Starting phenix.real_space_refine on Sun Sep 13 10:38:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hjq_0236/09_2026/6hjq_0236.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjq_0236/09_2026/6hjq_0236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2026/6hjq_0236.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2026/6hjq_0236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2026/6hjq_0236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2026/6hjq_0236.map" model { file = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2026/6hjq_0236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2026/6hjq_0236.cif" } resolution = 4.1 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= 0.003 sd= 0.175 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 90 5.16 5 C 14118 2.51 5 N 3780 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22530 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "B" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1569 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 1, 'TRANS': 201} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "H" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "I" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "K" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "J" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "L" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "C" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "E" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1569 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 1, 'TRANS': 201} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1569 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 1, 'TRANS': 201} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.82, per 1000 atoms: 0.21 Number of scatterers: 22530 At special positions: 0 Unit cell: (171.402, 176.792, 196.196, 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 90 16.00 O 4542 8.00 N 3780 7.00 C 14118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 143 " - pdb=" SG CYS G 199 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 143 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 143 " - pdb=" SG CYS K 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 137 " distance=2.01 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.02 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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 O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 4 " " BMA X 3 " - " MAN X 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " 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 Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " BETA1-6 " NAG N 1 " - " FUC N 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG M 1 " - " ASN A 15 " " NAG N 1 " - " ASN A 27 " " NAG O 1 " - " ASN A 91 " " NAG P 1 " - " ASN A 290 " " NAG Q 1 " - " ASN B 154 " " NAG R 1 " - " ASN C 15 " " NAG S 1 " - " ASN C 27 " " NAG T 1 " - " ASN C 91 " " NAG U 1 " - " ASN C 290 " " NAG V 1 " - " ASN E 15 " " NAG W 1 " - " ASN E 27 " " NAG X 1 " - " ASN E 91 " " NAG Y 1 " - " ASN E 290 " " NAG Z 1 " - " ASN D 154 " " NAG a 1 " - " ASN F 154 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.1 seconds 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5280 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 66 sheets defined 19.4% alpha, 31.7% 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 60 through 67 Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 39 through 59 removed outlier: 4.025A pdb=" N MET B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 125 removed outlier: 4.597A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.868A pdb=" N ASP B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.572A pdb=" N TYR B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.977A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.742A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.507A pdb=" N ASP G 90 " --> pdb=" O ARG G 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 87 through 91' Processing helix chain 'G' and resid 188 through 192 removed outlier: 4.147A pdb=" N LEU G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 129 removed outlier: 3.725A pdb=" N LEU H 126 " --> pdb=" O SER H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 4.001A pdb=" N TYR H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.977A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.742A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.508A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'I' and resid 188 through 192 removed outlier: 4.146A pdb=" N LEU I 192 " --> pdb=" O SER I 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.976A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.742A pdb=" N LYS K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.507A pdb=" N ASP K 90 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR K 91 " --> pdb=" O ALA K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 87 through 91' Processing helix chain 'K' and resid 188 through 192 removed outlier: 4.146A pdb=" N LEU K 192 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 removed outlier: 3.725A pdb=" N LEU J 126 " --> pdb=" O SER J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 4.001A pdb=" N TYR J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.725A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 removed outlier: 4.000A pdb=" N TYR L 187 " --> pdb=" O SER L 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 101 through 110 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'D' and resid 39 through 59 removed outlier: 4.024A pdb=" N MET D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 125 removed outlier: 4.597A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 174 removed outlier: 3.869A pdb=" N ASP D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.572A pdb=" N TYR D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 59 removed outlier: 4.025A pdb=" N MET F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 125 removed outlier: 4.597A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 158 through 161 Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.868A pdb=" N ASP F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 181 Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.572A