Starting phenix.real_space_refine on Thu Mar 5 03:21:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m8l_23719/03_2026/7m8l_23719.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m8l_23719/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m8l_23719/03_2026/7m8l_23719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m8l_23719/03_2026/7m8l_23719.map" model { file = "/net/cci-nas-00/data/ceres_data/7m8l_23719/03_2026/7m8l_23719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m8l_23719/03_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-5986/lib/python3.9/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 dihedrals: 15 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.53, per 1000 atoms: 0.24 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: 1.85 Conformation dependent library (CDL) restraints added in 812.5 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: 0.93 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: 3.81 Time building geometry restraints manager: 2.31 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 - 21.39: 11396 21.39 - 42.77: 238 42.77 - 64.16: 84 64.16 - 85.55: 48 85.55 - 106.93: 27 Dihedral angle restraints: 11793 sinusoidal: 5121 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 11790 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: 0.04 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: 2.060 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.110 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 12.535 106.932 7506 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 covalent geometry : bond 0.02136 (19194) covalent geometry : angle 1.84380 (26088) SS BOND : bond 0.01108 ( 21) SS BOND : angle 3.01019 ( 42) hydrogen bonds : bond 0.15724 ( 684) hydrogen bonds : angle 8.18736 ( 1719) link_ALPHA1-3 : bond 0.08211 ( 6) link_ALPHA1-3 : angle 4.44048 ( 18) link_ALPHA1-6 : bond 0.06486 ( 6) link_ALPHA1-6 : angle 3.69320 ( 18) link_BETA1-4 : bond 0.07454 ( 15) link_BETA1-4 : angle 5.47145 ( 45) link_NAG-ASN : bond 0.07779 ( 15) link_NAG-ASN : angle 2.16940 ( 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 : 0.862 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: 0.1725 time to fit residues: 152.6710 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 : 0.912 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 R 79 GLN R 92 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105834 restraints weight = 31000.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104807 restraints weight = 59501.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105342 restraints weight = 59545.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105281 restraints weight = 38105.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105795 restraints weight = 33130.824| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19257 Z= 0.180 Angle : 0.804 17.877 26256 Z= 0.398 Chirality : 0.050 0.282 2982 Planarity : 0.005 0.045 3282 Dihedral : 11.313 88.979 3423 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.52 % Favored : 97.35 % Rotamer: Outliers : 1.88 % Allowed : 10.53 % Favored : 87.58 % 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: 0.39 (0.17), residues: 2301 helix: 2.16 (0.37), residues: 156 sheet: 0.20 (0.17), residues: 957 loop : 0.19 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 587 TYR 0.021 0.002 TYR G 100 PHE 0.036 0.002 PHE K 72 TRP 0.038 0.002 TRP R 94 HIS 0.008 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00385 (19194) covalent geometry : angle 0.74698 (26088) SS BOND : bond 0.00399 ( 21) SS BOND : angle 1.27974 ( 42) hydrogen bonds : bond 0.04665 ( 684) hydrogen bonds : angle 6.40108 ( 1719) link_ALPHA1-3 : bond 0.01769 ( 6) link_ALPHA1-3 : angle 0.99709 ( 18) link_ALPHA1-6 : bond 0.01111 ( 6) link_ALPHA1-6 : angle 1.79830 ( 18) link_BETA1-4 : bond 0.02065 ( 15) link_BETA1-4 : angle 4.27240 ( 45) link_NAG-ASN : bond 0.01082 ( 15) link_NAG-ASN : angle 5.70403 ( 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: 37 poor density : 429 time to evaluate : 0.708 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: 0.7002 (mt-10) cc_final: 0.6734 (mp0) REVERT: G 53 ARG cc_start: 0.5735 (ttp-170) cc_final: 0.5492 (ptm-80) REVERT: J 60 PRO cc_start: 0.5519 (Cg_exo) cc_final: 0.5308 (Cg_endo) REVERT: D 565 THR cc_start: 0.8716 (p) cc_final: 0.8308 (t) REVERT: D 597 TRP cc_start: 0.6249 (m-90) cc_final: 0.5832 (m100) REVERT: M 3 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8209 (mp10) REVERT: M 6 GLU cc_start: 0.8315 (mp0) cc_final: 0.7999 (mp0) REVERT: M 17 THR cc_start: 0.8543 (m) cc_final: 0.8236 (p) REVERT: M 74 ASP cc_start: 0.6414 (t0) cc_final: 0.5462 (p0) REVERT: B 100 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6847 (mp0) REVERT: B 150 ASP cc_start: 0.7579 (m-30) cc_final: 0.7371 (m-30) REVERT: K 80 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5692 (tp30) REVERT: E 565 THR cc_start: 0.8542 (p) cc_final: 0.8122 (t) REVERT: E 597 TRP cc_start: 0.6329 (m-90) cc_final: 0.5853 (m100) REVERT: N 3 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8186 (mp10) REVERT: N 6 GLU cc_start: 0.8189 (mp0) cc_final: 0.7870 (mp0) REVERT: N 17 THR cc_start: 0.8500 (m) cc_final: 0.8214 (p) REVERT: N 74 ASP cc_start: 0.6391 (t0) cc_final: 0.5645 (p0) REVERT: N 83 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6872 (ttm-80) REVERT: Q 39 LYS cc_start: 0.8055 (mttt) cc_final: 0.7800 (mttt) REVERT: C 100 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7145 (mp0) REVERT: I 33 LYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5209 (mptt) REVERT: F 565 THR cc_start: 0.8708 (p) cc_final: 0.8383 (t) REVERT: F 578 GLU cc_start: 0.7557 (tt0) cc_final: 0.7225 (tt0) REVERT: F 597 TRP cc_start: 0.6438 (m-90) cc_final: 0.5915 (m100) REVERT: O 3 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8192 (mp10) REVERT: O 6 GLU cc_start: 0.8432 (mp0) cc_final: 0.8111 (mp0) REVERT: O 74 ASP cc_start: 0.6346 (t0) cc_final: 0.5467 (p0) REVERT: R 98 TYR cc_start: 0.8509 (m-80) cc_final: 0.8255 (m-80) REVERT: R 105 GLU cc_start: 0.5512 (mm-30) cc_final: 0.5022 (mm-30) outliers start: 37 outliers final: 25 residues processed: 447 average time/residue: 0.1744 time to fit residues: 111.8060 Evaluate side-chains 394 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 368 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 32 LYS 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: 5.9990 chunk 17 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 197 optimal weight: 0.0770 chunk 121 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 ASN D 595 GLN M 41 GLN M 79 HIS P 79 GLN ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN H 3 GLN E 514 ASN N 79 HIS Q 79 GLN I 3 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.098450 restraints weight = 31339.