Starting phenix.real_space_refine on Fri Sep 19 03:40:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hjq_0236/09_2025/6hjq_0236.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjq_0236/09_2025/6hjq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2025/6hjq_0236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2025/6hjq_0236.map" model { file = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2025/6hjq_0236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjq_0236/09_2025/6hjq_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.55, per 1000 atoms: 0.20 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: 1.91 Conformation dependent library (CDL) restraints added in 990.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.91 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: 4.14 Time building geometry restraints manager: 2.52 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 - 20.77: 13600 20.77 - 41.53: 480 41.53 - 62.30: 68 62.30 - 83.07: 42 83.07 - 103.83: 33 Dihedral angle restraints: 14223 sinusoidal: 5958 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 14220 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: 12.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.490 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 12.717 103.832 8853 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 aren 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 covalent geometry : bond 0.00570 (23028) covalent geometry : angle 0.94023 (31302) SS BOND : bond 0.00752 ( 30) SS BOND : angle 1.45606 ( 60) hydrogen bonds : bond 0.19161 ( 852) hydrogen bonds : angle 7.47762 ( 2466) link_ALPHA1-3 : bond 0.06152 ( 3) link_ALPHA1-3 : angle 7.55410 ( 9) link_BETA1-4 : bond 0.01368 ( 21) link_BETA1-4 : angle 2.90263 ( 63) link_BETA1-6 : bond 0.00201 ( 3) link_BETA1-6 : angle 4.81926 ( 9) link_NAG-ASN : bond 0.00703 ( 15) link_NAG-ASN : angle 4.41552 ( 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 : 0.893 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: 0.8308 (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: 0.8771 (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: 0.2462 time to fit residues: 79.8798 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 : 0.902 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 108 GLN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.047640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.033011 restraints weight = 156201.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.034030 restraints weight = 83270.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.034695 restraints weight = 55971.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.035108 restraints weight = 43318.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.035384 restraints weight = 36931.444| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23100 Z= 0.142 Angle : 0.681 11.484 31488 Z= 0.348 Chirality : 0.046 0.306 3594 Planarity : 0.004 0.054 3996 Dihedral : 10.744 78.113 3936 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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 aren not related in a simple way. whole: -1.83 (0.15), residues: 2847 helix: 0.13 (0.22), residues: 471 sheet: -0.80 (0.16), residues: 915 loop : -1.97 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG J 212 TYR 0.012 0.001 TYR H 91 PHE 0.012 0.001 PHE E 213 TRP 0.015 0.001 TRP C 153 HIS 0.004 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00291 (23028) covalent geometry : angle 0.66647 (31302) SS BOND : bond 0.00491 ( 30) SS BOND : angle 1.03524 ( 60) hydrogen bonds : bond 0.05401 ( 852) hydrogen bonds : angle 5.87634 ( 2466) link_ALPHA1-3 : bond 0.04917 ( 3) link_ALPHA1-3 : angle 2.53997 ( 9) link_BETA1-4 : bond 0.00724 ( 21) link_BETA1-4 : angle 1.91495 ( 63) link_BETA1-6 : bond 0.00382 ( 3) link_BETA1-6 : angle 2.28352 ( 9) link_NAG-ASN : bond 0.00477 ( 15) link_NAG-ASN : angle 2.58792 ( 