pdb=" N TYR F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 11 removed outlier: 3.532A pdb=" N GLY A 10 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 23 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.405A pdb=" N LEU A 46 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N CYS A 278 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 57 removed outlier: 6.790A pdb=" N LEU A 54 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU A 98 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP A 234 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU A 98 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP A 234 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.952A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB3, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AB4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.781A pdb=" N THR G 119 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.781A pdb=" N THR G 119 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE G 111 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 153 through 157 Processing sheet with id=AC1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.569A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.687A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR H 53 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 115 through 119 removed outlier: 5.312A pdb=" N SER H 132 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU H 182 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL H 134 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU H 180 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU H 136 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER H 178 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN H 138 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU H 176 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 145 through 151 Processing sheet with id=AC5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.782A pdb=" N THR I 119 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.782A pdb=" N THR I 119 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE I 111 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 153 through 157 Processing sheet with id=AD2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.782A pdb=" N THR K 119 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.782A pdb=" N THR K 119 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE K 111 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR K 179 " --> pdb=" O ASP K 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR K 179 " --> pdb=" O ASP K 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 153 through 157 Processing sheet with id=AD8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.569A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.687A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 115 through 119 removed outlier: 5.311A pdb=" N SER J 132 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU J 182 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL J 134 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU J 180 " --> pdb=" O VAL J 134 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU J 136 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER J 178 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN J 138 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU J 176 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 145 through 151 Processing sheet with id=AE3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.569A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.688A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.312A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 145 through 151 Processing sheet with id=AE7, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.515A pdb=" N GLY C 10 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 23 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AE9, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AF1, first strand: chain 'C' and resid 46 through 49 removed outlier: 5.405A pdb=" N LEU C 46 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 54 through 57 removed outlier: 6.789A pdb=" N LEU C 54 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU C 98 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP C 234 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE C 258 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU C 98 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP C 234 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AF6, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.952A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 164 through 168 Processing sheet with id=AF8, first strand: chain 'C' and resid 287 through 288 Processing sheet with id=AF9, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AG1, first strand: chain 'E' and resid 7 through 11 removed outlier: 3.531A pdb=" N GLY E 10 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY F 23 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AG3, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AG4, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.405A pdb=" N LEU E 46 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N CYS E 278 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 54 through 57 removed outlier: 6.790A pdb=" N LEU E 54 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU E 98 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP E 234 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU E 98 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP E 234 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AG9, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.952A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 164 through 168 Processing sheet with id=AH2, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AH3, first strand: chain 'E' and resid 295 through 296 939 hydrogen bonds defined for protein. 