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.098719 restraints weight = 70044.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099497 restraints weight = 59170.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099486 restraints weight = 39299.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100068 restraints weight = 33795.940| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19257 Z= 0.234 Angle : 0.780 14.946 26256 Z= 0.385 Chirality : 0.049 0.266 2982 Planarity : 0.005 0.044 3282 Dihedral : 10.398 84.038 3423 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.09 % Rotamer: Outliers : 3.41 % Allowed : 12.77 % Favored : 83.82 % 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: -0.16 (0.17), residues: 2301 helix: 1.38 (0.38), residues: 174 sheet: -0.34 (0.16), residues: 1065 loop : 0.11 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 587 TYR 0.027 0.002 TYR L 92 PHE 0.018 0.002 PHE K 72 TRP 0.029 0.003 TRP K 36 HIS 0.008 0.002 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00546 (19194) covalent geometry : angle 0.74163 (26088) SS BOND : bond 0.00459 ( 21) SS BOND : angle 1.40156 ( 42) hydrogen bonds : bond 0.04570 ( 684) hydrogen bonds : angle 5.90029 ( 1719) link_ALPHA1-3 : bond 0.01706 ( 6) link_ALPHA1-3 : angle 1.13023 ( 18) link_ALPHA1-6 : bond 0.00846 ( 6) link_ALPHA1-6 : angle 1.94748 ( 18) link_BETA1-4 : bond 0.01695 ( 15) link_BETA1-4 : angle 3.85910 ( 45) link_NAG-ASN : bond 0.00809 ( 15) link_NAG-ASN : angle 4.17831 ( 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 456 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 389 time to evaluate : 0.584 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: 0.7154 (mt-10) cc_final: 0.6901 (mp0) REVERT: A 184 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 261 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: J 32 LYS cc_start: 0.8521 (pttp) cc_final: 0.8020 (mmtt) REVERT: D 565 THR cc_start: 0.8826 (p) cc_final: 0.8330 (t) REVERT: D 578 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7440 (tt0) REVERT: D 597 TRP cc_start: 0.6411 (m-90) cc_final: 0.5946 (m100) REVERT: M 3 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8346 (mp10) REVERT: M 6 GLU cc_start: 0.8456 (mp0) cc_final: 0.8085 (mp0) REVERT: M 17 THR cc_start: 0.8551 (m) cc_final: 0.8235 (p) REVERT: M 74 ASP cc_start: 0.6315 (t0) cc_final: 0.5660 (p0) REVERT: B 100 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7063 (mp0) REVERT: K 80 GLU cc_start: 0.6140 (mm-30) cc_final: 0.5813 (tp30) REVERT: E 565 THR cc_start: 0.8711 (p) cc_final: 0.8265 (t) REVERT: E 597 TRP cc_start: 0.6378 (m-90) cc_final: 0.5978 (m100) REVERT: N 3 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8245 (mp10) REVERT: N 6 GLU cc_start: 0.8260 (mp0) cc_final: 0.7776 (mp0) REVERT: N 17 THR cc_start: 0.8614 (m) cc_final: 0.8342 (p) REVERT: N 74 ASP cc_start: 0.6564 (t0) cc_final: 0.5843 (p0) REVERT: C 100 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7365 (mp0) REVERT: C 130 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7283 (mtm-85) REVERT: L 32 LYS cc_start: 0.8407 (ptmm) cc_final: 0.7965 (mmtt) REVERT: L 92 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.4653 (m-80) REVERT: F 565 THR cc_start: 0.8734 (p) cc_final: 0.8365 (t) REVERT: F 578 GLU cc_start: 0.7535 (tt0) cc_final: 0.7320 (tt0) REVERT: F 597 TRP cc_start: 0.6423 (m-90) cc_final: 0.5977 (m100) REVERT: O 3 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8219 (mp10) REVERT: O 6 GLU cc_start: 0.8524 (mp0) cc_final: 0.8207 (mp0) REVERT: O 74 ASP cc_start: 0.6556 (t0) cc_final: 0.5778 (p0) REVERT: R 98 TYR cc_start: 0.8518 (m-80) cc_final: 0.8209 (m-80) outliers start: 67 outliers final: 43 residues processed: 424 average time/residue: 0.1598 time to fit residues: 99.2171 Evaluate side-chains 401 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 354 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 101 SER 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 R residue 21 LEU 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: 0.6980 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 201 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 79 HIS P 79 GLN P 92 ASN N 41 GLN N 78 ASN N 79 HIS Q 37 GLN Q 79 GLN O 79 HIS R 37 GLN R 79 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100991 restraints weight = 31564.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100709 restraints weight = 74995.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101376 restraints weight = 63065.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101357 restraints weight = 41450.