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 140 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.912 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: G 34 MET cc_start: 0.8762 (mmm) cc_final: 0.8549 (tpp) REVERT: H 4 MET cc_start: 0.8636 (mmm) cc_final: 0.8160 (mmm) REVERT: H 146 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7867 (ttpp) REVERT: H 193 TYR cc_start: 0.7810 (m-10) cc_final: 0.7445 (m-80) REVERT: H 211 ASN cc_start: 0.6477 (m-40) cc_final: 0.6160 (p0) REVERT: I 34 MET cc_start: 0.9065 (mmm) cc_final: 0.8718 (mmt) REVERT: I 215 GLU cc_start: 0.5674 (pt0) cc_final: 0.5102 (mm-30) REVERT: K 34 MET cc_start: 0.9089 (mmm) cc_final: 0.8414 (mmt) REVERT: K 77 ASN cc_start: 0.9339 (m-40) cc_final: 0.8811 (t0) REVERT: K 99 MET cc_start: 0.9039 (mmt) cc_final: 0.8498 (mmm) REVERT: K 215 GLU cc_start: 0.6452 (pt0) cc_final: 0.5945 (mm-30) REVERT: J 4 MET cc_start: 0.8174 (mmm) cc_final: 0.7826 (mmm) REVERT: L 4 MET cc_start: 0.8804 (mmm) cc_final: 0.8443 (mmm) REVERT: L 24 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7788 (ttm-80) REVERT: L 193 TYR cc_start: 0.7659 (m-10) cc_final: 0.6191 (m-80) REVERT: D 149 MET cc_start: 0.8962 (mmt) cc_final: 0.8557 (mmm) REVERT: F 59 MET cc_start: 0.9010 (mmm) cc_final: 0.8750 (mmm) REVERT: F 149 MET cc_start: 0.9045 (mmt) cc_final: 0.8687 (mmm) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2187 time to fit residues: 43.6723 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 : 0.674 ------------------------------------------------------------------------------- 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: 4.9990 chunk 111 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN G 109 ASN G 200 ASN H 6 GLN H 37 GLN I 77 ASN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 37 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 161 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 = 0.3103 r_free = 0.3103 target = 0.044635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.029753 restraints weight = 158192.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.030653 restraints weight = 89171.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.031212 restraints weight = 62140.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031602 restraints weight = 49643.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.031797 restraints weight = 42688.176| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23100 Z= 0.289 Angle : 0.756 10.137 31488 Z= 0.383 Chirality : 0.046 0.207 3594 Planarity : 0.005 0.052 3996 Dihedral : 9.694 69.679 3936 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.13 % Allowed : 3.14 % Favored : 96.74 % 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 aren not related in a simple way. whole: -1.43 (0.15), residues: 2847 helix: 0.87 (0.23), residues: 474 sheet: -0.67 (0.16), residues: 939 loop : -1.79 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 143 TYR 0.019 0.002 TYR F 157 PHE 0.022 0.002 PHE I 106 TRP 0.019 0.002 TRP K 112 HIS 0.007 0.002 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00632 (23028) covalent geometry : angle 0.74216 (31302) SS BOND : bond 0.00683 ( 30) SS BOND : angle 1.10913 ( 60) hydrogen bonds : bond 0.05605 ( 852) hydrogen bonds : angle 5.71091 ( 2466) link_ALPHA1-3 : bond 0.03775 ( 3) link_ALPHA1-3 : angle 2.92592 ( 9) link_BETA1-4 : bond 0.00664 ( 21) link_BETA1-4 : angle 1.76030 ( 63) link_BETA1-6 : bond 0.00289 ( 3) link_BETA1-6 : angle 2.98053 ( 9) link_NAG-ASN : bond 0.00668 ( 15) link_NAG-ASN : angle 2.67359 ( 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 99 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.942 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: G 34 MET cc_start: 0.9094 (mmm) cc_final: 0.8723 (mmt) REVERT: G 99 MET cc_start: 0.9219 (mmm) cc_final: 0.8666 (mmm) REVERT: H 4 MET cc_start: 0.8525 (mmm) cc_final: 0.8066 (mmm) REVERT: H 146 LYS cc_start: 0.8244 (mmtp) cc_final: 0.7698 (tmmt) REVERT: H 193 TYR cc_start: 0.7462 (m-10) cc_final: 0.7020 (m-80) REVERT: I 34 MET cc_start: 0.9183 (mmm) cc_final: 0.8807 (mmt) REVERT: I 215 GLU cc_start: 0.5503 (pt0) cc_final: 0.4749 (mm-30) REVERT: K 34 MET cc_start: 0.9223 (mmm) cc_final: 0.8978 (mmt) REVERT: K 46 GLU cc_start: 0.8195 (tt0) cc_final: 0.7718 (tt0) REVERT: K 211 ASP cc_start: 0.7695 (m-30) cc_final: 0.7400 (t0) REVERT: J 4 MET cc_start: 0.8464 (mmm) cc_final: 0.8084 (mmm) REVERT: L 4 MET cc_start: 0.8774 (mmm) cc_final: 0.8196 (mmm) REVERT: L 193 TYR cc_start: 0.7427 (m-10) cc_final: 0.6735 (m-80) REVERT: E 230 MET cc_start: 0.9034 (mtp) cc_final: 0.8697 (mtm) REVERT: D 59 MET cc_start: 0.9069 (mmm) cc_final: 0.8716 (mmt) REVERT: D 149 MET cc_start: 0.9005 (mmt) cc_final: 0.8735 (mmm) REVERT: F 59 MET cc_start: 0.9138 (mmm) cc_final: 0.8904 (mmm) REVERT: F 149 MET cc_start: 0.9072 (mmt) cc_final: 0.8692 (mmm) outliers start: 3 outliers final: 0 residues processed: 99 average time/residue: 0.1989 time to fit residues: 28.8483 Evaluate side-chains 66 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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: 8.9990 chunk 100 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 77 ASN I 174 GLN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN J 190 HIS L 6 GLN L 37 GLN ** 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 = 0.3122 r_free = 0.3122 target = 0.045224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.030317 restraints weight = 155944.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.031231 restraints weight = 87701.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.031814 restraints weight = 60983.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.032118 restraints weight = 48311.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.032416 restraints weight = 42410.667| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23100 Z= 0.179 Angle : 0.644 9.743 31488 Z= 0.327 Chirality : 0.044 0.190 3594 Planarity : 0.004 0.046 3996 Dihedral : 9.030 63.348 3936 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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 aren not related in a simple way. whole: -1.08 (0.16), residues: 2847 helix: 1.50 (0.24), residues: 474 sheet: -0.54 (0.16), residues: 969 loop : -1.63 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 104 TYR 0.013 0.001 TYR F 157 PHE 0.013 0.001 PHE A 213 TRP 0.013 0.001 TRP C 153 HIS 0.007 0.001 HIS H 190 Details of bonding type rmsd covalent geometry : bond 0.00388 (23028) covalent geometry : angle 0.63113 (31302) SS BOND : bond 0.00597 ( 30) SS BOND : angle 1.09001 ( 60) hydrogen bonds : bond 0.05049 ( 852) hydrogen bonds : angle 5.35062 ( 2466) link_ALPHA1-3 : bond 0.04004 ( 3) link_ALPHA1-3 : angle 2.86356 ( 9) link_BETA1-4 : bond 0.00554 ( 21) link_BETA1-4 : angle 1.62061 ( 63) link_BETA1-6 : bond 0.00338 ( 3) link_BETA1-6 : angle 2.38090 ( 9) link_NAG-ASN : bond 0.00475 ( 15) link_NAG-ASN : angle 2.22971 ( 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 : 1.151 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: B 17 MET cc_start: 0.9016 (ttt) cc_final: 0.8724 (ttt) REVERT: G 99 MET cc_start: 0.9059 (mmm) cc_final: 0.8662 (mmm) REVERT: H 193 TYR cc_start: 0.7419 (m-10) cc_final: 0.7060 (m-80) REVERT: I 3 GLN cc_start: 0.8194 (pm20) cc_final: 0.7978 (pm20) REVERT: I 34 MET cc_start: 0.9223 (mmm) cc_final: 0.8679 (mmt) REVERT: I 77 ASN cc_start: 0.9381 (m-40) cc_final: 0.8828 (t0) REVERT: I 215 GLU cc_start: 0.5506 (pt0) cc_final: 0.4727 (mm-30) REVERT: K 34 MET cc_start: 0.9365 (mmm) cc_final: 0.8884 (mmt) REVERT: K 46 GLU cc_start: 0.8254 (tt0) cc_final: 0.7709 (tt0) REVERT: K 211 ASP cc_start: 0.7552 (m-30) cc_final: 0.7177 (t0) REVERT: J 4 MET cc_start: 0.8439 (mmm) cc_final: 0.8062 (tpp) REVERT: J 150 LYS cc_start: 0.9076 (ptpp) cc_final: 0.8709 (mmmm) REVERT: L 4 MET cc_start: 0.8728 (mmm) cc_final: 0.8316 (tpp) REVERT: C 317 MET cc_start: 