2466 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: 4.38 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7128 1.34 - 1.46: 5661 1.46 - 1.58: 10116 1.58 - 1.70: 3 1.70 - 1.83: 120 Bond restraints: 23028 Sorted by residual: bond pdb=" C1 MAN T 4 " pdb=" C2 MAN T 4 " ideal model delta sigma weight residual 1.526 1.635 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C1 MAN X 4 " pdb=" C2 MAN X 4 " ideal model delta sigma weight residual 1.526 1.634 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C1 MAN O 4 " pdb=" C2 MAN O 4 " ideal model delta sigma weight residual 1.526 1.634 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C1 MAN T 4 " pdb=" O5 MAN T 4 " ideal model delta sigma weight residual 1.399 1.498 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C1 MAN X 4 " pdb=" O5 MAN X 4 " ideal model delta sigma weight residual 1.399 1.498 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 23023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 30202 2.28 - 4.56: 910 4.56 - 6.84: 146 6.84 - 9.11: 35 9.11 - 11.39: 9 Bond angle restraints: 31302 Sorted by residual: angle pdb=" C GLY D 134 " pdb=" N ASN D 135 " pdb=" CA ASN D 135 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C GLY B 134 " pdb=" N ASN B 135 " pdb=" CA ASN B 135 " ideal model delta sigma weight residual 121.54 130.94 -9.40 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C GLY F 134 " pdb=" N ASN F 135 " pdb=" CA ASN F 135 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" N GLY A 249 " pdb=" CA GLY A 249 " pdb=" C GLY A 249 " ideal model delta sigma weight residual 113.18 124.57 -11.39 2.37e+00 1.78e-01 2.31e+01 angle pdb=" N GLY C 249 " pdb=" CA GLY C 249 " pdb=" C GLY C 249 " ideal model delta sigma weight residual 113.18 124.56 -11.38 2.37e+00 1.78e-01 2.30e+01 ... (remaining 31297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 12627 15.41 - 30.83: 555 30.83 - 46.24: 150 46.24 - 61.66: 24 61.66 - 77.07: 15 Dihedral angle restraints: 13371 sinusoidal: 5106 harmonic: 8265 Sorted by residual: dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 143.60 -50.60 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 143.60 -50.60 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 143.58 -50.58 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 13368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3138 0.088 - 0.177: 414 0.177 - 0.265: 30 0.265 - 0.353: 9 0.353 - 0.442: 3 Chirality restraints: 3594 Sorted by residual: chirality pdb=" C3 BMA T 3 " pdb=" C2 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" O3 BMA T 3 " both_signs ideal model delta sigma weight residual False 2.41 1.97 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" C3 BMA O 3 " pdb=" C2 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" O3 BMA O 3 " both_signs ideal model delta sigma weight residual False 2.41 1.97 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C3 BMA X 3 " pdb=" C2 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" O3 BMA X 3 " both_signs ideal model delta sigma weight residual False 2.41 1.97 0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 3591 not shown) Planarity restraints: 4011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.130 2.00e-02 2.50e+03 1.14e-01 1.64e+02 pdb=" C7 NAG S 2 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.130 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG N 2 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " -0.130 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG W 2 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " 0.024 2.00e-02 2.50e+03 ... (remaining 4008 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.10: 3 2.10 - 2.80: 5961 2.80 - 3.50: 28694 3.50 - 4.20: 50702 4.20 - 4.90: 86582 Nonbonded interactions: 171942 Sorted by model distance: nonbonded pdb=" CG2 THR E 6 " pdb=" O PHE F 138 " model vdw 1.406 3.460 nonbonded pdb=" CG2 THR C 6 " pdb=" O PHE D 138 " model vdw 1.411 3.460 nonbonded pdb=" CG2 THR A 6 " pdb=" O PHE B 138 " model vdw 1.439 3.460 nonbonded pdb=" OG SER F 151 " pdb=" O THR F 156 " model vdw 2.203 3.040 nonbonded pdb=" OG SER B 151 " pdb=" O THR B 156 " model vdw 2.203 3.040 ... (remaining 171937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 13.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.570 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.006 0.109 23100 Z= 0.283 Angle : 0.975 11.663 31488 Z= 0.495 Chirality : 0.059 0.442 3594 Planarity : 0.007 0.114 3996 Dihedral : 10.065 77.071 8001 Min Nonbonded Distance : 1.406 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.31 % Rotamer: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -3.06 (0.13), residues: 2847 helix: -2.12 (0.17), residues: 477 sheet: -1.30 (0.16), residues: 897 loop : -2.50 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 212 TYR 0.026 0.003 TYR E 102 PHE 0.022 0.003 PHE F 9 TRP 0.027 0.003 TRP A 255 HIS 0.009 0.002 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.28 (23028) covalent geometry : angle 0.94023 / 0.49 (31302) SS BOND : bond 0.00752 / 0.53 ( 30) SS BOND : angle 1.45606 / 0.93 ( 60) hydrogen bonds : bond 0.19161 / 12.66 ( 852) hydrogen bonds : angle 7.47762 / 5.17 ( 2466) link_ALPHA1-3 : bond 0.06152 / 3.08 ( 3) link_ALPHA1-3 : angle 7.55410 / 3.83 ( 9) link_BETA1-4 : bond 0.01368 / 0.89 ( 21) link_BETA1-4 : angle 2.90263 / 2.04 ( 63) link_BETA1-6 : bond 0.00201 / 0.10 ( 3) link_BETA1-6 : angle 4.81926 / 2.87 ( 9) link_NAG-ASN : bond 0.00703 / 0.41 ( 15) link_NAG-ASN : angle 4.41552 / 2.66 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 235 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 MET cc_start: 0.9015 (mmm) cc_final: 0.8682 (mmt) REVERT: G 46 GLU cc_start: 0.8309 (tt0) cc_final: 0.8106 (tt0) REVERT: G 76 LYS cc_start: 0.9606 (mttt) cc_final: 0.9376 (mttm) REVERT: H 4 MET cc_start: 0.8625 (mmm) cc_final: 0.8210 (mmm) REVERT: H 136 LEU cc_start: 0.8253 (tp) cc_final: 0.8014 (tt) REVERT: H 146 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7883 (tptt) REVERT: H 193 TYR cc_start: 0.7756 (m-10) cc_final: 0.7370 (m-80) REVERT: H 211 ASN cc_start: 0.6687 (m-40) cc_final: 0.6244 (p0) REVERT: I 3 GLN cc_start: 0.8166 (pm20) cc_final: 0.7011 (pm20) REVERT: I 34 MET cc_start: 0.9256 (mmm) cc_final: 0.8868 (mmt) REVERT: I 99 MET cc_start: 0.8975 (mmt) cc_final: 0.8772 (mmm) REVERT: I 198 ILE cc_start: 0.9026 (mt) cc_final: 0.8826 (pt) REVERT: I 213 ARG cc_start: 0.7606 (ttt180) cc_final: 0.6702 (tpt170) REVERT: I 215 GLU cc_start: 0.5589 (pt0) cc_final: 0.5015 (mm-30) REVERT: K 1 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8494 (tm-30) REVERT: K 3 GLN cc_start: 0.8109 (pm20) cc_final: 0.7161 (pm20) REVERT: K 34 MET cc_start: 0.9184 (mmm) cc_final: 0.8866 (mmt) REVERT: K 99 MET cc_start: 0.8919 (mmt) cc_final: 0.8564 (mmm) REVERT: K 198 ILE cc_start: 0.9122 (mt) cc_final: 0.8917 (pt) REVERT: K 213 ARG cc_start: 0.7828 (ttt180) cc_final: 0.6690 (tpt170) REVERT: K 215 GLU cc_start: 0.6477 (pt0) cc_final: 0.5982 (mm-30) REVERT: J 146 LYS cc_start: 0.8505 (mmtp) cc_final: 0.8125 (tmmt) REVERT: L 4 MET cc_start: 0.8819 (mmm) cc_final: 0.8571 (mmm) REVERT: L 136 LEU cc_start: 0.8929 (tp) cc_final: 0.8677 (tt) REVERT: L 193 TYR cc_start: 0.7710 (m-10) cc_final: 0.7091 (m-80) REVERT: D 149 MET cc_start: 0.9013 (mmt) cc_final: 0.8708 (mmm) REVERT: F 149 MET cc_start: 0.9070 (mmt) cc_final: 0.8691 (mmm) outliers start: 3 outliers final: 3 residues processed: 238 average time/residue: 0.2281 time to fit residues: 75.5244 Evaluate side-chains 92 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS A 250 ASN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 207 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 167 GLN H 190 HIS I 77 ASN I 158 ASN K 77 ASN K 158 ASN K 207 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN J 167 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 161 GLN L 167 GLN C 108 GLN C 250 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN E 250 ASN ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.047640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.032990 restraints weight = 156277.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.034007 restraints weight = 83574.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.034660 restraints weight = 56142.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.035095 restraints weight = 43566.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.035364 restraints weight = 37028.282| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23100 Z= 0.131 Angle : 0.678 11.377 31488 Z= 0.345 Chirality : 0.045 0.228 3594 Planarity : 0.004 0.053 3996 Dihedral : 5.353 20.946 3084 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -1.80 (0.15), residues: 2847 helix: 0.18 (0.22), residues: 471 sheet: -0.78 (0.16), residues: 915 loop : -1.96 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 212 TYR 0.013 0.001 TYR J 187 PHE 0.012 0.001 PHE L 119 TRP 0.016 0.001 TRP C 153 HIS 0.003 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (23028) covalent geometry : angle 0.66528 / 0.34 (31302) SS BOND : bond 0.00479 / 0.32 ( 30) SS BOND : angle 1.02149 / 0.71 ( 60) hydrogen bonds : bond 0.05323 / 3.54 ( 852) hydrogen bonds : angle 5.85068 / 4.07 ( 2466) link_ALPHA1-3 : bond 0.02555 / 1.29 ( 3) link_ALPHA1-3 : angle 2.37990 / 1.33 ( 9) link_BETA1-4 : bond 0.00656 / 0.43 ( 21) link_BETA1-4 : angle 1.62830 / 1.13 ( 63) link_BETA1-6 : bond 0.00451 / 0.23 ( 3) link_BETA1-6 : angle 2.03069 / 1.31 ( 9) link_NAG-ASN : bond 0.00478 / 0.27 ( 15) link_NAG-ASN : angle 2.61516 / 1.61 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.840 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: G 34 MET cc_start: 0.8759 (mmm) cc_final: 0.8547 (tpp) REVERT: H 4 MET cc_start: 0.8640 (mmm) cc_final: 0.8160 (mmm) REVERT: H 146 LYS cc_start: 0.8268 (mmtp) cc_final: 0.7893 (ttpp) REVERT: H 193 TYR cc_start: 0.7808 (m-10) cc_final: 0.7423 (m-80) REVERT: H 211 ASN cc_start: 0.6456 (m-40) cc_final: 0.6142 (p0) REVERT: I 34 MET cc_start: 0.9063 (mmm) cc_final: 0.8714 (mmt) REVERT: I 215 GLU cc_start: 0.5684 (pt0) cc_final: 0.5105 (mm-30) REVERT: K 34 MET cc_start: 0.9073 (mmm) cc_final: 0.8290 (mmt) REVERT: K 77 ASN cc_start: 0.9339 (m-40) cc_final: 0.8815 (t0) REVERT: K 99 MET cc_start: 0.9045 (mmt) cc_final: 0.8503 (mmm) REVERT: K 215 GLU cc_start: 0.6461 (pt0) cc_final: 0.6005 (mm-30) REVERT: J 4 MET cc_start: 0.8172 (mmm) cc_final: 0.7822 (mmm) REVERT: L 4 MET cc_start: 0.8804 (mmm) cc_final: 0.8443 (mmm) REVERT: L 24 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7779 (ttm-80) REVERT: L 193 TYR cc_start: 0.7682 (m-10) cc_final: 0.6844 (m-80) REVERT: D 149 MET cc_start: 0.8984 (mmt) cc_final: 0.8645 (mmm) REVERT: F 59 MET cc_start: 0.9002 (mmm) cc_final: 0.8759 (mmm) REVERT: F 149 MET cc_start: 0.9046 (mmt) cc_final: 0.8683 (mmm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2126 time to fit residues: 43.0625 Evaluate side-chains 83 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 85 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 169 optimal weight: 0.0020 chunk 231 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN G 109 ASN H 6 GLN H 37 GLN I 77 ASN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 37 GLN J 190 HIS L 6 GLN L 37 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 169 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.031459 restraints weight = 155686.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.032407 restraints weight = 86145.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.033019 restraints weight = 59186.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033415 restraints weight = 46532.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.033663 restraints weight = 39985.469| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23100 Z= 0.159 Angle : 0.638 9.914 31488 Z= 0.325 Chirality : 0.043 0.180 3594 Planarity : 0.004 0.048 3996 Dihedral : 5.057 20.225 3084 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -1.29 (0.15), residues: 2847 helix: 1.10 (0.24), residues: 474 sheet: -0.65 (0.16), residues: 972 loop : -1.70 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 143 TYR 0.013 0.001 TYR J 91 PHE 0.014 0.001 PHE I 106 TRP 0.014 0.001 TRP C 153 HIS 0.006 0.001 HIS J 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (23028) covalent geometry : angle 0.62511 / 0.32 (31302) SS BOND : bond 0.00493 / 0.32 ( 30) SS BOND : angle 1.03107 / 0.66 ( 60) hydrogen bonds : bond 0.05050 / 3.35 ( 852) hydrogen bonds : angle 5.48334 / 3.82 ( 2466) link_ALPHA1-3 : bond 0.01727 / 0.87 ( 3) link_ALPHA1-3 : angle 2.92632 / 1.77 ( 9) link_BETA1-4 : bond 0.00516 / 0.35 ( 21) link_BETA1-4 : angle 1.47354 / 1.02 ( 63) link_BETA1-6 : bond 0.00369 / 0.19 ( 3) link_BETA1-6 : angle 2.30185 / 1.45 ( 9) link_NAG-ASN : bond 0.00403 / 0.24 ( 15) link_NAG-ASN : angle 2.35675 / 1.