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102125 restraints weight = 34801.159| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19257 Z= 0.140 Angle : 0.688 12.345 26256 Z= 0.334 Chirality : 0.046 0.264 2982 Planarity : 0.005 0.056 3282 Dihedral : 9.577 77.446 3423 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.61 % Favored : 97.26 % Rotamer: Outliers : 3.10 % Allowed : 13.59 % Favored : 83.31 % 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 (0.18), residues: 2301 helix: 1.91 (0.38), residues: 168 sheet: -0.13 (0.16), residues: 1035 loop : -0.20 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 596 TYR 0.020 0.002 TYR K 92 PHE 0.014 0.001 PHE K 72 TRP 0.022 0.001 TRP R 94 HIS 0.009 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00306 (19194) covalent geometry : angle 0.65470 (26088) SS BOND : bond 0.00304 ( 21) SS BOND : angle 1.03041 ( 42) hydrogen bonds : bond 0.03626 ( 684) hydrogen bonds : angle 5.56289 ( 1719) link_ALPHA1-3 : bond 0.01603 ( 6) link_ALPHA1-3 : angle 1.05545 ( 18) link_ALPHA1-6 : bond 0.01011 ( 6) link_ALPHA1-6 : angle 1.95335 ( 18) link_BETA1-4 : bond 0.01589 ( 15) link_BETA1-4 : angle 3.41129 ( 45) link_NAG-ASN : bond 0.00692 ( 15) link_NAG-ASN : angle 3.58467 ( 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 457 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 396 time to evaluate : 0.721 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: A 100 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6676 (mp0) REVERT: A 184 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8866 (pp) REVERT: A 231 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: A 261 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: J 32 LYS cc_start: 0.8489 (pttp) cc_final: 0.8013 (mmtt) REVERT: D 565 THR cc_start: 0.8799 (p) cc_final: 0.8331 (t) REVERT: D 597 TRP cc_start: 0.6333 (m-90) cc_final: 0.5854 (m100) REVERT: M 6 GLU cc_start: 0.8392 (mp0) cc_final: 0.8082 (mp0) REVERT: M 17 THR cc_start: 0.8468 (m) cc_final: 0.7982 (p) REVERT: M 74 ASP cc_start: 0.6318 (t0) cc_final: 0.5687 (p0) REVERT: P 10 THR cc_start: 0.8486 (m) cc_final: 0.8059 (p) REVERT: B 100 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: H 57 ARG cc_start: 0.7177 (mtp180) cc_final: 0.6919 (ttt-90) REVERT: E 565 THR cc_start: 0.8678 (p) cc_final: 0.8247 (t) REVERT: E 597 TRP cc_start: 0.6384 (m-90) cc_final: 0.5971 (m100) REVERT: N 3 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8288 (mp10) REVERT: N 6 GLU cc_start: 0.8256 (mp0) cc_final: 0.7800 (mp0) REVERT: N 17 THR cc_start: 0.8695 (m) cc_final: 0.8436 (p) REVERT: N 74 ASP cc_start: 0.6491 (t0) cc_final: 0.5807 (p0) REVERT: C 130 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7175 (mtm-85) REVERT: C 261 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: L 32 LYS cc_start: 0.8388 (ptmm) cc_final: 0.7945 (mmtt) REVERT: F 565 THR cc_start: 0.8637 (p) cc_final: 0.8368 (t) REVERT: F 597 TRP cc_start: 0.6383 (m-90) cc_final: 0.5968 (m100) REVERT: O 6 GLU cc_start: 0.8481 (mp0) cc_final: 0.8184 (mp0) REVERT: O 74 ASP cc_start: 0.6428 (t0) cc_final: 0.5758 (p0) REVERT: O 75 THR cc_start: 0.7926 (p) cc_final: 0.7700 (t) REVERT: O 106 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: R 98 TYR cc_start: 0.8458 (m-80) cc_final: 0.8110 (m-80) outliers start: 61 outliers final: 36 residues processed: 428 average time/residue: 0.1582 time to fit residues: 99.9222 Evaluate side-chains 409 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 366 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 86 VAL 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 M residue 119 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 103 GLU 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 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 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 79 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 106 GLU 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: 3.9990 chunk 176 optimal weight: 9.9990 chunk 203 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 41 GLN M 79 HIS P 79 GLN N 79 HIS Q 32 ASN Q 79 GLN Q 92 ASN L 43 GLN O 79 HIS O 114 GLN R 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094951 restraints weight = 31465.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094332 restraints weight = 69541.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095521 restraints weight = 62389.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095683 restraints weight = 37294.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097584 restraints weight = 31276.409| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19257 Z= 0.255 Angle : 0.766 12.003 26256 Z= 0.374 Chirality : 0.049 0.275 2982 Planarity : 0.006 0.061 3282 Dihedral : 9.497 74.383 3423 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.56 % Favored : 96.26 % Rotamer: Outliers : 4.17 % Allowed : 13.69 % Favored : 82.14 % 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: -0.42 (0.18), residues: 2301 helix: 1.33 (0.38), residues: 174 sheet: -0.35 (0.16), residues: 1062 loop : -0.31 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 596 TYR 0.039 0.002 TYR I 85 PHE 0.015 0.002 PHE H 113 TRP 0.028 0.002 TRP H 39 HIS 0.008 0.002 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00600 (19194) covalent geometry : angle 0.73826 (26088) SS BOND : bond 0.00460 ( 21) SS BOND : angle 1.28518 ( 42) hydrogen bonds : bond 0.04456 ( 684) hydrogen bonds : angle 5.52606 ( 1719) link_ALPHA1-3 : bond 0.01542 ( 6) link_ALPHA1-3 : angle 1.35893 ( 18) link_ALPHA1-6 : bond 0.00863 ( 6) link_ALPHA1-6 : angle 2.05836 ( 18) link_BETA1-4 : bond 0.01511 ( 15) link_BETA1-4 : angle 3.63796 ( 45) link_NAG-ASN : bond 0.00575 ( 15) link_NAG-ASN : angle 2.96793 ( 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 448 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 366 time to evaluate : 0.721 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 99 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.5826 (m-10) REVERT: A 100 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7117 (mp0) REVERT: A 184 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8832 (pp) REVERT: A 261 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: J 32 LYS cc_start: 0.8545 (pttp) cc_final: 0.8090 (mmtt) REVERT: D 565 THR cc_start: 0.8858 (p) cc_final: 0.8358 (t) REVERT: D 578 GLU cc_start: 0.7785 (tt0) cc_final: 0.7556 (tt0) REVERT: D 597 TRP cc_start: 0.6464 (m-90) cc_final: 0.6008 (m100) REVERT: M 6 GLU cc_start: 0.8473 (mp0) cc_final: 0.8099 (mp0) REVERT: M 17 THR cc_start: 0.8548 (m) cc_final: 0.8329 (t) REVERT: M 74 ASP cc_start: 0.6436 (t0) cc_final: 0.5872 (p0) REVERT: P 10 THR cc_start: 0.8591 (m) cc_final: 0.8231 (p) REVERT: B 99 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6241 (m-10) REVERT: B 100 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: B 231 GLU cc_start: 0.7098 (mp0) cc_final: 0.6867 (mp0) REVERT: H 57 