0.8892 (ttt) cc_final: 0.8581 (ttm) REVERT: E 230 MET cc_start: 0.9014 (mtp) cc_final: 0.8726 (mtm) REVERT: D 59 MET cc_start: 0.9048 (mmm) cc_final: 0.8780 (mmt) REVERT: D 149 MET cc_start: 0.8903 (mmt) cc_final: 0.8649 (mmm) REVERT: F 59 MET cc_start: 0.9157 (mmm) cc_final: 0.8859 (mmm) REVERT: F 149 MET cc_start: 0.9017 (mmt) cc_final: 0.8612 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2268 time to fit residues: 35.1346 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 : 1.026 ------------------------------------------------------------------------------- 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: 0.9990 chunk 227 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN ** A 296 GLN ** 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 109 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN L 167 GLN C 32 HIS ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** 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 = 0.3078 r_free = 0.3078 target = 0.044144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.029143 restraints weight = 156426.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.030013 restraints weight = 90327.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.030580 restraints weight = 63598.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.030946 restraints weight = 50762.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.031065 restraints weight = 43948.269| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 23100 Z= 0.258 Angle : 0.703 9.408 31488 Z= 0.357 Chirality : 0.045 0.186 3594 Planarity : 0.004 0.048 3996 Dihedral : 8.700 58.886 3936 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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 aren not related in a simple way. whole: -0.99 (0.16), residues: 2847 helix: 1.60 (0.25), residues: 474 sheet: -0.43 (0.17), residues: 945 loop : -1.63 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.015 0.002 TYR H 86 PHE 0.016 0.002 PHE B 140 TRP 0.014 0.002 TRP E 153 HIS 0.007 0.002 HIS H 190 Details of bonding type rmsd covalent geometry : bond 0.00563 (23028) covalent geometry : angle 0.69043 (31302) SS BOND : bond 0.00718 ( 30) SS BOND : angle 1.37977 ( 60) hydrogen bonds : bond 0.05187 ( 852) hydrogen bonds : angle 5.40817 ( 2466) link_ALPHA1-3 : bond 0.03699 ( 3) link_ALPHA1-3 : angle 2.70822 ( 9) link_BETA1-4 : bond 0.00591 ( 21) link_BETA1-4 : angle 1.63200 ( 63) link_BETA1-6 : bond 0.00308 ( 3) link_BETA1-6 : angle 2.69260 ( 9) link_NAG-ASN : bond 0.00604 ( 15) link_NAG-ASN : angle 2.29889 ( 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 95 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.929 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 99 MET cc_start: 0.9159 (mmm) cc_final: 0.8624 (mmm) REVERT: H 193 TYR cc_start: 0.7090 (m-10) cc_final: 0.6481 (m-80) REVERT: I 34 MET cc_start: 0.9316 (mmm) cc_final: 0.8896 (mmt) REVERT: I 77 ASN cc_start: 0.9349 (m-40) cc_final: 0.8879 (t0) REVERT: I 99 MET cc_start: 0.9050 (mmm) cc_final: 0.8834 (mmm) REVERT: I 215 GLU cc_start: 0.5575 (pt0) cc_final: 0.4660 (mm-30) REVERT: K 34 MET cc_start: 0.9386 (mmm) cc_final: 0.9041 (mmt) REVERT: K 46 GLU cc_start: 0.8151 (tt0) cc_final: 0.7638 (tt0) REVERT: K 211 ASP cc_start: 0.7395 (m-30) cc_final: 0.6993 (t0) REVERT: J 4 MET cc_start: 0.8538 (mmm) cc_final: 0.8116 (tpp) REVERT: J 150 LYS cc_start: 0.9115 (ptpp) cc_final: 0.8656 (mmmm) REVERT: L 4 MET cc_start: 0.8680 (mmm) cc_final: 0.8252 (tpp) REVERT: E 230 MET cc_start: 0.9020 (mtp) cc_final: 0.8752 (mtm) REVERT: D 59 MET cc_start: 0.8918 (mmm) cc_final: 0.8683 (mmt) REVERT: F 59 MET cc_start: 0.9111 (mmm) cc_final: 0.8861 (mmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2158 time to fit residues: 30.2512 Evaluate side-chains 64 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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: 5.