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.883 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: G 34 MET cc_start: 0.8937 (mmm) cc_final: 0.8464 (mmt) REVERT: G 99 MET cc_start: 0.9011 (mmm) cc_final: 0.8673 (mmm) REVERT: H 4 MET cc_start: 0.8613 (mmm) cc_final: 0.8155 (mmm) REVERT: H 193 TYR cc_start: 0.7820 (m-10) cc_final: 0.7391 (m-80) REVERT: I 3 GLN cc_start: 0.8002 (pm20) cc_final: 0.7740 (pm20) REVERT: I 34 MET cc_start: 0.9102 (mmm) cc_final: 0.8730 (mmt) REVERT: I 215 GLU cc_start: 0.5898 (pt0) cc_final: 0.5238 (mm-30) REVERT: K 46 GLU cc_start: 0.8302 (tt0) cc_final: 0.7720 (tt0) REVERT: K 77 ASN cc_start: 0.9359 (m-40) cc_final: 0.8859 (t0) REVERT: K 99 MET cc_start: 0.9029 (mmt) cc_final: 0.8470 (mmm) REVERT: K 211 ASP cc_start: 0.7784 (m-30) cc_final: 0.7503 (t0) REVERT: K 215 GLU cc_start: 0.6552 (pt0) cc_final: 0.5940 (mm-30) REVERT: L 4 MET cc_start: 0.8818 (mmm) cc_final: 0.8493 (tpp) REVERT: L 193 TYR cc_start: 0.7480 (m-10) cc_final: 0.7001 (m-80) REVERT: E 230 MET cc_start: 0.8912 (mtp) cc_final: 0.8580 (mtm) REVERT: D 149 MET cc_start: 0.8968 (mmt) cc_final: 0.8700 (mmm) REVERT: F 59 MET cc_start: 0.9128 (mmm) cc_final: 0.8883 (mmm) REVERT: F 149 MET cc_start: 0.9057 (mmt) cc_final: 0.8688 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2110 time to fit residues: 32.9020 Evaluate side-chains 73 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 265 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 ASN H 37 GLN I 77 ASN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN J 37 GLN L 37 GLN L 161 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.030518 restraints weight = 155812.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.031431 restraints weight = 87595.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.032034 restraints weight = 60714.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.032427 restraints weight = 47981.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.032614 restraints weight = 41294.200| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23100 Z= 0.195 Angle : 0.648 9.590 31488 Z= 0.331 Chirality : 0.044 0.194 3594 Planarity : 0.004 0.048 3996 Dihedral : 5.043 20.805 3084 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.96 (0.16), residues: 2847 helix: 1.57 (0.25), residues: 474 sheet: -0.47 (0.16), residues: 969 loop : -1.55 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 143 TYR 0.015 0.002 TYR F 157 PHE 0.012 0.001 PHE A 213 TRP 0.015 0.001 TRP C 153 HIS 0.007 0.001 HIS J 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (23028) covalent geometry : angle 0.63752 / 0.33 (31302) SS BOND : bond 0.00538 / 0.35 ( 30) SS BOND : angle 0.96208 / 0.64 ( 60) hydrogen bonds : bond 0.04961 / 3.30 ( 852) hydrogen bonds : angle 5.25555 / 3.67 ( 2466) link_ALPHA1-3 : bond 0.01003 / 0.50 ( 3) link_ALPHA1-3 : angle 2.36010 / 1.36 ( 9) link_BETA1-4 : bond 0.00509 / 0.35 ( 21) link_BETA1-4 : angle 1.35237 / 0.93 ( 63) link_BETA1-6 : bond 0.00333 / 0.17 ( 3) link_BETA1-6 : angle 2.25202 / 1.41 ( 9) link_NAG-ASN : bond 0.00485 / 0.29 ( 15) link_NAG-ASN : angle 2.20327 / 1.39 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.9027 (ttt) cc_final: 0.8785 (ttt) REVERT: G 46 GLU cc_start: 0.8426 (tt0) cc_final: 0.7887 (tt0) REVERT: G 99 MET cc_start: 0.9112 (mmm) cc_final: 0.8569 (mmm) REVERT: H 4 MET cc_start: 0.8521 (mmm) cc_final: 0.8182 (mmm) REVERT: H 193 TYR cc_start: 0.7444 (m-10) cc_final: 0.6932 (m-80) REVERT: H 195 CYS cc_start: 0.4271 (p) cc_final: 0.4061 (p) REVERT: I 3 GLN cc_start: 0.8102 (pm20) cc_final: 0.7842 (pm20) REVERT: I 34 MET cc_start: 0.9228 (mmm) cc_final: 0.8737 (mmt) REVERT: I 77 ASN cc_start: 0.9354 (m-40) cc_final: 0.8858 (t0) REVERT: I 215 GLU cc_start: 0.5683 (pt0) cc_final: 0.4950 (mm-30) REVERT: K 3 GLN cc_start: 0.7917 (pm20) cc_final: 0.7675 (pm20) REVERT: K 46 GLU cc_start: 0.8151 (tt0) cc_final: 0.7656 (tt0) REVERT: K 77 ASN cc_start: 0.9380 (m-40) cc_final: 0.8935 (t0) REVERT: K 99 MET cc_start: 0.9061 (mmt) cc_final: 0.8360 (mmm) REVERT: K 211 ASP cc_start: 0.7376 (m-30) cc_final: 0.7089 (t0) REVERT: J 150 LYS cc_start: 0.9065 (ptpp) cc_final: 0.8715 (mmmm) REVERT: L 4 MET cc_start: 0.8749 (mmm) cc_final: 0.8342 (tpp) REVERT: L 193 TYR cc_start: 0.7313 (m-10) cc_final: 0.6793 (m-80) REVERT: E 230 MET cc_start: 0.8959 (mtp) cc_final: 0.8711 (mtm) REVERT: D 149 MET cc_start: 0.8897 (mmt) cc_final: 0.8660 (mmm) REVERT: F 59 MET cc_start: 0.9122 (mmm) cc_final: 0.8869 (mmm) REVERT: F 149 MET cc_start: 0.9003 (mmt) cc_final: 0.8660 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2054 time to fit residues: 31.8191 Evaluate side-chains 72 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 5 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 145 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 174 GLN ** K 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN L 190 HIS C 32 HIS C 130 HIS ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 HIS ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.030451 restraints weight = 155829.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.031378 restraints weight = 86449.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.031956 restraints weight = 59659.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.032355 restraints weight = 47366.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032586 restraints weight = 40802.087| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23100 Z= 0.201 Angle : 0.639 9.357 31488 Z= 0.327 Chirality : 0.044 0.161 3594 Planarity : 0.004 0.046 3996 Dihedral : 4.998 21.269 3084 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.81 (0.16), residues: 2847 helix: 1.79 (0.25), residues: 474 sheet: -0.36 (0.17), residues: 963 loop : -1.49 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 104 TYR 0.013 0.002 TYR F 157 PHE 0.014 0.001 PHE B 140 TRP 0.014 0.001 TRP C 153 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (23028) covalent geometry : angle 0.62851 / 0.32 (31302) SS BOND : bond 0.00585 / 0.39 ( 30) SS BOND : angle 1.36641 / 0.86 ( 60) hydrogen bonds : bond 0.04900 / 3.25 ( 852) hydrogen bonds : angle 5.15329 / 3.60 ( 2466) link_ALPHA1-3 : bond 0.00858 / 0.43 ( 3) link_ALPHA1-3 : angle 2.06294 / 1.16 ( 9) link_BETA1-4 : bond 0.00498 / 0.34 ( 21) link_BETA1-4 : angle 1.34844 / 0.92 ( 63) link_BETA1-6 : bond 0.00276 / 0.14 ( 3) link_BETA1-6 : angle 2.24250 / 1.41 ( 9) link_NAG-ASN : bond 0.00473 / 0.29 ( 15) link_NAG-ASN : angle 2.11337 / 1.