ARG cc_start: 0.7332 (mtp180) cc_final: 0.7029 (ttt-90) REVERT: H 84 LEU cc_start: 0.7132 (pp) cc_final: 0.6715 (pp) REVERT: K 32 LYS cc_start: 0.8565 (ptmm) cc_final: 0.8184 (mmtt) REVERT: E 565 THR cc_start: 0.8559 (p) cc_final: 0.8134 (t) REVERT: E 597 TRP cc_start: 0.6468 (m-90) cc_final: 0.6062 (m100) REVERT: N 6 GLU cc_start: 0.8382 (mp0) cc_final: 0.7800 (mp0) REVERT: N 17 THR cc_start: 0.8717 (m) cc_final: 0.8388 (p) REVERT: N 74 ASP cc_start: 0.6300 (t0) cc_final: 0.6009 (p0) REVERT: N 75 THR cc_start: 0.8221 (p) cc_final: 0.8007 (t) REVERT: Q 103 ARG cc_start: 0.8237 (mmm-85) cc_final: 0.7817 (ttp80) REVERT: C 261 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: L 32 LYS cc_start: 0.8545 (ptmm) cc_final: 0.8030 (mmtt) REVERT: L 91 GLN cc_start: 0.6110 (pp30) cc_final: 0.5640 (pp30) REVERT: L 92 TYR cc_start: 0.5664 (OUTLIER) cc_final: 0.4924 (m-80) REVERT: F 547 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7798 (mp) REVERT: F 565 THR cc_start: 0.8611 (p) cc_final: 0.8298 (t) REVERT: F 597 TRP cc_start: 0.6368 (m-90) cc_final: 0.6004 (m100) REVERT: O 6 GLU cc_start: 0.8521 (mp0) cc_final: 0.8179 (mp0) REVERT: O 74 ASP cc_start: 0.6520 (t0) cc_final: 0.5902 (p0) REVERT: O 100 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7742 (mm-30) REVERT: R 61 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8113 (mtm110) REVERT: R 98 TYR cc_start: 0.8502 (m-80) cc_final: 0.8229 (m-80) outliers start: 82 outliers final: 57 residues processed: 411 average time/residue: 0.1558 time to fit residues: 94.7630 Evaluate side-chains 414 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 349 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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 93 THR 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 J residue 86 VAL 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 564 GLU 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 46 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain B residue 96 VAL 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 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 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 558 LEU 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 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 96 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 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 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: 1.9990 chunk 98 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 ASN M 79 HIS P 79 GLN N 79 HIS Q 27 GLN Q 79 GLN L 43 GLN F 516 HIS F 551 GLN O 79 HIS O 114 GLN R 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100653 restraints weight = 31261.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101383 restraints weight = 73958.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100697 restraints weight = 48006.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100471 restraints weight = 38676.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101140 restraints weight = 29650.584| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19257 Z= 0.149 Angle : 0.681 11.189 26256 Z= 0.332 Chirality : 0.047 0.262 2982 Planarity : 0.005 0.059 3282 Dihedral : 8.979 69.724 3423 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.65 % Rotamer: Outliers : 3.36 % Allowed : 14.76 % Favored : 81.88 % 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: -0.36 (0.18), residues: 2301 helix: 1.62 (0.39), residues: 174 sheet: -0.24 (0.16), residues: 1011 loop : -0.41 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 587 TYR 0.018 0.002 TYR H 100 PHE 0.015 0.001 PHE K 72 TRP 0.045 0.002 TRP J 36 HIS 0.009 0.002 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00336 (19194) covalent geometry : angle 0.65179 (26088) SS BOND : bond 0.00328 ( 21) SS BOND : angle 1.20687 ( 42) hydrogen bonds : bond 0.03550 ( 684) hydrogen bonds : angle 5.35948 ( 1719) link_ALPHA1-3 : bond 0.01621 ( 6) link_ALPHA1-3 : angle 1.30961 ( 18) link_ALPHA1-6 : bond 0.01013 ( 6) link_ALPHA1-6 : angle 2.01327 ( 18) link_BETA1-4 : bond 0.01572 ( 15) link_BETA1-4 : angle 3.35413 ( 45) link_NAG-ASN : bond 0.00514 ( 15) link_NAG-ASN : angle 3.01287 ( 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 440 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 374 time to evaluate : 0.755 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: 0.6948 (OUTLIER) cc_final: 0.6069 (m-10) REVERT: A 100 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6779 (mp0) REVERT: A 184 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8810 (pp) REVERT: A 261 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: A 265 LYS cc_start: 0.8711 (mttt) cc_final: 0.8352 (mttt) REVERT: J 32 LYS cc_start: 0.8487 (pttp) cc_final: 0.8026 (mmtt) REVERT: D 565 THR cc_start: 0.8750 (p) cc_final: 0.8301 (t) REVERT: D 578 GLU cc_start: 0.7633 (tt0) cc_final: 0.7389 (tt0) REVERT: D 597 TRP cc_start: 0.6523 (m-90) cc_final: 0.6012 (m100) REVERT: M 6 GLU cc_start: 0.8468 (mp0) cc_final: 0.8137 (mp0) REVERT: P 10 THR cc_start: 0.8558 (m) cc_final: 0.8206 (p) REVERT: B 99 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.5992 (m-10) REVERT: B 231 GLU cc_start: 0.7095 (mp0) cc_final: 0.6750 (mp0) REVERT: H 57 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6818 (ttt180) REVERT: K 32 LYS cc_start: 0.8429 (ptmm) cc_final: 0.8174 (mmtt) REVERT: E 565 THR cc_start: 0.8538 (p) cc_final: 0.8166 (t) REVERT: E 597 TRP cc_start: 0.6503 (m-90) cc_final: 0.6077 (m100) REVERT: N 6 GLU cc_start: 0.8403 (mp0) cc_final: 0.7896 (mp0) REVERT: N 17 THR cc_start: 0.8691 (m) cc_final: 0.8393 (p) REVERT: Q 39 LYS cc_start: 0.8069 (mttt) cc_final: 0.7719 (mttp) REVERT: C 155 LYS cc_start: 0.9047 (mttt) cc_final: 0.8805 (mttm) REVERT: C 231 GLU cc_start: 0.7218 (mp0) cc_final: 0.6803 (mp0) REVERT: C 261 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: L 32 LYS cc_start: 0.8427 (ptmm) cc_final: 0.7991 (mmtt) REVERT: L 91 GLN cc_start: 0.6018 (pp30) cc_final: 0.5601 (pp30) REVERT: L 92 TYR cc_start: 0.5492 (OUTLIER) cc_final: 0.4742 (m-80) REVERT: F 547 