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 H 156 GLN I 174 GLN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN L 156 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 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.043913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.028948 restraints weight = 157708.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.029806 restraints weight = 90704.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.030364 restraints weight = 63834.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.030725 restraints weight = 50950.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.030972 restraints weight = 44182.221| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 23100 Z= 0.251 Angle : 0.685 9.215 31488 Z= 0.348 Chirality : 0.045 0.196 3594 Planarity : 0.004 0.045 3996 Dihedral : 8.297 58.873 3936 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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 aren not related in a simple way. whole: -0.92 (0.16), residues: 2847 helix: 1.72 (0.25), residues: 474 sheet: -0.36 (0.17), residues: 936 loop : -1.62 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 87 TYR 0.016 0.002 TYR H 86 PHE 0.014 0.002 PHE K 95 TRP 0.017 0.002 TRP A 153 HIS 0.006 0.002 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00549 (23028) covalent geometry : angle 0.67329 (31302) SS BOND : bond 0.00599 ( 30) SS BOND : angle 1.17942 ( 60) hydrogen bonds : bond 0.05150 ( 852) hydrogen bonds : angle 5.30664 ( 2466) link_ALPHA1-3 : bond 0.03695 ( 3) link_ALPHA1-3 : angle 2.68911 ( 9) link_BETA1-4 : bond 0.00570 ( 21) link_BETA1-4 : angle 1.60657 ( 63) link_BETA1-6 : bond 0.00303 ( 3) link_BETA1-6 : angle 2.54554 ( 9) link_NAG-ASN : bond 0.00562 ( 15) link_NAG-ASN : angle 2.15779 ( 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 84 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.872 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: I 34 MET cc_start: 0.9349 (mmm) cc_final: 0.8938 (mmt) REVERT: I 77 ASN cc_start: 0.9364 (m-40) cc_final: 0.8918 (t0) REVERT: K 34 MET cc_start: 0.9366 (mmm) cc_final: 0.9068 (mmt) REVERT: K 46 GLU cc_start: 0.8231 (tt0) cc_final: 0.7643 (tt0) REVERT: K 99 MET cc_start: 0.8604 (mpp) cc_final: 0.8268 (mpp) REVERT: K 211 ASP cc_start: 0.7124 (m-30) cc_final: 0.6659 (t0) REVERT: J 4 MET cc_start: 0.8524 (mmm) cc_final: 0.8080 (tpp) REVERT: C 317 MET cc_start: 0.8906 (ttt) cc_final: 0.8640 (ttm) REVERT: E 230 MET cc_start: 0.9033 (mtp) cc_final: 0.8787 (mtm) REVERT: F 59 MET cc_start: 0.9124 (mmm) cc_final: 0.8843 (mmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1903 time to fit residues: 24.3872 Evaluate side-chains 60 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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: 7.9990 chunk 125 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 237 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 111 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.044178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.029212 restraints weight = 155711.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.030079 restraints weight = 89039.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.030647 restraints weight = 62441.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.031031 restraints weight = 49787.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.031270 restraints weight = 42994.565| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23100 Z= 0.199 Angle : 0.649 9.719 31488 Z= 0.328 Chirality : 0.044 0.192 3594 Planarity : 0.004 0.045 3996 Dihedral : 7.849 58.029 3936 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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 aren not related in a simple way. whole: -0.76 (0.16), residues: 2847 helix: 1.98 (0.25), residues: 477 sheet: -0.33 (0.17), residues: 948 loop : -1.52 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 116 TYR 0.013 0.001 TYR H 193 PHE 0.012 0.001 