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.779 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: B 17 MET cc_start: 0.9008 (ttt) cc_final: 0.8766 (ttt) REVERT: G 99 MET cc_start: 0.9121 (mmm) cc_final: 0.8665 (mmm) REVERT: H 193 TYR cc_start: 0.7400 (m-10) cc_final: 0.6970 (m-80) REVERT: I 3 GLN cc_start: 0.8061 (pm20) cc_final: 0.7811 (pm20) REVERT: I 34 MET cc_start: 0.9276 (mmm) cc_final: 0.8865 (mmt) REVERT: I 77 ASN cc_start: 0.9324 (m-40) cc_final: 0.8860 (t0) REVERT: I 215 GLU cc_start: 0.5699 (pt0) cc_final: 0.4823 (mm-30) REVERT: K 46 GLU cc_start: 0.8136 (tt0) cc_final: 0.7651 (tt0) REVERT: K 77 ASN cc_start: 0.9369 (m-40) cc_final: 0.8997 (t0) REVERT: K 99 MET cc_start: 0.8993 (mmt) cc_final: 0.8259 (mmm) REVERT: K 211 ASP cc_start: 0.7388 (m-30) cc_final: 0.7040 (t0) REVERT: J 4 MET cc_start: 0.8732 (mmm) cc_final: 0.8460 (tpp) REVERT: J 150 LYS cc_start: 0.9097 (ptpp) cc_final: 0.8644 (mmmm) REVERT: L 4 MET cc_start: 0.8650 (mmm) cc_final: 0.8259 (tpp) REVERT: L 123 ASP cc_start: 0.8857 (p0) cc_final: 0.8590 (p0) REVERT: L 193 TYR cc_start: 0.7201 (m-10) cc_final: 0.6873 (m-80) REVERT: C 317 MET cc_start: 0.8764 (ttp) cc_final: 0.8551 (ttm) REVERT: E 230 MET cc_start: 0.8974 (mtp) cc_final: 0.8733 (mtm) REVERT: D 149 MET cc_start: 0.8882 (mmt) cc_final: 0.8673 (mmm) REVERT: F 59 MET cc_start: 0.9067 (mmm) cc_final: 0.8857 (mmm) REVERT: F 149 MET cc_start: 0.9012 (mmt) cc_final: 0.8776 (mmm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1936 time to fit residues: 26.8798 Evaluate side-chains 69 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 164 optimal weight: 6.9990 chunk 252 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 GLN H 37 GLN I 174 GLN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.031284 restraints weight = 157383.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.032276 restraints weight = 84783.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.032919 restraints weight = 57517.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.033323 restraints weight = 44915.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.033553 restraints weight = 38558.202| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23100 Z= 0.112 Angle : 0.570 8.855 31488 Z= 0.291 Chirality : 0.043 0.156 3594 Planarity : 0.004 0.044 3996 Dihedral : 4.703 23.423 3084 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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 (0.16), residues: 2847 helix: 2.03 (0.25), residues: 495 sheet: -0.17 (0.17), residues: 960 loop : -1.48 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 67 TYR 0.010 0.001 TYR H 193 PHE 0.011 0.001 PHE B 140 TRP 0.010 0.001 TRP E 153 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (23028) covalent geometry : angle 0.56198 / 0.29 (31302) SS BOND : bond 0.00403 / 0.27 ( 30) SS BOND : angle 1.02393 / 0.63 ( 60) hydrogen bonds : bond 0.04482 / 2.97 ( 852) hydrogen bonds : angle 4.86822 / 3.41 ( 2466) link_ALPHA1-3 : bond 0.00826 / 0.41 ( 3) link_ALPHA1-3 : angle 1.70995 / 1.00 ( 9) link_BETA1-4 : bond 0.00470 / 0.32 ( 21) link_BETA1-4 : angle 1.25634 / 0.87 ( 63) link_BETA1-6 : bond 0.00384 / 0.19 ( 3) link_BETA1-6 : angle 1.83792 / 1.16 ( 9) link_NAG-ASN : bond 0.00281 / 0.17 ( 15) link_NAG-ASN : angle 1.77402 / 1.13 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.843 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 317 MET cc_start: 0.8862 (ttt) cc_final: 0.8638 (ttm) REVERT: G 34 MET cc_start: 0.9298 (mmt) cc_final: 0.9070 (mmt) REVERT: G 99 MET cc_start: 0.9039 (mmm) cc_final: 0.8585 (mmm) REVERT: H 4 MET cc_start: 0.8500 (mmm) cc_final: 0.8212 (tpp) REVERT: H 146 LYS cc_start: 0.7837 (mppt) cc_final: 0.7165 (tmmt) REVERT: H 150 LYS cc_start: 0.8947 (pttm) cc_final: 0.8392 (mmmm) REVERT: H 193 TYR cc_start: 0.7489 (m-10) cc_final: 0.6880 (m-80) REVERT: H 195 CYS cc_start: 0.2863 (p) cc_final: -0.0221 (p) REVERT: I 3 GLN cc_start: 0.8149 (pm20) cc_final: 0.7863 (pm20) REVERT: I 34 MET cc_start: 0.9334 (mmm) cc_final: 0.8984 (mmt) REVERT: I 77 ASN cc_start: 0.9353 (m-40) cc_final: 0.8921 (t0) REVERT: I 151 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7973 (tm-30) REVERT: K 3 GLN cc_start: 0.7906 (pm20) cc_final: 0.7625 (pm20) REVERT: K 46 GLU cc_start: 0.8229 (tt0) cc_final: 0.7660 (tt0) REVERT: K 77 ASN cc_start: 0.9357 (m-40) cc_final: 0.9011 (t0) REVERT: K 211 ASP cc_start: 0.7115 (m-30) cc_final: 0.6800 (t0) REVERT: J 4 MET cc_start: 0.8711 (mmm) cc_final: 0.7924 (mmm) REVERT: J 150 LYS cc_start: 0.9096 (ptpp) cc_final: 0.8760 (mmmm) REVERT: L 4 MET cc_start: 0.8676 (mmm) cc_final: 0.8328 (tpp) REVERT: L 193 TYR cc_start: 0.7409 (m-10) cc_final: 0.6735 (m-80) REVERT: E 230 MET cc_start: 0.8922 (mtp) cc_final: 0.8685 (mtm) REVERT: F 59 MET cc_start: 0.9043 (mmm) cc_final: 0.8792 (mmm) REVERT: F 149 MET cc_start: 0.8957 (mmt) cc_final: 0.8628 (mmm) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1841 time to fit residues: 28.2394 Evaluate side-chains 74 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 191 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 183 HIS ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 174 GLN I 200 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN L 156 GLN L 167 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.044844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.030056 restraints weight = 159163.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.030962 restraints weight = 90536.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.031539 restraints weight = 63250.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.031916 restraints weight = 50342.