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7695 (mp) REVERT: F 565 THR cc_start: 0.8654 (p) cc_final: 0.8355 (t) REVERT: F 597 TRP cc_start: 0.6396 (m-90) cc_final: 0.6017 (m100) REVERT: O 6 GLU cc_start: 0.8484 (mp0) cc_final: 0.8237 (mp0) REVERT: O 74 ASP cc_start: 0.6606 (t0) cc_final: 0.5944 (p0) REVERT: R 61 ARG cc_start: 0.8376 (mtm110) cc_final: 0.8024 (mtm110) REVERT: R 98 TYR cc_start: 0.8427 (m-80) cc_final: 0.8144 (m-80) outliers start: 66 outliers final: 50 residues processed: 415 average time/residue: 0.1627 time to fit residues: 99.3461 Evaluate side-chains 415 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 358 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 115 GLU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 547 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 78 ASN Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU 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 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 63 PHE 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 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 65 SER 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 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: 6.9990 chunk 173 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 78 ASN M 79 HIS P 79 GLN N 79 HIS Q 27 GLN Q 79 GLN O 79 HIS R 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094898 restraints weight = 31739.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094051 restraints weight = 77426.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094759 restraints weight = 65088.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.096676 restraints weight = 41136.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096930 restraints weight = 26568.344| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19257 Z= 0.247 Angle : 0.756 12.041 26256 Z= 0.369 Chirality : 0.049 0.284 2982 Planarity : 0.006 0.057 3282 Dihedral : 9.041 66.876 3423 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.74 % Favored : 96.05 % 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: -0.59 (0.18), residues: 2301 helix: 1.42 (0.39), residues: 174 sheet: -0.43 (0.16), residues: 1011 loop : -0.53 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 587 TYR 0.022 0.002 TYR H 100 PHE 0.016 0.002 PHE K 72 TRP 0.057 0.003 TRP J 36 HIS 0.005 0.001 HIS D 549 Details of bonding type rmsd covalent geometry : bond 0.00585 (19194) covalent geometry : angle 0.72470 (26088) SS BOND : bond 0.00465 ( 21) SS BOND : angle 1.51653 ( 42) hydrogen bonds : bond 0.04246 ( 684) hydrogen bonds : angle 5.42159 ( 1719) link_ALPHA1-3 : bond 0.01556 ( 6) link_ALPHA1-3 : angle 1.49933 ( 18) link_ALPHA1-6 : bond 0.00822 ( 6) link_ALPHA1-6 : angle 2.00271 ( 18) link_BETA1-4 : bond 0.01500 ( 15) link_BETA1-4 : angle 3.58122 ( 45) link_NAG-ASN : bond 0.00566 ( 15) link_NAG-ASN : angle 3.35557 ( 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 442 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 361 time to evaluate : 0.700 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: 0.7304 (OUTLIER) cc_final: 0.6035 (m-10) REVERT: A 100 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7010 (mp0) REVERT: A 184 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8965 (pp) REVERT: A 231 GLU cc_start: 0.6939 (mp0) cc_final: 0.6682 (mp0) REVERT: A 261 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: J 32 LYS cc_start: 0.8556 (pttp) cc_final: 0.8136 (mmtt) REVERT: D 565 THR cc_start: 0.8836 (p) cc_final: 0.8331 (t) REVERT: D 578 GLU cc_start: 0.7688 (tt0) cc_final: 0.7448 (tt0) REVERT: D 597 TRP cc_start: 0.6537 (m-90) cc_final: 0.6110 (m100) REVERT: M 6 GLU cc_start: 0.8471 (mp0) cc_final: 0.8053 (mp0) REVERT: M 74 ASP cc_start: 0.6796 (t0) cc_final: 0.5408 (p0) REVERT: M 79 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6282 (m-70) REVERT: M 83 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6775 (ttm-80) REVERT: P 10 THR cc_start: 0.8784 (m) cc_final: 0.8441 (p) REVERT: B 99 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6301 (m-10) REVERT: B 184 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8943 (pt) REVERT: B 231 GLU cc_start: 0.7176 (mp0) cc_final: 0.6871 (mp0) REVERT: H 54 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6628 (tt) REVERT: H 57 ARG cc_start: 0.7332 (mtp180) cc_final: 0.7003 (ttt180) REVERT: H 84 LEU cc_start: 0.7055 (pp) cc_final: 0.6794 (pp) REVERT: K 32 LYS cc_start: 0.8499 (ptmm) cc_final: 0.8220 (mmtt) REVERT: E 565 THR cc_start: 0.8585 (p) cc_final: 0.8173 (t) REVERT: E 597 TRP cc_start: 0.6548 (m-90) cc_final: 0.6190 (m100) REVERT: N 6 GLU cc_start: 0.8412 (mp0) cc_final: 0.7872 (mp0) REVERT: N 74 ASP cc_start: 0.6707 (t0) cc_final: 0.5863 (p0) REVERT: C 231 GLU cc_start: 0.7150 (mp0) cc_final: 0.6640 (mp0) REVERT: C 261 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: L 32 LYS cc_start: 0.8560 (ptmm) cc_final: 0.8038 (mmtt) REVERT: L 91 GLN cc_start: 0.6291 (pp30) cc_final: 0.5729 (pp30) REVERT: L 92 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4838 (m-80) REVERT: F 547 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7814 (mp) REVERT: F 565 THR cc_start: 0.8597 (p) cc_final: 0.8275 (t) REVERT: F 597 TRP cc_start: 0.6457 (m-90) cc_final: 0.6085 (m100) REVERT: O 6 GLU cc_start: 0.8556 (mp0) cc_final: 0.8166 (mp0) REVERT: R 70 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7115 (mm-30) REVERT: R 98 TYR cc_start: 0.8478 (m-80) cc_final: 0.8164 (m-80) outliers start: 81 outliers final: 58 residues processed: 413 average time/residue: 0.1611 time to fit residues: 98.3475 Evaluate side-chains 416 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 348 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 90 HIS Chi-restraints excluded: chain D residue 545 GLU 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 79 HIS 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 69 THR Chi-restraints excluded: chain P residue 78 LEU 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 184 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL 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 63 PHE 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 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 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 O residue 85 THR Chi-restraints excluded: chain O residue 116 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: 8.9990 chunk 177 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 79 HIS N 79 HIS Q 27 GLN Q 79 GLN O 78 ASN R 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098006 restraints weight = 31561.