PHE I 95 TRP 0.015 0.001 TRP E 153 HIS 0.006 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00436 (23028) covalent geometry : angle 0.63733 (31302) SS BOND : bond 0.00625 ( 30) SS BOND : angle 1.29962 ( 60) hydrogen bonds : bond 0.04912 ( 852) hydrogen bonds : angle 5.12081 ( 2466) link_ALPHA1-3 : bond 0.03655 ( 3) link_ALPHA1-3 : angle 2.76665 ( 9) link_BETA1-4 : bond 0.00536 ( 21) link_BETA1-4 : angle 1.55715 ( 63) link_BETA1-6 : bond 0.00346 ( 3) link_BETA1-6 : angle 2.34252 ( 9) link_NAG-ASN : bond 0.00474 ( 15) link_NAG-ASN : angle 2.01045 ( 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 : 1.097 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: H 4 MET cc_start: 0.8405 (mmm) cc_final: 0.8055 (tpp) REVERT: H 195 CYS cc_start: 0.2344 (p) cc_final: 0.1831 (p) REVERT: I 34 MET cc_start: 0.9333 (mmm) cc_final: 0.8958 (mmt) REVERT: I 77 ASN cc_start: 0.9289 (m-40) cc_final: 0.8931 (t0) REVERT: K 1 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8744 (tm-30) REVERT: K 3 GLN cc_start: 0.8307 (pm20) cc_final: 0.7530 (pm20) REVERT: K 34 MET cc_start: 0.9343 (mmm) cc_final: 0.9084 (mmt) REVERT: K 46 GLU cc_start: 0.8221 (tt0) cc_final: 0.7738 (tt0) REVERT: K 211 ASP cc_start: 0.6999 (m-30) cc_final: 0.6557 (t0) REVERT: J 4 MET cc_start: 0.8500 (mmm) cc_final: 0.8088 (tpp) REVERT: J 150 LYS cc_start: 0.9019 (ptpp) cc_final: 0.8296 (mmtp) REVERT: L 4 MET cc_start: 0.8662 (mmp) cc_final: 0.8452 (mmm) REVERT: E 230 MET cc_start: 0.8985 (mtp) cc_final: 0.8759 (mtm) REVERT: F 59 MET cc_start: 0.9071 (mmm) cc_final: 0.8784 (mmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1969 time to fit residues: 26.7201 Evaluate side-chains 65 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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: 9.9990 chunk 59 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 190 HIS ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN J 37 GLN J 156 GLN L 37 GLN C 150 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.043071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.028470 restraints weight = 163884.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.029257 restraints weight = 98876.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.029761 restraints weight = 71605.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.030092 restraints weight = 58130.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.030283 restraints weight = 50926.215| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 23100 Z= 0.386 Angle : 0.832 10.467 31488 Z= 0.420 Chirality : 0.048 0.221 3594 Planarity : 0.005 0.046 3996 Dihedral : 8.204 59.982 3936 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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 aren not related in a simple way. whole: -1.17 (0.16), residues: 2847 helix: 1.35 (0.24), residues: 474 sheet: -0.52 (0.17), residues: 942 loop : -1.72 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 116 TYR 0.021 0.003 TYR L 86 PHE 0.020 0.002 PHE B 3 TRP 0.019 0.002 TRP E 153 HIS 0.008 0.002 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00846 (23028) covalent geometry : angle 0.82080 (31302) SS BOND : bond 0.00785 ( 30) SS BOND : angle 1.48346 ( 60) hydrogen bonds : bond 0.05612 ( 852) hydrogen bonds : angle 5.55758 ( 2466) link_ALPHA1-3 : bond 0.03388 ( 3) link_ALPHA1-3 : angle 2.24990 ( 9) link_BETA1-4 : bond 0.00721 ( 21) link_BETA1-4 : angle 1.66547 ( 63) link_BETA1-6 : bond 0.00259 ( 3) link_BETA1-6 : angle 2.99717 ( 9) link_NAG-ASN : bond 0.00804 ( 15) link_NAG-ASN : angle 2.45773 ( 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 72 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.789 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: I 34 MET cc_start: 0.9391 (mmm) cc_final: 0.9009 (mmt) REVERT: I 77 ASN cc_start: 0.9213 (m-40) cc_final: 0.8931 (t0) REVERT: K 34 MET cc_start: 0.9389 (mmm) cc_final: 0.9068 (mmt) REVERT: K 211 ASP cc_start: 