYS cc_start: 0.8445 (ptmm) cc_final: 0.8230 (mmtt) REVERT: E 565 THR cc_start: 0.8580 (p) cc_final: 0.8186 (t) REVERT: E 597 TRP cc_start: 0.6542 (m-90) cc_final: 0.6182 (m100) REVERT: N 6 GLU cc_start: 0.8268 (mp0) cc_final: 0.7929 (mp0) REVERT: N 74 ASP cc_start: 0.6571 (t0) cc_final: 0.5836 (p0) REVERT: N 79 HIS cc_start: 0.6918 (m-70) cc_final: 0.6629 (m-70) REVERT: C 99 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6570 (m-80) REVERT: C 130 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7290 (mtm-85) REVERT: C 231 GLU cc_start: 0.7238 (mp0) cc_final: 0.6728 (mp0) REVERT: C 261 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: L 92 TYR cc_start: 0.5698 (OUTLIER) cc_final: 0.5203 (m-80) REVERT: F 547 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7680 (mp) REVERT: F 565 THR cc_start: 0.8487 (p) cc_final: 0.8192 (t) REVERT: F 587 ARG cc_start: 0.7718 (ttm110) cc_final: 0.7506 (mtp-110) REVERT: F 597 TRP cc_start: 0.6397 (m-90) cc_final: 0.6071 (m100) REVERT: O 74 ASP cc_start: 0.7027 (t0) cc_final: 0.6351 (t0) REVERT: O 100 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7701 (mm-30) REVERT: R 70 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7152 (mm-30) REVERT: R 98 TYR cc_start: 0.8375 (m-80) cc_final: 0.8099 (m-80) outliers start: 69 outliers final: 49 residues processed: 413 average time/residue: 0.1577 time to fit residues: 97.2458 Evaluate side-chains 409 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 349 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 162 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 158 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 79 HIS H 3 GLN Q 27 GLN Q 79 GLN R 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096308 restraints weight = 31368.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095585 restraints weight = 74680.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096597 restraints weight = 65886.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096716 restraints weight = 42062.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097712 restraints weight = 34407.772| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19257 Z= 0.185 Angle : 0.745 16.605 26256 Z= 0.363 Chirality : 0.047 0.504 2982 Planarity : 0.005 0.068 3282 Dihedral : 5.255 25.867 2577 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.69 % Favored : 96.09 % Rotamer: Outliers : 3.05 % Allowed : 15.93 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: -0.61 (0.18), residues: 2301 helix: 1.40 (0.39), residues: 180 sheet: -0.43 (0.17), residues: 960 loop : -0.57 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 78 TYR 0.021 0.002 TYR J 50 PHE 0.021 0.001 PHE K 72 TRP 0.059 0.002 TRP J 36 HIS 0.004 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (19194) covalent geometry : angle 0.71422 / 0.36 (26088) SS BOND : bond 0.00391 / 0.23 ( 21) SS BOND : angle 1.69474 / 1.00 ( 42) hydrogen bonds : bond 0.03848 / 2.57 ( 684) hydrogen bonds : angle 5.35505 / 3.71 ( 1719) link_ALPHA1-3 : bond 0.00956 / 0.56 ( 6) link_ALPHA1-3 : angle 1.90758 / 1.11 ( 18) link_ALPHA1-6 : bond 0.00435 / 0.25 ( 6) link_ALPHA1-6 : angle 1.46878 / 0.86 ( 18) link_BETA1-4 : bond 0.01409 / 1.17 ( 15) link_BETA1-4 : angle 3.02977 / 1.93 ( 45) link_NAG-ASN : bond 0.00436 / 0.24 ( 15) link_NAG-ASN : angle 3.70807 / 3.09 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 351 time to evaluate : 0.791 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 99 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6080 (m-10) REVERT: A 100 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6885 (mp0) REVERT: A 231 GLU cc_start: 0.7030 (mp0) cc_final: 0.6696 (mp0) REVERT: A 261 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: J 32 LYS cc_start: 0.8491 (pttp) cc_final: 0.8151 (mmtt) REVERT: D 565 THR cc_start: 0.8803 (p) cc_final: 0.8322 (t) REVERT: D 597 TRP cc_start: 0.6310 (m-90) cc_final: 0.5894 (m100) REVERT: M 6 GLU cc_start: 0.8367 (mp0) cc_final: 0.8137 (mp0) REVERT: M 74 ASP cc_start: 0.6643 (t0) cc_final: 0.5372 (p0) REVERT: M 79 HIS cc_start: 0.6606 (m-70) cc_final: 0.6267 (m170) REVERT: B 99 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6236 (m-10) REVERT: B 231 GLU cc_start: 0.7094 (mp0) cc_final: 0.6796 (mp0) REVERT: H 33 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.4792 (mmtp) REVERT: H 54 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6620 (tt) REVERT: H 57 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6906 (ttt180) REVERT: E 565 THR cc_start: 0.8636 (p) cc_final: 0.8228 (t) REVERT: E 597 TRP cc_start: 0.6551 (m-90) cc_final: 0.6194 (m100) REVERT: N 6 GLU cc_start: 0.8388 (mp0) cc_final: 0.7942 (mp0) REVERT: N 74 ASP cc_start: 0.6425 (t0) cc_final: 0.5718 (p0) REVERT: N 79 HIS cc_start: 0.6905 (m-70) cc_final: 0.6517 (m170) REVERT: C 99 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: C 130 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7130 (mtm-85) REVERT: C 231 GLU cc_start: 0.7153 (mp0) cc_final: 0.6640 (mp0) REVERT: C 261 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: L 92 TYR cc_start: 0.5802 (OUTLIER) cc_final: 0.5302 (m-80) REVERT: F 547 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7575 (mp) REVERT: F 565 THR cc_start: 0.8594 (p) cc_final: 0.8238 (t) REVERT: F 587 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7508 (mtp-110) REVERT: F 597 TRP cc_start: 0.6368 (m-90) cc_final: 0.6069 (m100) REVERT: O 79 HIS cc_start: 0.7183 (p90) cc_final: 0.6957 (p-80) REVERT: R 70 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7192 (mm-30) outliers start: 60 outliers final: 47 residues processed: 393 average time/residue: 0.1598 time to fit residues: 93.6933 Evaluate side-chains 400 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 343 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 97 TRP Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 107 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 158 optimal weight: 0.1980 chunk 159 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN D 516 HIS Q 79 GLN R 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098273 restraints weight = 31599.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099160 restraints weight = 76068.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099093 restraints weight = 51783.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098518 restraints weight = 43588.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099152 restraints weight = 32814.850| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19257 Z= 0.179 Angle : 0.746 17.984 26256 Z= 0.363 Chirality : 0.047 0.338 2982 Planarity : 0.005 0.064 3282 Dihedral : 5.242 25.948 2577 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.61 % Favored : 96.18 % Rotamer: Outliers : 3.26 % Allowed : 16.08 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 are not related in a simple way. whole: -0.63 (0.18), residues: 2301 helix: 1.47 (0.39), residues: 180 sheet: -0.46 (0.17), residues: 957 loop : -0.57 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 587 TYR 0.023 0.002 TYR K 50 PHE 0.026 0.002 PHE G 30 TRP 0.069 0.002 TRP J 36 HIS 0.007 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (19194) covalent geometry : angle 0.71104 / 0.36 (26088) SS BOND : bond 0.00381 / 0.23 ( 21) SS BOND : angle 1.76636 / 1.03 ( 42) hydrogen bonds : bond 0.03698 / 2.47 ( 684) hydrogen bonds : angle 5.31049 / 3.68 ( 1719) link_ALPHA1-3 : bond 0.00969 / 0.58 ( 6) link_ALPHA1-3 : angle 1.86184 / 1.09 ( 18) link_ALPHA1-6 : bond 0.00415 / 0.25 ( 6) link_ALPHA1-6 : angle 1.47004 / 0.86 ( 18) link_BETA1-4 : bond 0.01362 / 1.13 ( 15) link_BETA1-4 : angle 2.97082 / 1.89 ( 45) link_NAG-ASN : bond 0.00455 / 0.28 ( 15) link_NAG-ASN : angle 4.16861 / 3.27 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.46 seconds wall clock time: 57 minutes 19.02 seconds (3439.02 seconds total)