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097279 restraints weight = 82917.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097988 restraints weight = 64820.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.100203 restraints weight = 42514.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099980 restraints weight = 25530.319| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19257 Z= 0.162 Angle : 0.736 21.746 26256 Z= 0.354 Chirality : 0.048 0.569 2982 Planarity : 0.006 0.133 3282 Dihedral : 8.718 62.750 3423 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.52 % Favored : 96.26 % Rotamer: Outliers : 3.72 % Allowed : 15.17 % Favored : 81.12 % 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: -0.49 (0.18), residues: 2301 helix: 1.66 (0.39), residues: 174 sheet: -0.37 (0.17), residues: 978 loop : -0.48 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 587 TYR 0.020 0.002 TYR J 50 PHE 0.017 0.001 PHE K 72 TRP 0.081 0.002 TRP K 36 HIS 0.017 0.001 HIS M 79 Details of bonding type rmsd covalent geometry : bond 0.00372 (19194) covalent geometry : angle 0.69294 (26088) SS BOND : bond 0.00435 ( 21) SS BOND : angle 1.87922 ( 42) hydrogen bonds : bond 0.03715 ( 684) hydrogen bonds : angle 5.35242 ( 1719) link_ALPHA1-3 : bond 0.01620 ( 6) link_ALPHA1-3 : angle 1.48222 ( 18) link_ALPHA1-6 : bond 0.00990 ( 6) link_ALPHA1-6 : angle 2.00081 ( 18) link_BETA1-4 : bond 0.01545 ( 15) link_BETA1-4 : angle 3.40491 ( 45) link_NAG-ASN : bond 0.00426 ( 15) link_NAG-ASN : angle 4.53954 ( 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 438 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 365 time to evaluate : 0.522 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: 0.7119 (OUTLIER) cc_final: 0.6026 (m-10) REVERT: A 100 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6851 (mp0) REVERT: A 184 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8861 (pp) REVERT: A 261 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: G 54 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6616 (tt) REVERT: J 32 LYS cc_start: 0.8527 (pttp) cc_final: 0.8120 (mmtt) REVERT: D 565 THR cc_start: 0.8793 (p) cc_final: 0.8313 (t) REVERT: D 597 TRP cc_start: 0.6336 (m-90) cc_final: 0.5858 (m100) REVERT: M 6 GLU cc_start: 0.8456 (mp0) cc_final: 0.8129 (mp0) REVERT: M 74 ASP cc_start: 0.6654 (t0) cc_final: 0.5373 (p0) REVERT: M 79 HIS cc_start: 0.6771 (OUTLIER) cc_final: 0.6513 (m170) REVERT: M 83 ARG cc_start: 0.7017 (ttm-80) cc_final: 0.6781 (ttm-80) REVERT: P 4 MET cc_start: 0.7956 (mmm) cc_final: 0.7660 (mmm) REVERT: P 10 THR cc_start: 0.8735 (m) cc_final: 0.8461 (p) REVERT: B 99 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6131 (m-10) REVERT: B 184 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8863 (pt) REVERT: B 231 GLU cc_start: 0.7186 (mp0) cc_final: 0.6853 (mp0) REVERT: H 57 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6939 (ttt180) REVERT: H 84 LEU cc_start: 0.7071 (pp) cc_final: 0.6771 (pp) REVERT: K 32 LYS cc_start: 0.8481 (ptmm) cc_final: 0.8216 (mmtt) REVERT: E 565 THR cc_start: 0.8511 (p) cc_final: 0.8130 (t) REVERT: E 597 TRP cc_start: 0.6482 (m-90) cc_final: 0.6106 (m100) REVERT: N 6 GLU cc_start: 0.8383 (mp0) cc_final: 0.7951 (mp0) REVERT: N 74 ASP cc_start: 0.6712 (t0) cc_final: 0.5791 (p0) REVERT: N 79 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.6531 (m170) REVERT: C 130 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7111 (mtm-85) REVERT: C 217 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8397 (t) REVERT: C 231 GLU cc_start: 0.7162 (mp0) cc_final: 0.6678 (mp0) REVERT: C 261 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: L 32 LYS cc_start: 0.8529 (ptmm) cc_final: 0.8026 (mmtt) REVERT: L 91 GLN cc_start: 0.6286 (pp30) cc_final: 0.5733 (pp30) REVERT: L 92 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.5017 (m-80) REVERT: F 547 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7587 (mp) REVERT: F 565 THR cc_start: 0.8692 (p) cc_final: 0.8387 (t) REVERT: F 597 TRP cc_start: 0.6343 (m-90) cc_final: 0.6022 (m100) REVERT: O 6 GLU cc_start: 0.8537 (mp0) cc_final: 0.8156 (mp0) REVERT: O 74 ASP cc_start: 0.7009 (t0) cc_final: 0.6699 (t0) REVERT: O 83 ARG cc_start: 0.7039 (ttm-80) cc_final: 0.6787 (ttm-80) REVERT: R 70 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7041 (mm-30) REVERT: R 98 TYR cc_start: 0.8377 (m-80) cc_final: 0.8078 (m-80) outliers start: 73 outliers final: 54 residues processed: 414 average time/residue: 0.1545 time to fit residues: 95.0812 Evaluate side-chains 418 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 351 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 88 MET 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 545 GLU 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 79 HIS 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 69 THR 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 184 LEU Chi-restraints excluded: chain B residue 217 THR 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 115 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 89 CYS 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 79 HIS 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 65 SER Chi-restraints excluded: chain C residue 82 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 217 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 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 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: 3.9990 chunk 165 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 79 HIS P 79 GLN N 79 HIS Q 27 GLN Q 79 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096470 restraints weight = 31594.