0.7024 (m-30) cc_final: 0.6498 (t0) REVERT: J 4 MET cc_start: 0.8508 (mmm) cc_final: 0.7685 (mmm) REVERT: L 4 MET cc_start: 0.8707 (mmp) cc_final: 0.8459 (mmm) REVERT: E 230 MET cc_start: 0.9128 (mtp) cc_final: 0.8915 (mtm) REVERT: F 59 MET cc_start: 0.9052 (mmm) cc_final: 0.8781 (mmm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1926 time to fit residues: 20.8306 Evaluate side-chains 57 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 0.9980 chunk 259 optimal weight: 0.9990 chunk 193 optimal weight: 0.0980 chunk 276 optimal weight: 0.7980 chunk 228 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 167 GLN I 109 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.044912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.029994 restraints weight = 152709.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.030900 restraints weight = 86055.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.031491 restraints weight = 59810.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031795 restraints weight = 47352.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.032099 restraints weight = 41469.611| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23100 Z= 0.119 Angle : 0.638 11.656 31488 Z= 0.319 Chirality : 0.044 0.178 3594 Planarity : 0.004 0.043 3996 Dihedral : 7.358 57.409 3936 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % 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 aren not related in a simple way. whole: -0.58 (0.16), residues: 2847 helix: 2.18 (0.25), residues: 477 sheet: -0.24 (0.17), residues: 945 loop : -1.41 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 127 TYR 0.031 0.001 TYR E 161 PHE 0.013 0.001 PHE B 9 TRP 0.016 0.001 TRP C 127 HIS 0.008 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00238 (23028) covalent geometry : angle 0.62829 (31302) SS BOND : bond 0.00544 ( 30) SS BOND : angle 1.02700 ( 60) hydrogen bonds : bond 0.04743 ( 852) hydrogen bonds : angle 4.94535 ( 2466) link_ALPHA1-3 : bond 0.03753 ( 3) link_ALPHA1-3 : angle 3.25211 ( 9) link_BETA1-4 : bond 0.00502 ( 21) link_BETA1-4 : angle 1.46648 ( 63) link_BETA1-6 : bond 0.00427 ( 3) link_BETA1-6 : angle 1.92081 ( 9) link_NAG-ASN : bond 0.00385 ( 15) link_NAG-ASN : angle 1.76087 ( 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 86 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.844 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: H 4 MET cc_start: 0.8362 (mmm) cc_final: 0.8094 (tpp) REVERT: H 146 LYS cc_start: 0.8015 (mppt) cc_final: 0.7504 (tppt) REVERT: I 34 MET cc_start: 0.9345 (mmm) cc_final: 0.8956 (mmt) REVERT: I 77 ASN cc_start: 0.9205 (m-40) cc_final: 0.8912 (t0) REVERT: K 3 GLN cc_start: 0.8134 (pm20) cc_final: 0.7894 (pm20) REVERT: K 34 MET cc_start: 0.9300 (mmm) cc_final: 0.8982 (mmt) REVERT: K 77 ASN cc_start: 0.9301 (m-40) cc_final: 0.9009 (t0) REVERT: K 211 ASP cc_start: 0.6987 (m-30) cc_final: 0.6505 (t0) REVERT: J 4 MET cc_start: 0.8478 (mmm) cc_final: 0.8106 (tpp) REVERT: J 150 LYS cc_start: 0.9068 (ptpp) cc_final: 0.8379 (mmtp) REVERT: L 4 MET cc_start: 0.8712 (mmp) cc_final: 0.8417 (mmm) REVERT: F 59 MET cc_start: 0.9029 (mmm) cc_final: 0.8686 (mmm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1930 time to fit residues: 24.9870 Evaluate side-chains 70 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.3082 r_free = 0.3082 target = 0.044253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.029746 restraints weight = 165483.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.030595 restraints weight = 96378.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.031108 restraints weight = 68463.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031485 restraints weight = 55479.