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.032163 restraints weight = 43570.783| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23100 Z= 0.215 Angle : 0.647 9.327 31488 Z= 0.329 Chirality : 0.044 0.169 3594 Planarity : 0.004 0.047 3996 Dihedral : 4.933 22.888 3084 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2847 helix: 1.93 (0.24), residues: 495 sheet: -0.15 (0.17), residues: 948 loop : -1.46 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 143 TYR 0.014 0.002 TYR K 94 PHE 0.012 0.002 PHE K 95 TRP 0.014 0.002 TRP C 153 HIS 0.006 0.001 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (23028) covalent geometry : angle 0.63787 / 0.33 (31302) SS BOND : bond 0.00591 / 0.38 ( 30) SS BOND : angle 1.13647 / 0.75 ( 60) hydrogen bonds : bond 0.04926 / 3.25 ( 852) hydrogen bonds : angle 5.01536 / 3.50 ( 2466) link_ALPHA1-3 : bond 0.00875 / 0.44 ( 3) link_ALPHA1-3 : angle 1.77027 / 1.06 ( 9) link_BETA1-4 : bond 0.00496 / 0.34 ( 21) link_BETA1-4 : angle 1.31428 / 0.90 ( 63) link_BETA1-6 : bond 0.00331 / 0.17 ( 3) link_BETA1-6 : angle 2.39970 / 1.50 ( 9) link_NAG-ASN : bond 0.00467 / 0.29 ( 15) link_NAG-ASN : angle 2.04760 / 1.31 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.937 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: H 4 MET cc_start: 0.8519 (mmm) cc_final: 0.8206 (tpp) REVERT: H 193 TYR cc_start: 0.7324 (m-10) cc_final: 0.6647 (m-80) REVERT: I 3 GLN cc_start: 0.8103 (pm20) cc_final: 0.7817 (pm20) REVERT: I 34 MET cc_start: 0.9347 (mmm) cc_final: 0.9008 (mmt) REVERT: I 77 ASN cc_start: 0.9300 (m-40) cc_final: 0.8901 (t0) REVERT: I 99 MET cc_start: 0.9225 (mmm) cc_final: 0.8260 (mmm) REVERT: K 3 GLN cc_start: 0.7946 (pm20) cc_final: 0.7654 (pm20) REVERT: K 46 GLU cc_start: 0.8241 (tt0) cc_final: 0.7626 (tt0) REVERT: K 77 ASN cc_start: 0.9391 (m-40) cc_final: 0.9067 (t0) REVERT: K 211 ASP cc_start: 0.7080 (m-30) cc_final: 0.6682 (t0) REVERT: J 150 LYS cc_start: 0.9189 (ptpp) cc_final: 0.8735 (mmmm) REVERT: L 193 TYR cc_start: 0.7317 (m-10) cc_final: 0.6752 (m-80) REVERT: E 230 MET cc_start: 0.9010 (mtp) cc_final: 0.8732 (mtm) REVERT: F 59 MET cc_start: 0.9119 (mmm) cc_final: 0.8874 (mmm) REVERT: F 98 LEU cc_start: 0.9461 (tp) cc_final: 0.9226 (tp) REVERT: F 149 MET cc_start: 0.8923 (mmt) cc_final: 0.8576 (mmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1925 time to fit residues: 25.8968 Evaluate side-chains 67 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 70 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 156 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN C 150 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.044026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.029521 restraints weight = 164808.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.030360 restraints weight = 96506.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.030896 restraints weight = 68738.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.031241 restraints weight = 55496.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031462 restraints weight = 48620.092| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 23100 Z= 0.324 Angle : 0.764 11.383 31488 Z= 0.389 Chirality : 0.046 0.184 3594 Planarity : 0.004 0.045 3996 Dihedral : 5.426 23.673 3084 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.88 (0.16), residues: 2847 helix: 1.65 (0.24), residues: 474 sheet: -0.31 (0.17), residues: 936 loop : -1.57 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 116 TYR 0.026 0.002 TYR E 161 PHE 0.018 0.002 PHE B 3 TRP 0.022 0.002 TRP C 153 HIS 0.007 0.002 HIS E 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.32 (23028) covalent geometry : angle 0.75428 / 0.39 (31302) SS BOND : bond 0.00721 / 0.46 ( 30) SS BOND : angle 1.47988 / 0.98 ( 60) hydrogen bonds : bond 0.05421 / 3.59 ( 852) hydrogen bonds : angle 5.33090 / 3.71 ( 2466) link_ALPHA1-3 : bond 0.00833 / 0.42 ( 3) link_ALPHA1-3 : angle 1.82987 / 1.08 ( 9) link_BETA1-4 : bond 0.00556 / 0.38 ( 21) link_BETA1-4 : angle 1.38831 / 0.95 ( 63) link_BETA1-6 : bond 0.00223 / 0.11 ( 3) link_BETA1-6 : angle 2.66039 / 1.66 ( 9) link_NAG-ASN : bond 0.00659 / 0.41 ( 15) link_NAG-ASN : angle 2.28026 / 1.47 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.842 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: H 4 MET cc_start: 0.8448 (mmm) cc_final: 0.8025 (mmm) REVERT: I 34 MET cc_start: 0.9381 (mmm) cc_final: 0.9014 (mmt) REVERT: I 77 ASN cc_start: 0.9268 (m-40) cc_final: 0.8930 (t0) REVERT: K 3 GLN cc_start: 0.8026 (pm20) cc_final: 0.7723 (pm20) REVERT: K 99 MET cc_start: 0.9143 (mmt) cc_final: 0.8524 (mmm) REVERT: K 211 ASP cc_start: 0.7181 (m-30) cc_final: 0.6701 (t0) REVERT: L 4 MET cc_start: 0.8534 (mmp) cc_final: 0.8221 (mmm) REVERT: E 230 MET cc_start: 0.9124 (mtp) cc_final: 0.8888 (mtm) REVERT: F 59 MET cc_start: 0.9158 (mmm) cc_final: 0.8866 (mmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1972 time to fit residues: 23.1353 Evaluate side-chains 58 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 89 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 101 optimal weight: 0.0170 chunk 121 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 174 GLN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.031147 restraints weight = 161984.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.032039 restraints weight = 93033.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.032603 restraints weight = 65513.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.032983 restraints weight = 52568.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.033206 restraints weight = 45699.829| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23100 Z= 0.118 Angle : 0.610 10.611 31488 Z= 0.309 Chirality : 0.043 0.164 3594 Planarity : 0.004 0.044 3996 Dihedral : 4.888 22.556 3084 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.41 (0.16), residues: 2847 helix: 2.27 (0.25), residues: 477 sheet: -0.06 (0.17), residues: 942 loop : -1.33 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 104 TYR 0.030 0.001 TYR A 161 PHE 0.010 0.001 PHE B 9 TRP 0.018 0.001 TRP A 127 HIS 0.010 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (23028) covalent geometry : angle 0.60286 / 0.31 (31302) SS BOND : bond 0.00451 / 0.31 ( 30) SS BOND : angle 0.95601 / 0.62 ( 60) hydrogen bonds : bond 0.04663 / 3.09 ( 852) hydrogen bonds : angle 4.86112 / 3.40 ( 2466) link_ALPHA1-3 : bond 0.00789 / 0.39 ( 3) link_ALPHA1-3 : angle 1.63690 / 0.97 ( 9) link_BETA1-4 : bond 0.00451 / 0.30 ( 21) link_BETA1-4 : angle 1.24489 / 0.86 ( 63) link_BETA1-6 : bond 0.00420 / 0.21 ( 3) link_BETA1-6 : angle 1.81630 / 1.16 ( 9) link_NAG-ASN : bond 0.00322 / 0.20 ( 15) link_NAG-ASN : angle 1.75535 / 1.11 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.876 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 317 MET