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096701 restraints weight = 81003.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097137 restraints weight = 58515.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096672 restraints weight = 42303.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097452 restraints weight = 33755.967| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19257 Z= 0.258 Angle : 0.786 18.760 26256 Z= 0.382 Chirality : 0.050 0.425 2982 Planarity : 0.006 0.146 3282 Dihedral : 8.783 59.775 3423 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.09 % Favored : 95.65 % Rotamer: Outliers : 3.97 % Allowed : 15.01 % 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: -0.66 (0.18), residues: 2301 helix: 1.47 (0.39), residues: 174 sheet: -0.51 (0.17), residues: 960 loop : -0.57 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 24 TYR 0.021 0.002 TYR K 50 PHE 0.021 0.002 PHE G 30 TRP 0.065 0.002 TRP K 36 HIS 0.019 0.002 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00615 (19194) covalent geometry : angle 0.74999 (26088) SS BOND : bond 0.00488 ( 21) SS BOND : angle 1.56209 ( 42) hydrogen bonds : bond 0.04340 ( 684) hydrogen bonds : angle 5.41625 ( 1719) link_ALPHA1-3 : bond 0.01565 ( 6) link_ALPHA1-3 : angle 1.63822 ( 18) link_ALPHA1-6 : bond 0.00794 ( 6) link_ALPHA1-6 : angle 1.94023 ( 18) link_BETA1-4 : bond 0.01490 ( 15) link_BETA1-4 : angle 3.60256 ( 45) link_NAG-ASN : bond 0.00442 ( 15) link_NAG-ASN : angle 4.06245 ( 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: 78 poor density : 355 time to evaluate : 0.685 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: 0.7355 (OUTLIER) cc_final: 0.6022 (m-10) REVERT: A 100 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7038 (mp0) REVERT: A 184 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8931 (pp) REVERT: A 231 GLU cc_start: 0.6987 (mp0) cc_final: 0.6630 (mp0) REVERT: A 261 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: G 54 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6817 (tt) REVERT: J 32 LYS cc_start: 0.8499 (pttp) cc_final: 0.8143 (mmtt) REVERT: D 565 THR cc_start: 0.8835 (p) cc_final: 0.8300 (t) REVERT: D 597 TRP cc_start: 0.6441 (m-90) cc_final: 0.6034 (m100) REVERT: M 6 GLU cc_start: 0.8475 (mp0) cc_final: 0.8122 (mp0) REVERT: M 74 ASP cc_start: 0.6528 (t0) cc_final: 0.5203 (p0) REVERT: P 24 ARG cc_start: 0.7569 (ttm110) cc_final: 0.7352 (ttm110) REVERT: P 70 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7742 (mm-30) REVERT: B 99 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6365 (m-10) REVERT: B 231 GLU cc_start: 0.7168 (mp0) cc_final: 0.6948 (mp0) REVERT: H 57 ARG cc_start: 0.7249 (mtp180) cc_final: 0.6907 (ttt180) REVERT: H 84 LEU cc_start: 0.7120 (pp) cc_final: 0.6800 (pp) REVERT: K 32 LYS cc_start: 0.8433 (ptmm) cc_final: 0.8206 (mmtt) REVERT: E 565 THR cc_start: 0.8632 (p) cc_final: 0.8215 (t) REVERT: E 597 TRP cc_start: 0.6584 (m-90) cc_final: 0.6249 (m100) REVERT: N 6 GLU cc_start: 0.8403 (mp0) cc_final: 0.7853 (mp0) REVERT: N 74 ASP cc_start: 0.6601 (t0) cc_final: 0.5824 (p0) REVERT: C 217 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8479 (t) REVERT: C 231 GLU cc_start: 0.7163 (mp0) cc_final: 0.6753 (mp0) REVERT: C 261 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: I 121 ASP cc_start: 0.7269 (t0) cc_final: 0.6633 (t0) REVERT: L 32 LYS cc_start: 0.8491 (ptmm) cc_final: 0.8056 (mmtt) REVERT: L 91 GLN cc_start: 0.6307 (pp30) cc_final: 0.5699 (pp30) REVERT: L 92 TYR cc_start: 0.5766 (OUTLIER) cc_final: 0.4934 (m-80) REVERT: F 547 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7722 (mp) REVERT: F 565 THR cc_start: 0.8600 (p) cc_final: 0.8269 (t) REVERT: F 597 TRP cc_start: 0.6466 (m-90) cc_final: 0.6147 (m100) REVERT: O 6 GLU cc_start: 0.8544 (mp0) cc_final: 0.8150 (mp0) REVERT: O 74 ASP cc_start: 0.6866 (t0) cc_final: 0.5883 (p0) REVERT: O 83 ARG cc_start: 0.7053 (ttm-80) cc_final: 0.6790 (ttm-80) REVERT: R 70 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7126 (mm-30) REVERT: R 98 TYR cc_start: 0.8459 (m-80) cc_final: 0.8168 (m-80) outliers start: 78 outliers final: 60 residues processed: 405 average time/residue: 0.1555 time to fit residues: 93.8640 Evaluate side-chains 413 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 344 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 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 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 97 TRP 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 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 69 THR 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 144 THR Chi-restraints excluded: chain B residue 217 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 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 E residue 595 GLN 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 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 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 217 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 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 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: 0.5980 chunk 26 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 158 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN D 516 HIS M 79 HIS P 79 GLN N 79 HIS Q 79 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099863 restraints weight = 31363.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101006 restraints weight = 74219.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100068 restraints weight = 43426.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100039 restraints weight = 33073.