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.031692 restraints weight = 48261.741| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23100 Z= 0.262 Angle : 0.706 10.483 31488 Z= 0.356 Chirality : 0.045 0.192 3594 Planarity : 0.004 0.045 3996 Dihedral : 7.496 57.797 3936 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % 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 aren not related in a simple way. whole: -0.75 (0.16), residues: 2847 helix: 1.93 (0.25), residues: 474 sheet: -0.31 (0.17), residues: 933 loop : -1.48 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 229 TYR 0.024 0.002 TYR E 161 PHE 0.015 0.002 PHE I 106 TRP 0.015 0.002 TRP C 153 HIS 0.006 0.002 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00578 (23028) covalent geometry : angle 0.69565 (31302) SS BOND : bond 0.00629 ( 30) SS BOND : angle 1.25649 ( 60) hydrogen bonds : bond 0.05118 ( 852) hydrogen bonds : angle 5.13732 ( 2466) link_ALPHA1-3 : bond 0.03463 ( 3) link_ALPHA1-3 : angle 2.65929 ( 9) link_BETA1-4 : bond 0.00562 ( 21) link_BETA1-4 : angle 1.56661 ( 63) link_BETA1-6 : bond 0.00359 ( 3) link_BETA1-6 : angle 2.58719 ( 9) link_NAG-ASN : bond 0.00549 ( 15) link_NAG-ASN : angle 2.07920 ( 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 75 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 MET cc_start: 0.8477 (mmm) cc_final: 0.8184 (tpp) REVERT: H 146 LYS cc_start: 0.8007 (mppt) cc_final: 0.7420 (tppt) REVERT: I 34 MET cc_start: 0.9347 (mmm) cc_final: 0.8972 (mmt) REVERT: I 77 ASN cc_start: 0.9229 (m-40) cc_final: 0.8910 (t0) REVERT: K 34 MET cc_start: 0.9342 (mmm) cc_final: 0.8993 (mmt) REVERT: K 77 ASN cc_start: 0.9337 (m-40) cc_final: 0.8987 (t0) REVERT: K 211 ASP cc_start: 0.7135 (m-30) cc_final: 0.6609 (t0) REVERT: J 4 MET cc_start: 0.8547 (mmm) cc_final: 0.8155 (tpp) REVERT: J 150 LYS cc_start: 0.9036 (ptpp) cc_final: 0.8382 (mmtp) REVERT: L 4 MET cc_start: 0.8768 (mmp) cc_final: 0.8398 (mmm) REVERT: F 59 MET cc_start: 0.9130 (mmm) cc_final: 0.8809 (mmm) REVERT: F 98 LEU cc_start: 0.9462 (tp) cc_final: 0.9243 (tp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1929 time to fit residues: 22.3905 Evaluate side-chains 65 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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: 4.9990 chunk 142 optimal weight: 10.0000 chunk 239 optimal weight: 0.6980 chunk 148 optimal weight: 0.0980 chunk 217 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3105 r_free = 0.3105 target = 0.044921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.030445 restraints weight = 162655.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.031316 restraints weight = 93815.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.031878 restraints weight = 66187.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.032237 restraints weight = 53058.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.032415 restraints weight = 46244.997| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23100 Z= 0.169 Angle : 0.640 10.261 31488 Z= 0.322 Chirality : 0.044 0.167 3594 Planarity : 0.004 0.042 3996 Dihedral : 7.209 57.581 3936 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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 aren not related in a simple way. whole: -0.56 (0.16), residues: 2847 helix: 2.15 (0.25), residues: 477 sheet: -0.22 (0.17), residues: 936 loop : -1.37 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 104 TYR 0.018 0.001 TYR E 161 PHE 0.015 0.001 PHE I 106 TRP 0.013 0.001 TRP C 127 HIS 0.006 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00371 (23028) covalent geometry : angle 0.62906 (31302) SS BOND : bond 0.00512 ( 30) SS BOND : angle 1.11194 ( 60) hydrogen bonds : bond 0.04819 ( 852) hydrogen bonds : angle 4.95164 ( 2466) link_ALPHA1-3 : bond 0.03457 ( 3) link_ALPHA1-3 : angle 2.91108 ( 9) link_BETA1-4 : bond 0.00495 ( 21) link_BETA1-4 : angle 1.47809 ( 63) link_BETA1-6 : bond 0.00377 ( 3) link_BETA1-6 : angle 2.19900 ( 9) link_NAG-ASN : bond 0.00420 ( 15) link_NAG-ASN : angle 1.88900 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3665.13 seconds wall clock time: 64 minutes 32.82 seconds (3872.82 seconds total)