cc_start: 0.9073 (ttt) cc_final: 0.8870 (ttm) REVERT: B 59 MET cc_start: 0.8946 (mmm) cc_final: 0.8708 (mmm) REVERT: G 3 GLN cc_start: 0.8180 (pm20) cc_final: 0.7276 (pm20) REVERT: H 4 MET cc_start: 0.8398 (mmm) cc_final: 0.8103 (tpp) REVERT: H 146 LYS cc_start: 0.7909 (mppt) cc_final: 0.7418 (tppt) REVERT: H 193 TYR cc_start: 0.6789 (m-10) cc_final: 0.6357 (m-80) REVERT: I 3 GLN cc_start: 0.8202 (pm20) cc_final: 0.7905 (pm20) REVERT: I 34 MET cc_start: 0.9358 (mmm) cc_final: 0.8987 (mmt) REVERT: I 77 ASN cc_start: 0.9265 (m-40) cc_final: 0.8944 (t0) REVERT: K 3 GLN cc_start: 0.8073 (pm20) cc_final: 0.7760 (pm20) REVERT: K 46 GLU cc_start: 0.8327 (tt0) cc_final: 0.7784 (tt0) REVERT: K 77 ASN cc_start: 0.9367 (m-40) cc_final: 0.9042 (t0) REVERT: K 99 MET cc_start: 0.9091 (mmt) cc_final: 0.8192 (mpp) REVERT: K 211 ASP cc_start: 0.7155 (m-30) cc_final: 0.6688 (t0) REVERT: J 4 MET cc_start: 0.8674 (mmm) cc_final: 0.7906 (mmm) REVERT: J 150 LYS cc_start: 0.9076 (ptpp) cc_final: 0.8640 (mmtm) REVERT: L 4 MET cc_start: 0.8720 (mmp) cc_final: 0.8444 (mmm) REVERT: L 127 LYS cc_start: 0.8660 (pttt) cc_final: 0.8437 (ptpp) REVERT: E 230 MET cc_start: 0.9091 (mtp) cc_final: 0.8862 (mtm) REVERT: F 59 MET cc_start: 0.9113 (mmm) cc_final: 0.8764 (mmm) REVERT: F 98 LEU cc_start: 0.9394 (tp) cc_final: 0.9177 (tp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1900 time to fit residues: 24.2069 Evaluate side-chains 68 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 181 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 ASN I 174 GLN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.030153 restraints weight = 165605.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.031022 restraints weight = 96236.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.031576 restraints weight = 68081.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.031918 restraints weight = 54671.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.032150 restraints weight = 47819.877| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 23100 Z= 0.227 Angle : 0.668 9.984 31488 Z= 0.338 Chirality : 0.044 0.162 3594 Planarity : 0.004 0.045 3996 Dihedral : 5.064 23.352 3084 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.54 (0.16), residues: 2847 helix: 2.13 (0.25), residues: 471 sheet: -0.13 (0.17), residues: 933 loop : -1.39 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 229 TYR 0.028 0.002 TYR A 161 PHE 0.013 0.002 PHE K 95 TRP 0.017 0.002 TRP E 153 HIS 0.006 0.001 HIS H 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.23 (23028) covalent geometry : angle 0.65995 / 0.34 (31302) SS BOND : bond 0.00589 / 0.39 ( 30) SS BOND : angle 1.12810 / 0.72 ( 60) hydrogen bonds : bond 0.04980 / 3.30 ( 852) hydrogen bonds : angle 5.00155 / 3.49 ( 2466) link_ALPHA1-3 : bond 0.00871 / 0.44 ( 3) link_ALPHA1-3 : angle 1.69850 / 1.03 ( 9) link_BETA1-4 : bond 0.00496 / 0.34 ( 21) link_BETA1-4 : angle 1.29014 / 0.89 ( 63) link_BETA1-6 : bond 0.00286 / 0.14 ( 3) link_BETA1-6 : angle 2.32722 / 1.46 ( 9) link_NAG-ASN : bond 0.00466 / 0.29 ( 15) link_NAG-ASN : angle 1.96234 / 1.26 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.882 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: H 4 MET cc_start: 0.8481 (mmm) cc_final: 0.8149 (tpp) REVERT: H 146 LYS cc_start: 0.7930 (mppt) cc_final: 0.7337 (tppt) REVERT: H 193 TYR cc_start: 0.6767 (m-10) cc_final: 0.6363 (m-80) REVERT: I 3 GLN cc_start: 0.8117 (pm20) cc_final: 0.7821 (pm20) REVERT: I 34 MET cc_start: 0.9376 (mmm) cc_final: 0.9008 (mmt) REVERT: I 77 ASN cc_start: 0.9261 (m-40) cc_final: 0.8955 (t0) REVERT: K 3 GLN cc_start: 0.8051 (pm20) cc_final: 0.7767 (pm20) REVERT: K 77 ASN cc_start: 0.9375 (m-40) cc_final: 0.9060 (t0) REVERT: K 99 MET cc_start: 0.9096 (mmt) cc_final: 0.8496 (mmm) REVERT: K 211 ASP cc_start: 0.7143 (m-30) cc_final: 0.6706 (t0) REVERT: J 4 MET cc_start: 0.8665 (mmm) cc_final: 0.7834 (mmm) REVERT: J 150 LYS cc_start: 0.9078 (ptpp) cc_final: 0.8680 (mmtm) REVERT: L 4 MET cc_start: 0.8763 (mmp) cc_final: 0.8411 (mmm) REVERT: E 230 MET cc_start: 0.9059 (mtp) cc_final: 0.8796 (mtm) REVERT: F 59 MET cc_start: 0.9136 (mmm) cc_final: 0.8826 (mmm) REVERT: F 86 ASP cc_start: 0.9036 (m-30) cc_final: 0.8754 (p0) REVERT: F 98 LEU cc_start: 0.9453 (tp) cc_final: 0.9236 (tp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1780 time to fit residues: 21.6955 Evaluate side-chains 67 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 139 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 247 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 174 GLN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.044809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.030275 restraints weight = 164200.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.031142 restraints weight = 95403.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.031696 restraints weight = 67646.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.032045 restraints weight = 54328.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.032218 restraints weight = 47432.940| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23100 Z= 0.205 Angle : 0.649 9.925 31488 Z= 0.330 Chirality : 0.044 0.162 3594 Planarity : 0.004 0.043 3996 Dihedral : 5.065 28.179 3084 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.54 (0.16), residues: 2847 helix: 2.16 (0.25), residues: 471 sheet: -0.15 (0.17), residues: 942 loop : -1.38 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 104 TYR 0.021 0.002 TYR A 161 PHE 0.012 0.001 PHE K 95 TRP 0.017 0.001 TRP E 153 HIS 0.015 0.001 HIS H 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (23028) covalent geometry : angle 0.64110 / 0.33 (31302) SS BOND : bond 0.00563 / 0.37 ( 30) SS BOND : angle 1.13899 / 0.71 ( 60) hydrogen bonds : bond 0.04870 / 3.23 ( 852) hydrogen bonds : angle 4.95104 / 3.46 ( 2466) link_ALPHA1-3 : bond 0.00841 / 0.42 ( 3) link_ALPHA1-3 : angle 1.66597 / 1.01 ( 9) link_BETA1-4 : bond 0.00472 / 0.32 ( 21) link_BETA1-4 : angle 1.27665 / 0.88 ( 63) link_BETA1-6 : bond 0.00303 / 0.15 ( 3) link_BETA1-6 : angle 2.16539 / 1.37 ( 9) link_NAG-ASN : bond 0.00444 / 0.27 ( 15) link_NAG-ASN : angle 1.93245 / 1.24 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3698.52 seconds wall clock time: 65 minutes 27.15 seconds (3927.15 seconds total)