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100306 restraints weight = 28908.205| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19257 Z= 0.163 Angle : 0.736 15.484 26256 Z= 0.358 Chirality : 0.048 0.299 2982 Planarity : 0.005 0.067 3282 Dihedral : 8.256 58.392 3423 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.48 % Rotamer: Outliers : 3.41 % Allowed : 16.23 % Favored : 80.36 % 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: -0.58 (0.18), residues: 2301 helix: 1.49 (0.39), residues: 180 sheet: -0.53 (0.17), residues: 981 loop : -0.44 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 83 TYR 0.021 0.002 TYR J 50 PHE 0.021 0.001 PHE G 30 TRP 0.056 0.002 TRP K 36 HIS 0.008 0.001 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00377 (19194) covalent geometry : angle 0.70292 (26088) SS BOND : bond 0.00344 ( 21) SS BOND : angle 1.72817 ( 42) hydrogen bonds : bond 0.03675 ( 684) hydrogen bonds : angle 5.33448 ( 1719) link_ALPHA1-3 : bond 0.01643 ( 6) link_ALPHA1-3 : angle 1.66758 ( 18) link_ALPHA1-6 : bond 0.00859 ( 6) link_ALPHA1-6 : angle 1.74332 ( 18) link_BETA1-4 : bond 0.01567 ( 15) link_BETA1-4 : angle 3.49210 ( 45) link_NAG-ASN : bond 0.00381 ( 15) link_NAG-ASN : angle 3.45980 ( 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 434 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 367 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.5973 (m-10) REVERT: A 100 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6755 (mp0) REVERT: A 184 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8906 (pp) REVERT: G 41 ARG cc_start: 0.6845 (ttp80) cc_final: 0.6575 (ptm160) REVERT: G 54 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6735 (tt) REVERT: J 32 LYS cc_start: 0.8475 (pttp) cc_final: 0.8129 (mmtt) REVERT: D 565 THR cc_start: 0.8782 (p) cc_final: 0.8300 (t) REVERT: D 597 TRP cc_start: 0.6304 (m-90) cc_final: 0.5907 (m100) REVERT: M 6 GLU cc_start: 0.8460 (mp0) cc_final: 0.8130 (mp0) REVERT: M 74 ASP cc_start: 0.6384 (t0) cc_final: 0.5023 (p0) REVERT: M 79 HIS cc_start: 0.6714 (OUTLIER) cc_final: 0.6386 (m170) REVERT: B 99 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.5720 (m-10) REVERT: B 100 GLU cc_start: 0.7014 (mp0) cc_final: 0.6796 (mm-30) REVERT: B 231 GLU cc_start: 0.7077 (mp0) cc_final: 0.6861 (mp0) REVERT: H 57 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6785 (ttt180) REVERT: H 84 LEU cc_start: 0.7039 (pp) cc_final: 0.6691 (pp) REVERT: E 565 THR cc_start: 0.8631 (p) cc_final: 0.8215 (t) REVERT: E 597 TRP cc_start: 0.6522 (m-90) cc_final: 0.6163 (m100) REVERT: N 6 GLU cc_start: 0.8398 (mp0) cc_final: 0.7938 (mp0) REVERT: N 74 ASP cc_start: 0.6783 (t0) cc_final: 0.5701 (p0) REVERT: N 79 HIS cc_start: 0.6397 (m-70) cc_final: 0.6051 (m170) REVERT: C 130 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7133 (mtm-85) REVERT: C 217 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8393 (t) REVERT: C 231 GLU cc_start: 0.6954 (mp0) cc_final: 0.6594 (mp0) REVERT: C 261 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: L 32 LYS cc_start: 0.8443 (ptmm) cc_final: 0.8078 (mmtt) REVERT: L 50 TYR cc_start: 0.6658 (p90) cc_final: 0.6453 (p90) REVERT: L 92 TYR cc_start: 0.5677 (OUTLIER) cc_final: 0.5195 (m-80) REVERT: F 547 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7564 (mp) REVERT: F 565 THR cc_start: 0.8712 (p) cc_final: 0.8375 (t) REVERT: F 597 TRP cc_start: 0.6421 (m-90) cc_final: 0.6078 (m100) REVERT: O 6 GLU cc_start: 0.8513 (mp0) cc_final: 0.8154 (mp0) REVERT: O 74 ASP cc_start: 0.6970 (t0) cc_final: 0.5839 (p0) REVERT: R 70 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7154 (mm-30) outliers start: 67 outliers final: 50 residues processed: 411 average time/residue: 0.1461 time to fit residues: 89.8903 Evaluate side-chains 414 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 354 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 89 CYS 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 M residue 24 VAL Chi-restraints excluded: chain M residue 79 HIS Chi-restraints excluded: chain M residue 87 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 144 THR Chi-restraints excluded: chain B residue 217 THR 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 K residue 76 ILE Chi-restraints excluded: chain E residue 558 LEU 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 65 SER Chi-restraints excluded: chain C residue 82 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 217 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 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 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: 10.0000 chunk 43 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 190 optimal weight: 0.1980 chunk 113 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 42 HIS M 79 HIS Q 79 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096862 restraints weight = 31581.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096181 restraints weight = 74102.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097126 restraints weight = 65445.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097200 restraints weight = 41391.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098062 restraints weight = 34835.977| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19257 Z= 0.186 Angle : 0.762 17.127 26256 Z= 0.369 Chirality : 0.050 0.788 2982 Planarity : 0.005 0.067 3282 Dihedral : 7.702 58.899 3423 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.91 % Favored : 95.83 % Rotamer: Outliers : 3.16 % Allowed : 16.59 % Favored : 80.25 % 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: -0.62 (0.18), residues: 2301 helix: 1.52 (0.39), residues: 180 sheet: -0.57 (0.17), residues: 981 loop : -0.46 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 78 TYR 0.022 0.002 TYR K 50 PHE 0.024 0.002 PHE H 113 TRP 0.051 0.002 TRP J 36 HIS 0.029 0.002 HIS M 79 Details of bonding type rmsd covalent geometry : bond 0.00436 (19194) covalent geometry : angle 0.72659 (26088) SS BOND : bond 0.00436 ( 21) SS BOND : angle 1.53190 ( 42) hydrogen bonds : bond 0.03850 ( 684) hydrogen bonds : angle 5.32417 ( 1719) link_ALPHA1-3 : bond 0.01614 ( 6) link_ALPHA1-3 : angle 1.86598 ( 18) link_ALPHA1-6 : bond 0.00727 ( 6) link_ALPHA1-6 : angle 1.76830 ( 18) link_BETA1-4 : bond 0.01532 ( 15) link_BETA1-4 : angle 3.63501 ( 45) link_NAG-ASN : bond 0.00389 ( 15) link_NAG-ASN : angle 3.83022 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3005.85 seconds wall clock time: 53 minutes 4.63 seconds (3184.63 seconds total)